sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | apbs 3.4.1-6 (amd64) Mon, 20 Jan 2025 14:31:19 +0000 | +==============================================================================+ Package: apbs Version: 3.4.1-6 Source Version: 3.4.1-6 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 20 Jan 2025 14:31:20 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup apbs_3.4.1-6 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup apbs_3.4.1-6 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 20 Jan 2025 14:31:21 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Ign:2 http://localhost:3142/debian sid InRelease Get:3 http://deb.debian.org/debian unstable InRelease [205 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-20-0805.29-F-2025-01-20-0805.29.pdiff [3153 B] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-20-0805.29-F-2025-01-20-0805.29.pdiff [3153 B] Get:6 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Ign:2 http://localhost:3142/debian sid InRelease Ign:2 http://localhost:3142/debian sid InRelease Err:2 http://localhost:3142/debian sid InRelease 503 Server reports unexpected range [IP: 127.0.0.1 3142] Fetched 272 kB in 7s (38.2 kB/s) Reading package lists... W: Failed to fetch http://localhost:3142/debian/dists/sid/InRelease 503 Server reports unexpected range [IP: 127.0.0.1 3142] W: Some index files failed to download. They have been ignored, or old ones used instead. Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Mon, 20 Jan 2025 14:31:30 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/apbs_3.4.1-6.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 20 Jan 2025 14:31:31 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkgconf, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, build-essential, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml Filtered Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkgconf, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx, swig, zlib1g-dev, build-essential, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive ./ InRelease Get:2 copy:/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive ./ Release [609 B] Ign:3 copy:/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive ./ Release.gpg Get:4 copy:/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive ./ Sources [950 B] Get:5 copy:/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive ./ Packages [961 B] Fetched 2520 B in 0s (128 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file fonts-font-awesome fonts-lato fonts-mathjax gettext gettext-base gfortran-14 gfortran-14-x86-64-linux-gnu groff-base ibverbs-providers intltool-debian libamd-comgr2 libamd3 libamdhip64-5 libarchive-zip-perl libarchive13t64 libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli1 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcom-err2 libcurl4t64 libcxsparse4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu72 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp26 libk5crypto3 libkeyutils1 libklu2 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldl3 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmaloc-dev libmaloc1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libparu1 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib librbio4 librdmacm1t64 librhash1 librtmp1 libspex3 libspqr4 libssh2-1t64 libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7 libsuperlu-dev libsuperlu7 libtirpc-common libtirpc-dev libtirpc3t64 libtool libuchardet0 libucx0 libumfpack6 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libyaml-0-2 libz3-4 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl pkgconf pkgconf-bin po-debconf procps pybind11-dev pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster python3-autocommand python3-babel python3-build python3-certifi python3-chardet python3-charset-normalizer python3-defusedxml python3-dev python3-docutils python3-idna python3-imagesize python3-inflect python3-installer python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-jinja2 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-toml python3-typeguard python3-typing-extensions python3-urllib3 python3-wheel python3-yaml python3-zipp python3.13 python3.13-dev python3.13-minimal sensible-utils sgml-base sphinx-common sphinx-rtd-theme-common swig tzdata xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit gettext-doc libasprintf-dev libgettextpo-dev gfortran-14-multilib gfortran-14-doc libcoarrays-dev groff lrzip liblapack-doc krb5-doc krb5-user libhwloc-contrib-plugins libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc libtool-doc openmpi-doc pciutils libsuperlu-doc gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv python3-pip python-build-doc python-charset-normalizer-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-installer-doc python-jinja2-doc python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-stemmer dvipng dvisvgm fonts-freefont-otf imagemagick latexmk sphinx-doc tex-gyre texlive-fonts-extra texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.13-venv python3.13-doc binfmt-support sgml-base-doc swig-doc swig-examples Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl krb5-locales libcoarrays-openmpi-dev publicsuffix libgraphblas-dev xauth libmail-sendmail-perl psmisc linux-sysctl-defaults libeigen3-dev libpaper-utils python3-pil python3-numpy The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file fonts-font-awesome fonts-lato fonts-mathjax gettext gettext-base gfortran-14 gfortran-14-x86-64-linux-gnu groff-base ibverbs-providers intltool-debian libamd-comgr2 libamd3 libamdhip64-5 libarchive-zip-perl libarchive13t64 libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli1 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcom-err2 libcurl4t64 libcxsparse4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu72 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp26 libk5crypto3 libkeyutils1 libklu2 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldl3 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmaloc-dev libmaloc1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libparu1 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib librbio4 librdmacm1t64 librhash1 librtmp1 libspex3 libspqr4 libssh2-1t64 libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7 libsuperlu-dev libsuperlu7 libtirpc-common libtirpc-dev libtirpc3t64 libtool libuchardet0 libucx0 libumfpack6 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libyaml-0-2 libz3-4 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl pkgconf pkgconf-bin po-debconf procps pybind11-dev pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster python3-autocommand python3-babel python3-build python3-certifi python3-chardet python3-charset-normalizer python3-defusedxml python3-dev python3-docutils python3-idna python3-imagesize python3-inflect python3-installer python3-jaraco.context python3-jaraco.functools python3-jaraco.text python3-jinja2 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-toml python3-typeguard python3-typing-extensions python3-urllib3 python3-wheel python3-yaml python3-zipp python3.13 python3.13-dev python3.13-minimal sbuild-build-depends-main-dummy sensible-utils sgml-base sphinx-common sphinx-rtd-theme-common swig tzdata xml-core zlib1g-dev 0 upgraded, 222 newly installed, 0 to remove and 0 not upgraded. Need to get 178 MB of archives. After this operation, 740 MB of additional disk space will be used. Get:1 copy:/build/apbs-PSc155/resolver-Yf8tsQ/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1012 B] Get:2 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:33 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Get:44 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.4-2 [2267 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get:54 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http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:76 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.6.0-1 [720 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-14 [837 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-14 [881 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-14 [11.7 MB] Get:89 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-14 [13.5 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2+b2 [62.2 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2+b2 [343 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-20+b1 [23.6 MB] Get:96 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:97 http://deb.debian.org/debian unstable/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [23.8 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libamd3 amd64 1:7.8.3+dfsg-2 [40.7 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:100 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-4 [104 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-4 [120 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libbtf2 amd64 1:7.8.3+dfsg-2 [24.7 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libcamd3 amd64 1:7.8.3+dfsg-2 [37.5 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libccolamd3 amd64 1:7.8.3+dfsg-2 [39.2 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [32.5 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libcholmod5 amd64 1:7.8.3+dfsg-2 [638 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libcxsparse4 amd64 1:7.8.3+dfsg-2 [84.2 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2+b2 [70.4 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-2 [165 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2+b2 [28.2 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2+b2 [43.4 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2+b2 [636 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 libklu2 amd64 1:7.8.3+dfsg-2 [90.6 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 libldl3 amd64 1:7.8.3+dfsg-2 [24.5 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 libmaloc1 amd64 1.5-2+b2 [84.5 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 libmaloc-dev amd64 1.5-2+b2 [1276 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.6-1 [652 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.6-3 [2360 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.6-3 [97.0 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:165 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-4 [616 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get:169 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get:173 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-2 [120 kB] Get:175 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:176 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get:177 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get:178 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:179 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:180 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get:181 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:182 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:183 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get:184 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-4 [468 kB] Get:185 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.6-1 [3962 kB] Get:186 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.6-3 [188 kB] Get:187 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get:188 http://deb.debian.org/debian unstable/main amd64 libumfpack6 amd64 1:7.8.3+dfsg-2 [280 kB] Get:189 http://deb.debian.org/debian unstable/main amd64 libparu1 amd64 1:7.8.3+dfsg-2 [65.1 kB] Get:190 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:191 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.1-3 [2151 kB] Get:192 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.1-3 [5013 kB] Get:193 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.1-2 [10.2 kB] Get:194 http://deb.debian.org/debian unstable/main amd64 librbio4 amd64 1:7.8.3+dfsg-2 [39.9 kB] Get:195 http://deb.debian.org/debian unstable/main amd64 libspex3 amd64 1:7.8.3+dfsg-2 [59.9 kB] Get:196 http://deb.debian.org/debian unstable/main amd64 libspqr4 amd64 1:7.8.3+dfsg-2 [146 kB] Get:197 http://deb.debian.org/debian unstable/main amd64 libsuitesparse-mongoose3 amd64 1:7.8.3+dfsg-2 [47.3 kB] Get:198 http://deb.debian.org/debian unstable/main amd64 libsuitesparse-dev amd64 1:7.8.3+dfsg-2 [1476 kB] Get:199 http://deb.debian.org/debian unstable/main amd64 libsuperlu7 amd64 7.0.0+dfsg1-2 [174 kB] Get:200 http://deb.debian.org/debian unstable/main amd64 libsuperlu-dev amd64 7.0.0+dfsg1-2 [21.9 kB] Get:201 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:202 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:203 http://deb.debian.org/debian unstable/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3+b1 [190 kB] Get:204 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:205 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get:206 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:207 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:208 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 2.13.6-1 [204 kB] Get:209 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get:210 http://deb.debian.org/debian unstable/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get:211 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.45.1-1 [56.7 kB] Get:212 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get:213 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get:214 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250108 [11.6 kB] Get:215 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.1-3 [507 kB] Get:216 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB] Get:217 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.13.6-1 [215 kB] Get:218 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get:219 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get:220 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get:221 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get:222 http://deb.debian.org/debian unstable/main amd64 swig amd64 4.3.0-0.1 [1502 kB] Preconfiguring packages ... Fetched 178 MB in 14s (12.7 MB/s) Selecting previously unselected package fonts-lato. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... Selecting previously unselected package python3-minimal. 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Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libibumad3:amd64 (52.0-2+b2) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libibmad5:amd64 (52.0-2+b2) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up libldl3:amd64 (1:7.8.3+dfsg-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 20 14:32:18 UTC 2025. Universal Time is now: Mon Jan 20 14:32:18 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libbtf2:amd64 (1:7.8.3+dfsg-2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libltdl7:amd64 (2.5.4-2) ... Setting up libgfortran5:amd64 (14.2.0-14) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.6-3) ... Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.4-2) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up openssl (3.4.0-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Setting up libmaloc-dev (1.5-2+b2) ... Setting up libblas-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpython3.13:amd64 (3.13.1-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-14) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libarpack2t64:amd64 (3.9.1-4) ... Setting up libamd3:amd64 (1:7.8.3+dfsg-2) ... Setting up libtool (2.5.4-2) ... Setting up libcolamd3:amd64 (1:7.8.3+dfsg-2) ... Setting up python3.13 (3.13.1-3) ... Setting up libspex3:amd64 (1:7.8.3+dfsg-2) ... Setting up libsuitesparse-mongoose3:amd64 (1:7.8.3+dfsg-2) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcxsparse4:amd64 (1:7.8.3+dfsg-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-wheel (0.45.1-1) ... Setting up libcamd3:amd64 (1:7.8.3+dfsg-2) ... Setting up libsuperlu7:amd64 (7.0.0+dfsg1-2) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-14) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.5.4-2) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-20+b1) ... Setting up python3-pyproject-hooks (1.2.0-1) ... Setting up python3-certifi (2024.12.14+ds-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up librbio4:amd64 (1:7.8.3+dfsg-2) ... Setting up libpython3.13-dev:amd64 (3.13.1-3) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libccolamd3:amd64 (1:7.8.3+dfsg-2) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up python3-build (1.2.2-1) ... Setting up gfortran-14 (14.2.0-14) ... Setting up libsuperlu-dev:amd64 (7.0.0+dfsg1-2) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libibverbs1:amd64 (52.0-2+b2) ... Setting up libcholmod5:amd64 (1:7.8.3+dfsg-2) ... Setting up libarpack2-dev:amd64 (3.9.1-4) ... Setting up libpython3-dev:amd64 (3.13.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:amd64 (8.11.1-1+b1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b2) ... Setting up libspqr4:amd64 (1:7.8.3+dfsg-2) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3.13-dev (3.13.1-3) ... Setting up openssh-client (1:9.9p1-3) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up pybind11-dev (2.13.6-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3+b1) ... Setting up libklu2:amd64 (1:7.8.3+dfsg-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up sphinx-common (8.1.3-4) ... Setting up python3-dev (3.13.1-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.6-1) ... Setting up libumfpack6:amd64 (1:7.8.3+dfsg-2) ... Setting up cmake (3.31.4-2) ... Setting up librdmacm1t64:amd64 (52.0-2+b2) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up python3-pybind11 (2.13.6-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up debhelper (13.24.1) ... Setting up libibverbs-dev:amd64 (52.0-2+b2) ... Setting up libparu1:amd64 (1:7.8.3+dfsg-2) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up dh-python (6.20250108) ... Setting up libsuitesparse-dev:amd64 (1:7.8.3+dfsg-2) ... Setting up pybuild-plugin-pyproject (6.20250108) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi40:amd64 (5.0.6-3) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up libpmix-dev:amd64 (5.0.6-1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up libopenmpi-dev:amd64 (5.0.6-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Setting up mpi-default-dev (1.18) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Mon, 20 Jan 2025 14:32:40 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 20 Jan 2025 14:32:40 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.23 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20241223 cmake_3.31.4-2 cmake-data_3.31.4-2 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-python_6.20250108 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-2 dirmngr_2.2.46-1+b1 docutils-common_0.21.2+dfsg-2 dpkg_1.22.14 dpkg-dev_1.22.14 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.45-3+b1 findutils_4.10.0-3 fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1 fonts-lato_2.015-1 fonts-mathjax_2.7.9+dfsg-1 g++_4:14.2.0-1 g++-13_13.3.0-12 g++-13-x86-64-linux-gnu_13.3.0-12 g++-14_14.2.0-14 g++-14-x86-64-linux-gnu_14.2.0-14 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-12 gcc-13-base_13.3.0-12 gcc-13-x86-64-linux-gnu_13.3.0-12 gcc-14_14.2.0-14 gcc-14-base_14.2.0-14 gcc-14-x86-64-linux-gnu_14.2.0-14 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gfortran-14_14.2.0-14 gfortran-14-x86-64-linux-gnu_14.2.0-14 gnupg_2.2.46-1 gnupg-l10n_2.2.46-1 gnupg-utils_2.2.46-1+b1 gpg_2.2.46-1+b1 gpg-agent_2.2.46-1+b1 gpg-wks-client_2.2.46-1+b1 gpgconf_2.2.46-1+b1 gpgsm_2.2.46-1+b1 gpgv_2.2.46-1+b1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hostname_3.25 ibverbs-providers_52.0-2+b2 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2 libamd3_1:7.8.3+dfsg-2 libamdhip64-5_5.7.1-5 libapt-pkg6.0t64_2.9.23 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libarpack2-dev_3.9.1-4 libarpack2t64_3.9.1-4 libasan8_14.2.0-14 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-14 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbinutils_2.43.50.20250108-1 libblas-dev_3.12.0-4 libblas3_3.12.0-4 libblkid1_2.40.4-1 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbtf2_1:7.8.3+dfsg-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc-l10n_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libcamd3_1:7.8.3+dfsg-2 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcbor0.10_0.10.2-2 libcc1-0_14.2.0-14 libccolamd3_1:7.8.3+dfsg-2 libcholmod5_1:7.8.3+dfsg-2 libcolamd3_1:7.8.3+dfsg-2 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libcurl4t64_8.11.1-1+b1 libcxsparse4_1:7.8.3+dfsg-2 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdpkg-perl_1.22.14 libdrm-amdgpu1_2.4.123-1 libdrm-common_2.4.123-1 libdrm2_2.4.123-1 libeatmydata1_131-2+b1 libedit2_3.1-20250104-1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libevent-core-2.1-7t64_2.1.12-stable-10+b1 libevent-dev_2.1.12-stable-10+b1 libevent-extra-2.1-7t64_2.1.12-stable-10+b1 libevent-openssl-2.1-7t64_2.1.12-stable-10+b1 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.6.4-1 libexpat1-dev_2.6.4-1 libfabric1_1.17.0-3.1 libffi8_3.4.6-1 libfido2-1_1.15.0-1+b1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-12 libgcc-14-dev_14.2.0-14 libgcc-s1_14.2.0-14 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran-14-dev_14.2.0-14 libgfortran5_14.2.0-14 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-14 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libgssapi-krb5-2_1.21.3-4 libhogweed6t64_3.10-1+b1 libhsa-runtime64-1_6.1.2-2 libhsakmt1_6.1.2+ds-1 libhwasan0_14.2.0-14 libhwloc-dev_2.11.2-1 libhwloc-plugins_2.11.2-1 libhwloc15_2.11.2-1 libibmad5_52.0-2+b2 libibumad3_52.0-2+b2 libibverbs-dev_52.0-2+b2 libibverbs1_52.0-2+b2 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-14 libjansson4_2.14-2+b3 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-mathjax_2.7.9+dfsg-1 libjs-sphinxdoc_8.1.3-4 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-perl_4.10000-1 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-4 libkeyutils1_1.6.3-4 libklu2_1:7.8.3+dfsg-2 libkrb5-3_1.21.3-4 libkrb5support0_1.21.3-4 libksba8_1.6.7-2+b1 liblapack-dev_3.12.0-4 liblapack3_3.12.0-4 libldap-2.5-0_2.5.19+dfsg-1 libldap2_2.6.9+dfsg-1 libldl3_1:7.8.3+dfsg-2 libllvm17t64_1:17.0.6-20+b1 liblsan0_14.2.0-14 libltdl-dev_2.5.4-2 libltdl7_2.5.4-2 liblz4-1_1.9.4-4 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmaloc-dev_1.5-2+b2 libmaloc1_1.5-2+b2 libmd0_1.1.0-2+b1 libmount1_2.40.4-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libmunge2_0.5.15-4+b1 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnl-3-200_3.7.0-0.3+b1 libnl-3-dev_3.7.0-0.3+b1 libnl-route-3-200_3.7.0-0.3+b1 libnl-route-3-dev_3.7.0-0.3+b1 libnpth0t64_1.8-2 libnuma-dev_2.0.18-1+b1 libnuma1_2.0.18-1+b1 libopenmpi-dev_5.0.6-3 libopenmpi40_5.0.6-3 libp11-kit0_0.25.5-3 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libparu1_1:7.8.3+dfsg-2 libpciaccess0_0.17-3+b3 libpcre2-8-0_10.44-5 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-1 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpmix-dev_5.0.6-1 libpmix2t64_5.0.6-1 libproc2-0_2:4.0.4-6 libpsl5t64_0.21.2-1.1+b1 libpsm-infinipath1_3.3+20.604758e7-6.3 libpsm2-2_11.2.185-2.1 libpython3-dev_3.13.1-2 libpython3-stdlib_3.13.1-2 libpython3.13_3.13.1-3 libpython3.13-dev_3.13.1-3 libpython3.13-minimal_3.13.1-3 libpython3.13-stdlib_3.13.1-3 libquadmath0_14.2.0-14 librbio4_1:7.8.3+dfsg-2 librdmacm1t64_52.0-2+b2 libreadline8t64_8.2-6 librhash1_1.4.5-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8+b1 libsasl2-modules-db_2.1.28+dfsg1-8+b1 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20250108-1 libsmartcols1_2.40.4-1 libspex3_1:7.8.3+dfsg-2 libspqr4_1:7.8.3+dfsg-2 libsqlite3-0_3.46.1-1 libssh2-1t64_1.11.1-1 libssl3t64_3.4.0-2 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 libsuitesparse-dev_1:7.8.3+dfsg-2 libsuitesparse-mongoose3_1:7.8.3+dfsg-2 libsuitesparseconfig7_1:7.8.3+dfsg-2 libsuperlu-dev_7.0.0+dfsg1-2 libsuperlu7_7.0.0+dfsg1-2 libsystemd0_257.2-2 libtasn1-6_4.19.0-3+b3 libtinfo6_6.5-2+b1 libtirpc-common_1.3.4+ds-1.3 libtirpc-dev_1.3.4+ds-1.3+b1 libtirpc3t64_1.3.4+ds-1.3+b1 libtool_2.5.4-2 libtsan2_14.2.0-14 libubsan1_14.2.0-14 libuchardet0_0.0.8-1+b2 libucx0_1.17.0+ds-3 libudev1_257.2-2 libumfpack6_1:7.8.3+dfsg-2 libunistring5_1.3-1 libuuid1_2.40.4-1 libuv1t64_1.48.0-7 libx11-6_2:1.8.10-2 libx11-data_2:1.8.10-2 libxau6_1:1.0.11-1 libxcb1_1.17.0-2+b1 libxdmcp6_1:1.1.5-1 libxext6_2:1.3.4-1+b3 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxnvctrl0_535.171.04-1+b1 libxxhash0_0.8.3-2 libyaml-0-2_0.2.5-2 libz3-4_4.13.3-1 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.10-1 locales-all_2.40-5 login_1:4.16.0-2+really2.40.4-1 login.defs_1:4.16.0-7 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mpi-default-dev_1.18 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1+b2 openmpi-bin_5.0.6-3 openmpi-common_5.0.6-3 openssh-client_1:9.9p1-3 openssl_3.4.0-2 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.1-1 perl-base_5.40.1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-1 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 pybind11-dev_2.13.6-1 pybuild-plugin-pyproject_6.20250108 python-babel-localedata_2.16.0-1 python3_3.13.1-2 python3-alabaster_0.7.16-0.1 python3-autocommand_2.2.2-3 python3-babel_2.16.0-1 python3-build_1.2.2-1 python3-certifi_2024.12.14+ds-1 python3-chardet_5.2.0+dfsg-2 python3-charset-normalizer_3.4.0-1+b1 python3-defusedxml_0.7.1-3 python3-dev_3.13.1-2 python3-docutils_0.21.2+dfsg-2 python3-idna_3.8-2 python3-imagesize_1.4.1-1 python3-inflect_7.3.1-2 python3-installer_0.7.0+dfsg1-3 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-jinja2_3.1.3-2 python3-markupsafe_2.1.5-1+b2 python3-minimal_3.13.1-2 python3-more-itertools_10.6.0-1 python3-packaging_24.2-1 python3-pkg-resources_75.6.0-1 python3-pybind11_2.13.6-1 python3-pygments_2.18.0+dfsg-2 python3-pyproject-hooks_1.2.0-1 python3-requests_2.32.3+dfsg-1 python3-roman_4.2-1 python3-setuptools_75.6.0-1 python3-snowballstemmer_2.2.0-4 python3-sphinx_8.1.3-4 python3-sphinx-rtd-theme_3.0.2+dfsg-2 python3-sphinxcontrib.jquery_4.1-5 python3-toml_0.10.2-1 python3-typeguard_4.4.1-1 python3-typing-extensions_4.12.2-2 python3-urllib3_2.3.0-1 python3-wheel_0.45.1-1 python3-yaml_6.0.2-1+b1 python3-zipp_3.21.0-1 python3.13_3.13.1-3 python3.13-dev_3.13.1-3 python3.13-minimal_3.13.1-3 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sphinx-common_8.1.3-4 sphinx-rtd-theme-common_3.0.2+dfsg-2 sqv_1.2.1-5 swig_4.3.0-0.1 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2025a-1 usr-is-merged_39+nmu2 util-linux_2.40.4-1 xml-core_0.19 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 20 Jan 2025 14:32:40 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: apbs Binary: apbs, python3-apbslib, libapbs-dev, libapbs3t64, apbs-data, apbs-doc, libfetk-dev, libfetk1.9t64 Architecture: any all Version: 3.4.1-6 Maintainer: Debichem Team Uploaders: Michael Banck Homepage: http://www.poissonboltzmann.org/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/debichem-team/apbs Vcs-Git: https://salsa.debian.org/debichem-team/apbs.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkgconf, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev Build-Depends-Indep: libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml Package-List: apbs deb science optional arch=any apbs-data deb science optional arch=all apbs-doc deb science optional arch=all libapbs-dev deb libdevel optional arch=any libapbs3t64 deb libs optional arch=any libfetk-dev deb libdevel optional arch=any libfetk1.9t64 deb libs optional arch=any python3-apbslib deb python optional arch=any Checksums-Sha1: 584fd36dc1424cb22fd8846f1cf2c7ead60ce0c6 85806314 apbs_3.4.1.orig.tar.gz 4b109e526ce154482edf6e8b03abd76f40778030 20434596 apbs_3.4.1-6.debian.tar.xz Checksums-Sha256: 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2 85806314 apbs_3.4.1.orig.tar.gz df65c5bef2933ad1c432861d6ad3d872594d2b54a5cdea220f8eb94518322244 20434596 apbs_3.4.1-6.debian.tar.xz Files: 5d2af7c3592f8c410a5df39887361520 85806314 apbs_3.4.1.orig.tar.gz a1d28397623bbd7fd390f4584ebe554f 20434596 apbs_3.4.1-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmcjhVMUHGRwYXJzb25z QGRlYmlhbi5vcmcACgkQVz7x5L1aAfrIpQ//e6kKJIFWg9YSKtGLTCnnmErFyhJY Ug14D8OiNyHQt0EQj1S8koWDElc6POr7xqWG+6OKzNuyw37PzZOOfg9MgICN27pw lXC7F/9iNTgCScNOUg+b+KNWQv0EomXjXQwfXmGbwY4OzGBpgSvmswhiPUrog4Wm zhnF1UMpixcKJPYF2kAlovLAZXD8DcEQN8qcMpUYhdncTTyuayL87U/sLXXduZum YzbiC6X0K/y1vqZwGkmBEAulYILyRKOSAt88TFPdDMNFp/wJe0FOWrDX+sqZ6Vnw oBUBkbA0CtaOr5PuVdz47fG/Q0Yv5g2SnOUJ1d1VpnPhRCU8XfelNSgiCRcaEiot AsYjNrd4EPqzXqeFiZZsZq15sX/IGrVnVFcgkrzIr748WtoYdIUBBrrPvHbifAEG 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fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying cmake.patch dpkg-source: info: applying docs.patch dpkg-source: info: applying open-U-obsolete.patch dpkg-source: info: applying gcc14.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 20 Jan 2025 14:32:44 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network apbs_3.4.1-6 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network apbs_3.4.1-6 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/apbs-PSc155/apbs-3.4.1 SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-47faea5b-e16f-4dcd-bfed-d425d668db5f SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building apbs using existing ./apbs_3.4.1.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: warning: ignoring deletion of file examples/hca-bind/UHBD/bindf.out.orig, use --include-removal to override dpkg-source: info: building apbs in apbs_3.4.1-6.debian.tar.xz dpkg-source: info: building apbs in apbs_3.4.1-6.dsc debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/apbs-PSc155/apbs-3.4.1' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None \ -DAPBS_STATIC_BUILD=Off \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETCHCONTENT_SOURCE_DIR_FETK=/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=None -DAPBS_STATIC_BUILD=Off -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETCHCONTENT_SOURCE_DIR_FETK=/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Install prefix: /usr -- -- APBS Static build: Off -- Building shared libs: ON -- Find-library suffixes: .so;.so;.a -- -- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2 CMake Deprecation Warning at debian/external_deps/fetk/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- FETK set_basic_vars_and_paths: FALSE, FETK -- Setting project paths -- Install prefix: /usr -- FETK static build: OFF -- Building shared libs: ON -- Find-library suffixes: .so;.so;.so;.a CMake Deprecation Warning at debian/external_deps/fetk/punc/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Configuring build for PUNC -- FETK set_basic_vars_and_paths: FALSE, punc -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- Will build vf2c -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T - Success -- Performing Test SUPERLU_HAS_CLEAN_ENUMS -- Performing Test SUPERLU_HAS_CLEAN_ENUMS - Success -- Performing Test SUPERLU_HAS_GLOBALLU_T -- Performing Test SUPERLU_HAS_GLOBALLU_T - Success -- Found SuperLU: /usr/include/superlu (found version "5.0") -- Found ARPACK: libraries at /usr/lib/x86_64-linux-gnu/libarpack.so -- Will build CGCODE -- Building vf2c -- Type: EXTERNAL_HEADERS -- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h -- Type: INTERNAL_HEADERS -- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h -- Type: SOURCES -- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c -- Building cgcode -- Type: INTERNAL_HEADERS -- Items: vcgcode.h -- Type: SOURCES -- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c -- Type: INTERNAL_HEADERS -- Items: /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/punccf.h -- Type: SOURCES -- Items: punc_base.c -- Type: EXTERNAL_HEADERS -- Items: punc/punc.h;punc/punc_base.h -- Type: INTERNAL_HEADERS -- Items: punc_base_p.h CMake Deprecation Warning at debian/external_deps/fetk/gamer/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src/gamercf.h -- Type: SOURCES -- Items: gamer_base.c -- Type: EXTERNAL_HEADERS -- Items: gamer/gamer.h;gamer/gamer_base.h -- Type: INTERNAL_HEADERS -- Items: gamer_base_p.h -- Type: SOURCES -- Items: triangle.c -- Type: EXTERNAL_HEADERS -- Items: gamer/triangle.h -- Type: INTERNAL_HEADERS -- Items: triangle_p.h -- Type: SOURCES -- Items: predicates.cpp;tetgen.cpp -- Type: EXTERNAL_HEADERS -- Items: gamer/tetgen.h -- Type: INTERNAL_HEADERS -- Items: tetgen_p.h -- Type: SOURCES -- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C -- Type: EXTERNAL_HEADERS -- Items: gamer/biom.h -- Type: INTERNAL_HEADERS -- Items: MarchingCube.h;PDB2Volume.h CMake Deprecation Warning at debian/external_deps/fetk/mc/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Configuring build for MC -- FETK set_basic_vars_and_paths: FALSE, mc -- Found UMFPACK: /usr/include/suitesparse -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.a -- Adding librt: /usr/lib/x86_64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- Found SuiteSparse: TRUE (found version "..") -- Type: INTERNAL_HEADERS -- Items: /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src/mccf.h -- Type: SOURCES -- Items: mc_base.c -- Type: EXTERNAL_HEADERS -- Items: mc/mc_base.h;mc/mc.h -- Type: INTERNAL_HEADERS -- Items: mc_base_p.h -- Type: SOURCES -- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c -- Type: EXTERNAL_HEADERS -- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h -- Type: INTERNAL_HEADERS -- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h -- Type: SOURCES -- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c -- Type: EXTERNAL_HEADERS -- Items: mc/whb.h -- Type: INTERNAL_HEADERS -- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h -- Type: SOURCES -- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c -- Type: EXTERNAL_HEADERS -- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h -- Type: INTERNAL_HEADERS -- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h -- Type: SOURCES -- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c -- Type: EXTERNAL_HEADERS -- Items: mc/gem.h;mc/vel.h;mc/ves.h -- Type: INTERNAL_HEADERS -- Items: gem_p.h;vel_p.h;ves_p.h -- Type: SOURCES -- Items: pde.c -- Type: EXTERNAL_HEADERS -- Items: mc/pde.h -- Type: INTERNAL_HEADERS -- Items: pde_p.h -- Type: SOURCES -- Items: am.c;lsolv.c;nsolv.c -- Type: EXTERNAL_HEADERS -- Items: mc/am.h;mc/nam.h -- Type: INTERNAL_HEADERS -- Items: am_p.h;nam_p.h -- Type: SOURCES -- Items: dyn.c;svio.c -- Type: EXTERNAL_HEADERS -- Items: mc/dyn.h -- Type: INTERNAL_HEADERS -- Items: dyn_p.h;svio_p.h -- Type: SOURCES -- Items: mcsh.c -- Type: EXTERNAL_HEADERS -- Items: mc/mcsh.h -- Type: INTERNAL_HEADERS -- Items: mcsh_p.h -- ############################################################# -- ** PROJECT NAME: APBS -- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver -- ** PROJECT URL: http://www.poissonboltzmann.org/ -- ** VERSION_DATA: 3.4.1 -- ** CURRENT_TIME: 2024-10-31T13:24:17 -- ** CURRENT_YEAR: 2024 -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found Intl: built in to C library -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.a -- Adding librt: /usr/lib/x86_64-linux-gnu/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- UMFPack libraries: /usr/lib/x86_64-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Building of iAPBS interface disabled CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_fem -- With source files vcsm.c;vfetk.c;vpee.c -- With external header files vcsm.h;vfetk.h;vpee.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic -- Added apbs_fem -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig (found version "4.3.0") -- Found Python3: /usr/bin/python3 (found suitable version "3.13.1", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.13 -- ***** Python3 library path is: /usr/lib/x86_64-linux-gnu/libpython3.13.so -- ***** Python3 library dir is: /usr/lib/x86_64-linux-gnu CMake Warning at /usr/lib/cmake/pybind11/pybind11Tools.cmake:24 (message): Set PYBIND11_PYTHON_VERSION to search for a specific version, not PYTHON_VERSION (which is an output). Assuming that is what you meant to do and continuing anyway. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Common.cmake:228 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) CMake Warning (dev) at /usr/lib/cmake/pybind11/FindPythonLibsNew.cmake:101 (message): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning, or preferably upgrade to using FindPython, either by calling it explicitly before pybind11, or by setting PYBIND11_FINDPYTHON ON before pybind11. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/lib/cmake/pybind11/pybind11Common.cmake:228 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.13.1", minimum required is "3.6") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.13.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.13.6") -- LIBS mc;util;dl;m;stdc++;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp -- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- ******* TESTING ADDED ***************** -- Found Python3: /usr/bin/python3 (found suitable exact version "3.13.1") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t born -- ******* FOUND TEST CASE actin, actin-dimer-auto -- TEST actin-dimer-auto_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t actin-dimer-auto -- ******* FOUND TEST CASE alkanes, alkanes -- TEST alkanes_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t FKBP -- ******* FOUND TEST CASE hca, hca-bind -- TEST hca-bind_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ionize -- ******* FOUND TEST CASE ion, ion-pmf -- TEST ion-pmf_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t ion-pmf -- ******* FOUND TEST CASE pka, pka-lig -- TEST pka-lig_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t pka-lig -- ******* FOUND TEST CASE point, point-pmf -- TEST point-pmf_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /build/apbs-PSc155/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/apbs-PSc155/apbs-3.4.1/tests/apbs_tester.py -e apbs -t solv -- Configuring done (10.9s) -- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB -- Build files have been written to: /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/apbs-PSc155/apbs-3.4.1 -B/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/CMakeFiles /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode 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directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 0%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT 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/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 2%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o -MF CMakeFiles/cgcode.dir/scg.c.o.d -o CMakeFiles/cgcode.dir/scg.c.o -c 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-Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o -MF CMakeFiles/vf2c.dir/iargc_.c.o.d -o CMakeFiles/vf2c.dir/iargc_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iargc_.c [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o -MF CMakeFiles/vf2c.dir/getenv_.c.o.d -o CMakeFiles/vf2c.dir/getenv_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getenv_.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o -MF CMakeFiles/vf2c.dir/signal_.c.o.d -o CMakeFiles/vf2c.dir/signal_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/signal_.c [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o -MF CMakeFiles/cgcode.dir/spcg.c.o.d -o CMakeFiles/cgcode.dir/spcg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcg.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o -MF CMakeFiles/vf2c.dir/s_stop.c.o.d -o CMakeFiles/vf2c.dir/s_stop.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o -MF CMakeFiles/vf2c.dir/s_paus.c.o.d -o CMakeFiles/vf2c.dir/s_paus.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o -MF CMakeFiles/vf2c.dir/cabs.c.o.d -o CMakeFiles/vf2c.dir/cabs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o -MF CMakeFiles/cgcode.dir/scgne.c.o.d -o CMakeFiles/cgcode.dir/scgne.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgne.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o -MF CMakeFiles/vf2c.dir/derf_.c.o.d -o CMakeFiles/vf2c.dir/derf_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derf_.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o cd 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o -MF CMakeFiles/vf2c.dir/erfc_.c.o.d -o CMakeFiles/vf2c.dir/erfc_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erfc_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o -MF CMakeFiles/cgcode.dir/spcgne.c.o.d -o CMakeFiles/cgcode.dir/spcgne.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgne.c cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o -MF CMakeFiles/vf2c.dir/sig_die.c.o.d -o CMakeFiles/vf2c.dir/sig_die.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o -MF CMakeFiles/cgcode.dir/sppcg.c.o.d -o CMakeFiles/cgcode.dir/sppcg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sppcg.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o -MF CMakeFiles/vf2c.dir/uninit.c.o.d -o CMakeFiles/vf2c.dir/uninit.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uninit.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o -MF CMakeFiles/cgcode.dir/spcgca.c.o.d -o CMakeFiles/cgcode.dir/spcgca.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o -MF CMakeFiles/vf2c.dir/pow_ci.c.o.d -o CMakeFiles/vf2c.dir/pow_ci.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o -MF CMakeFiles/cgcode.dir/sdpchb.c.o.d -o CMakeFiles/cgcode.dir/sdpchb.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o -MF CMakeFiles/vf2c.dir/pow_hh.c.o.d -o CMakeFiles/vf2c.dir/pow_hh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o -MF CMakeFiles/cgcode.dir/scbfix.c.o.d -o CMakeFiles/cgcode.dir/scbfix.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o -MF CMakeFiles/vf2c.dir/pow_ii.c.o.d -o CMakeFiles/vf2c.dir/pow_ii.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o -MF CMakeFiles/vf2c.dir/pow_ri.c.o.d -o CMakeFiles/vf2c.dir/pow_ri.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o -MF CMakeFiles/cgcode.dir/sckchb.c.o.d -o CMakeFiles/cgcode.dir/sckchb.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o -MF CMakeFiles/vf2c.dir/pow_zi.c.o.d -o CMakeFiles/vf2c.dir/pow_zi.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o -MF CMakeFiles/cgcode.dir/scgchk.c.o.d -o CMakeFiles/cgcode.dir/scgchk.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o -MF CMakeFiles/vf2c.dir/pow_zz.c.o.d -o CMakeFiles/vf2c.dir/pow_zz.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o -MF CMakeFiles/cgcode.dir/sonest.c.o.d -o CMakeFiles/cgcode.dir/sonest.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sonest.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o -MF CMakeFiles/cgcode.dir/msstop.c.o.d -o CMakeFiles/cgcode.dir/msstop.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o -MF CMakeFiles/vf2c.dir/c_abs.c.o.d -o CMakeFiles/vf2c.dir/c_abs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_abs.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o -MF CMakeFiles/cgcode.dir/r1mach.c.o.d -o CMakeFiles/cgcode.dir/r1mach.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/r1mach.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o -MF CMakeFiles/vf2c.dir/c_cos.c.o.d -o CMakeFiles/vf2c.dir/c_cos.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o -MF CMakeFiles/cgcode.dir/sratqr.c.o.d -o CMakeFiles/cgcode.dir/sratqr.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o -MF CMakeFiles/vf2c.dir/c_div.c.o.d -o CMakeFiles/vf2c.dir/c_div.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o -MF CMakeFiles/vf2c.dir/c_exp.c.o.d -o CMakeFiles/vf2c.dir/c_exp.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_exp.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o -MF CMakeFiles/cgcode.dir/dcgdrv.c.o.d -o CMakeFiles/cgcode.dir/dcgdrv.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o -MF CMakeFiles/vf2c.dir/c_log.c.o.d -o CMakeFiles/vf2c.dir/c_log.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o -MF CMakeFiles/vf2c.dir/c_sin.c.o.d -o CMakeFiles/vf2c.dir/c_sin.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o -MF CMakeFiles/cgcode.dir/dcg.c.o.d -o CMakeFiles/cgcode.dir/dcg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o -MF CMakeFiles/vf2c.dir/c_sqrt.c.o.d -o CMakeFiles/vf2c.dir/c_sqrt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o -MF CMakeFiles/cgcode.dir/dcr.c.o.d -o CMakeFiles/cgcode.dir/dcr.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o -MF CMakeFiles/vf2c.dir/z_abs.c.o.d -o CMakeFiles/vf2c.dir/z_abs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o -MF CMakeFiles/vf2c.dir/z_cos.c.o.d -o CMakeFiles/vf2c.dir/z_cos.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o -MF CMakeFiles/vf2c.dir/z_div.c.o.d -o CMakeFiles/vf2c.dir/z_div.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_div.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o -MF CMakeFiles/vf2c.dir/z_exp.c.o.d -o CMakeFiles/vf2c.dir/z_exp.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o -MF CMakeFiles/cgcode.dir/dcrind.c.o.d -o CMakeFiles/cgcode.dir/dcrind.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcrind.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o -MF CMakeFiles/vf2c.dir/z_log.c.o.d -o CMakeFiles/vf2c.dir/z_log.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_log.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o -MF CMakeFiles/cgcode.dir/dpcg.c.o.d -o CMakeFiles/cgcode.dir/dpcg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o -MF CMakeFiles/vf2c.dir/z_sqrt.c.o.d -o CMakeFiles/vf2c.dir/z_sqrt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o -MF CMakeFiles/vf2c.dir/r_abs.c.o.d -o CMakeFiles/vf2c.dir/r_abs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o -MF CMakeFiles/vf2c.dir/r_acos.c.o.d -o CMakeFiles/vf2c.dir/r_acos.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o -MF CMakeFiles/cgcode.dir/dcgnr.c.o.d -o CMakeFiles/cgcode.dir/dcgnr.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o -MF CMakeFiles/vf2c.dir/r_asin.c.o.d -o CMakeFiles/vf2c.dir/r_asin.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_asin.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o -MF CMakeFiles/vf2c.dir/r_atan.c.o.d -o CMakeFiles/vf2c.dir/r_atan.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o -MF CMakeFiles/cgcode.dir/dcgne.c.o.d -o CMakeFiles/cgcode.dir/dcgne.c.o -c 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o -MF CMakeFiles/vf2c.dir/r_cnjg.c.o.d -o CMakeFiles/vf2c.dir/r_cnjg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o -MF CMakeFiles/vf2c.dir/r_cos.c.o.d -o CMakeFiles/vf2c.dir/r_cos.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cos.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o -MF CMakeFiles/vf2c.dir/r_cosh.c.o.d -o CMakeFiles/vf2c.dir/r_cosh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o -MF CMakeFiles/cgcode.dir/dpcgne.c.o.d -o CMakeFiles/cgcode.dir/dpcgne.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o -MF CMakeFiles/vf2c.dir/r_dim.c.o.d -o CMakeFiles/vf2c.dir/r_dim.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_dim.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o -MF CMakeFiles/vf2c.dir/r_exp.c.o.d -o CMakeFiles/vf2c.dir/r_exp.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_exp.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o -MF CMakeFiles/vf2c.dir/r_imag.c.o.d -o CMakeFiles/vf2c.dir/r_imag.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o -MF CMakeFiles/vf2c.dir/r_int.c.o.d -o CMakeFiles/vf2c.dir/r_int.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_int.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o -MF CMakeFiles/cgcode.dir/dppcg.c.o.d -o CMakeFiles/cgcode.dir/dppcg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dppcg.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o -MF CMakeFiles/vf2c.dir/r_lg10.c.o.d -o CMakeFiles/vf2c.dir/r_lg10.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o -MF CMakeFiles/vf2c.dir/r_log.c.o.d -o 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24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o -MF CMakeFiles/vf2c.dir/r_nint.c.o.d -o CMakeFiles/vf2c.dir/r_nint.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd 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/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o -MF CMakeFiles/vf2c.dir/r_sign.c.o.d -o CMakeFiles/vf2c.dir/r_sign.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sign.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o -MF CMakeFiles/vf2c.dir/r_sin.c.o.d -o CMakeFiles/vf2c.dir/r_sin.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sin.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o -MF CMakeFiles/vf2c.dir/r_sinh.c.o.d -o CMakeFiles/vf2c.dir/r_sinh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o -MF CMakeFiles/cgcode.dir/ddpchb.c.o.d -o CMakeFiles/cgcode.dir/ddpchb.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o -MF CMakeFiles/vf2c.dir/r_sqrt.c.o.d -o CMakeFiles/vf2c.dir/r_sqrt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c [ 27%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o -MF CMakeFiles/cgcode.dir/dcbfix.c.o.d -o CMakeFiles/cgcode.dir/dcbfix.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o -MF CMakeFiles/vf2c.dir/r_tan.c.o.d -o CMakeFiles/vf2c.dir/r_tan.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tan.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o -MF CMakeFiles/vf2c.dir/r_tanh.c.o.d -o CMakeFiles/vf2c.dir/r_tanh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c [ 27%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o -MF CMakeFiles/vf2c.dir/d_abs.c.o.d -o CMakeFiles/vf2c.dir/d_abs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o -MF CMakeFiles/cgcode.dir/dcgchk.c.o.d -o CMakeFiles/cgcode.dir/dcgchk.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o -MF CMakeFiles/vf2c.dir/d_acos.c.o.d -o CMakeFiles/vf2c.dir/d_acos.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o -MF CMakeFiles/cgcode.dir/donest.c.o.d -o CMakeFiles/cgcode.dir/donest.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o -MF CMakeFiles/vf2c.dir/d_asin.c.o.d -o CMakeFiles/vf2c.dir/d_asin.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_asin.c [ 29%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o -MF CMakeFiles/cgcode.dir/mdstop.c.o.d -o CMakeFiles/cgcode.dir/mdstop.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o -MF CMakeFiles/vf2c.dir/d_atan.c.o.d -o CMakeFiles/vf2c.dir/d_atan.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o -MF CMakeFiles/cgcode.dir/d1mach.c.o.d -o CMakeFiles/cgcode.dir/d1mach.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/d1mach.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o -MF CMakeFiles/vf2c.dir/d_atn2.c.o.d -o CMakeFiles/vf2c.dir/d_atn2.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o -MF CMakeFiles/cgcode.dir/dratqr.c.o.d -o CMakeFiles/cgcode.dir/dratqr.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o -MF CMakeFiles/vf2c.dir/d_cnjg.c.o.d -o CMakeFiles/vf2c.dir/d_cnjg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o -MF CMakeFiles/vf2c.dir/d_cos.c.o.d -o CMakeFiles/vf2c.dir/d_cos.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cos.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o -MF CMakeFiles/vf2c.dir/d_cosh.c.o.d -o CMakeFiles/vf2c.dir/d_cosh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 31%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o -MF CMakeFiles/cgcode.dir/depsln.c.o.d -o CMakeFiles/cgcode.dir/depsln.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o -MF CMakeFiles/vf2c.dir/d_dim.c.o.d -o CMakeFiles/vf2c.dir/d_dim.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_dim.c [ 31%] Linking C shared library libcgcode.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o -MF CMakeFiles/vf2c.dir/d_exp.c.o.d -o CMakeFiles/vf2c.dir/d_exp.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_exp.c /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/cgcode.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_symlink_library libcgcode.so.1.9.3 libcgcode.so.1.9 libcgcode.so [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o -MF CMakeFiles/vf2c.dir/d_imag.c.o.d -o CMakeFiles/vf2c.dir/d_imag.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_imag.c make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 32%] Built target cgcode make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 33%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o -MF CMakeFiles/gamer.dir/base/gamer_base.c.o.d -o CMakeFiles/gamer.dir/base/gamer_base.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base/gamer_base.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o -MF CMakeFiles/vf2c.dir/d_int.c.o.d -o CMakeFiles/vf2c.dir/d_int.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 33%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o -MF CMakeFiles/gamer.dir/triangle/triangle.c.o.d -o CMakeFiles/gamer.dir/triangle/triangle.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle/triangle.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o -MF CMakeFiles/vf2c.dir/d_lg10.c.o.d -o CMakeFiles/vf2c.dir/d_lg10.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o -MF CMakeFiles/vf2c.dir/d_log.c.o.d -o CMakeFiles/vf2c.dir/d_log.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o -MF CMakeFiles/vf2c.dir/d_mod.c.o.d -o CMakeFiles/vf2c.dir/d_mod.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o -MF CMakeFiles/vf2c.dir/d_nint.c.o.d -o CMakeFiles/vf2c.dir/d_nint.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_nint.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o -MF CMakeFiles/vf2c.dir/d_prod.c.o.d -o CMakeFiles/vf2c.dir/d_prod.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o -MF CMakeFiles/vf2c.dir/d_sign.c.o.d -o CMakeFiles/vf2c.dir/d_sign.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC 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CMakeFiles/vf2c.dir/d_sinh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o -MF CMakeFiles/vf2c.dir/d_sqrt.c.o.d -o CMakeFiles/vf2c.dir/d_sqrt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o -MF CMakeFiles/vf2c.dir/d_tan.c.o.d -o CMakeFiles/vf2c.dir/d_tan.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tan.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o -MF CMakeFiles/vf2c.dir/d_tanh.c.o.d -o CMakeFiles/vf2c.dir/d_tanh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o -MF CMakeFiles/vf2c.dir/i_abs.c.o.d -o CMakeFiles/vf2c.dir/i_abs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o -MF CMakeFiles/vf2c.dir/i_dim.c.o.d -o CMakeFiles/vf2c.dir/i_dim.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dim.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o -MF CMakeFiles/vf2c.dir/i_dnnt.c.o.d -o CMakeFiles/vf2c.dir/i_dnnt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o -MF CMakeFiles/vf2c.dir/i_indx.c.o.d -o CMakeFiles/vf2c.dir/i_indx.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_indx.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o -MF CMakeFiles/vf2c.dir/i_len.c.o.d -o CMakeFiles/vf2c.dir/i_len.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o -MF CMakeFiles/vf2c.dir/i_mod.c.o.d -o CMakeFiles/vf2c.dir/i_mod.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o -MF CMakeFiles/vf2c.dir/i_nint.c.o.d -o CMakeFiles/vf2c.dir/i_nint.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_nint.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o -MF CMakeFiles/vf2c.dir/i_sign.c.o.d -o CMakeFiles/vf2c.dir/i_sign.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_sign.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o -MF CMakeFiles/vf2c.dir/lbitbits.c.o.d -o CMakeFiles/vf2c.dir/lbitbits.c.o -c 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object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o -MF CMakeFiles/vf2c.dir/h_abs.c.o.d -o CMakeFiles/vf2c.dir/h_abs.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o -MF CMakeFiles/vf2c.dir/h_dnnt.c.o.d -o CMakeFiles/vf2c.dir/h_dnnt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o -MF CMakeFiles/vf2c.dir/h_indx.c.o.d -o CMakeFiles/vf2c.dir/h_indx.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_indx.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o -MF CMakeFiles/vf2c.dir/h_len.c.o.d -o CMakeFiles/vf2c.dir/h_len.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o -MF CMakeFiles/vf2c.dir/h_mod.c.o.d -o CMakeFiles/vf2c.dir/h_mod.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o -MF CMakeFiles/vf2c.dir/h_nint.c.o.d -o CMakeFiles/vf2c.dir/h_nint.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o -MF CMakeFiles/vf2c.dir/h_sign.c.o.d -o CMakeFiles/vf2c.dir/h_sign.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o -MF CMakeFiles/vf2c.dir/l_ge.c.o.d -o CMakeFiles/vf2c.dir/l_ge.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o -MF CMakeFiles/vf2c.dir/l_gt.c.o.d -o CMakeFiles/vf2c.dir/l_gt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o -MF CMakeFiles/vf2c.dir/l_le.c.o.d -o CMakeFiles/vf2c.dir/l_le.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o -MF CMakeFiles/vf2c.dir/l_lt.c.o.d -o CMakeFiles/vf2c.dir/l_lt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_lt.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o -MF CMakeFiles/vf2c.dir/hl_ge.c.o.d -o CMakeFiles/vf2c.dir/hl_ge.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o -MF CMakeFiles/vf2c.dir/hl_gt.c.o.d -o CMakeFiles/vf2c.dir/hl_gt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o -MF CMakeFiles/vf2c.dir/hl_le.c.o.d -o CMakeFiles/vf2c.dir/hl_le.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_le.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o -MF CMakeFiles/vf2c.dir/hl_lt.c.o.d -o CMakeFiles/vf2c.dir/hl_lt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o -MF CMakeFiles/vf2c.dir/ef1asc_.c.o.d -o CMakeFiles/vf2c.dir/ef1asc_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o -MF CMakeFiles/vf2c.dir/ef1cmc_.c.o.d -o CMakeFiles/vf2c.dir/ef1cmc_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o -MF CMakeFiles/vf2c.dir/f77_aloc.c.o.d 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_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o -MF CMakeFiles/vf2c.dir/s_copy.c.o.d -o CMakeFiles/vf2c.dir/s_copy.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_copy.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o -MF CMakeFiles/vf2c.dir/dtime_.c.o.d -o CMakeFiles/vf2c.dir/dtime_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dtime_.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o -MF CMakeFiles/vf2c.dir/etime_.c.o.d -o CMakeFiles/vf2c.dir/etime_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o -MF CMakeFiles/vf2c.dir/backspac.c.o.d -o CMakeFiles/vf2c.dir/backspac.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function ‘f_back’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c:47:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 47 | fread((char *)&n,sizeof(uiolen),1,f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o -MF CMakeFiles/vf2c.dir/close.c.o.d -o CMakeFiles/vf2c.dir/close.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/close.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o -MF CMakeFiles/vf2c.dir/dfe.c.o.d -o CMakeFiles/vf2c.dir/dfe.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dfe.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o cd 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o -MF CMakeFiles/vf2c.dir/due.c.o.d -o CMakeFiles/vf2c.dir/due.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/due.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o -MF CMakeFiles/vf2c.dir/endfile.c.o.d -o CMakeFiles/vf2c.dir/endfile.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/endfile.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o -MF CMakeFiles/vf2c.dir/err.c.o.d -o CMakeFiles/vf2c.dir/err.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/err.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o -MF CMakeFiles/vf2c.dir/fmt.c.o.d -o CMakeFiles/vf2c.dir/fmt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o -MF CMakeFiles/vf2c.dir/fmtlib.c.o.d -o CMakeFiles/vf2c.dir/fmtlib.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o -MF CMakeFiles/vf2c.dir/ftell_.c.o.d -o CMakeFiles/vf2c.dir/ftell_.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ftell_.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o -MF CMakeFiles/vf2c.dir/iio.c.o.d -o CMakeFiles/vf2c.dir/iio.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iio.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o -MF CMakeFiles/vf2c.dir/ilnw.c.o.d -o CMakeFiles/vf2c.dir/ilnw.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ilnw.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o -MF CMakeFiles/vf2c.dir/inquire.c.o.d -o CMakeFiles/vf2c.dir/inquire.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/inquire.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o cd 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o -MF CMakeFiles/vf2c.dir/lwrite.c.o.d -o CMakeFiles/vf2c.dir/lwrite.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o -MF CMakeFiles/vf2c.dir/open.c.o.d -o CMakeFiles/vf2c.dir/open.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/open.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o -MF CMakeFiles/vf2c.dir/rdfmt.c.o.d -o CMakeFiles/vf2c.dir/rdfmt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o -MF CMakeFiles/vf2c.dir/rewind.c.o.d -o CMakeFiles/vf2c.dir/rewind.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rewind.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o -MF CMakeFiles/vf2c.dir/rsfe.c.o.d -o CMakeFiles/vf2c.dir/rsfe.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o -MF CMakeFiles/vf2c.dir/rsli.c.o.d -o CMakeFiles/vf2c.dir/rsli.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsli.c [ 52%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -MF CMakeFiles/gamer.dir/tetgen/predicates.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o -MF CMakeFiles/vf2c.dir/rsne.c.o.d -o CMakeFiles/vf2c.dir/rsne.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o -MF CMakeFiles/vf2c.dir/sfe.c.o.d -o CMakeFiles/vf2c.dir/sfe.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sfe.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o -MF CMakeFiles/vf2c.dir/sue.c.o.d -o CMakeFiles/vf2c.dir/sue.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o -MF CMakeFiles/vf2c.dir/typesize.c.o.d -o CMakeFiles/vf2c.dir/typesize.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/typesize.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o -MF CMakeFiles/vf2c.dir/uio.c.o.d -o CMakeFiles/vf2c.dir/uio.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o -MF CMakeFiles/vf2c.dir/util.c.o.d -o CMakeFiles/vf2c.dir/util.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/util.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o -MF CMakeFiles/vf2c.dir/wref.c.o.d -o CMakeFiles/vf2c.dir/wref.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o -MF CMakeFiles/vf2c.dir/wrtfmt.c.o.d -o CMakeFiles/vf2c.dir/wrtfmt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wrtfmt.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o -MF CMakeFiles/vf2c.dir/wsfe.c.o.d -o CMakeFiles/vf2c.dir/wsfe.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o -MF CMakeFiles/vf2c.dir/wsle.c.o.d -o CMakeFiles/vf2c.dir/wsle.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsle.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o -MF CMakeFiles/vf2c.dir/wsne.c.o.d -o CMakeFiles/vf2c.dir/wsne.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsne.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o -MF CMakeFiles/vf2c.dir/xwsne.c.o.d -o CMakeFiles/vf2c.dir/xwsne.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o -MF CMakeFiles/vf2c.dir/main.c.o.d -o CMakeFiles/vf2c.dir/main.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c [ 56%] Linking C shared library libvf2c.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_link_script CMakeFiles/vf2c.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/vf2c.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o 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CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o 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CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_symlink_library libvf2c.so.1.9.3 libvf2c.so.1.9 libvf2c.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 56%] Built target vf2c make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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Scanning dependencies of target apbslib_swig_compilation make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 56%] Swig compile apbslib.i for python cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python && /usr/bin/cmake -E touch /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp cd 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'/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 56%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o -MF CMakeFiles/punc.dir/base/punc_base.c.o.d -o CMakeFiles/punc.dir/base/punc_base.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base/punc_base.c [ 56%] Linking C shared library libpunc.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/punc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/punc.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_symlink_library libpunc.so.1.9.3 libpunc.so.1.9 libpunc.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 56%] Built target punc make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o -MF CMakeFiles/mc.dir/base/mc_base.c.o.d -o CMakeFiles/mc.dir/base/mc_base.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc_base.c [ 57%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o -MF CMakeFiles/mc.dir/bam/bmat.c.o.d -o CMakeFiles/mc.dir/bam/bmat.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_galerkin’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function ‘sprintf’, inlined from ‘Bmat_galerkin’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 31 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 57%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o -MF CMakeFiles/mc.dir/bam/bsolv.c.o.d -o CMakeFiles/mc.dir/bam/bsolv.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 922 | sprintf(rn,"Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function ‘sprintf’, inlined from ‘Bvec_bcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 919 | sprintf(rn,"--->Bvec_bcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_bcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:28: warning: ‘%s’ directive writing up to 79 bytes into a region of size 73 [-Wformat-overflow=] 631 | sprintf(rn,"Bvec_cg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 87 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 628 | sprintf(rn,"--->Bvec_cg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 1422 | sprintf(rn,"Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cgnr’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 1419 | sprintf(rn,"--->Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cgnr’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 57%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o -MF CMakeFiles/mc.dir/bam/bvec.c.o.d -o CMakeFiles/mc.dir/bam/bvec.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec.c [ 58%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o -MF CMakeFiles/mc.dir/bam/mat.c.o.d -o CMakeFiles/mc.dir/bam/mat.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mat.c [ 58%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -MF CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘void tetgenmesh::constrainedfacets()’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20804:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20804 | equatptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20809:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20809 | horizptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20810:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20810 | belowptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20811:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20811 | aboveptlist = new list("point *"); | ^~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘long int tetgenmesh::reconstructmesh()’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:24383:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 24383 | markerlist = new list("int"); | ^~~~~ [ 58%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && 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-I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o -MF CMakeFiles/mc.dir/bam/slu.c.o.d -o CMakeFiles/mc.dir/bam/slu.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/slu.c [ 59%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse 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-I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o -MF CMakeFiles/mc.dir/bam/vec.c.o.d -o CMakeFiles/mc.dir/bam/vec.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec.c [ 59%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse 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-I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o -MF CMakeFiles/mc.dir/bam/zslu.c.o.d -o CMakeFiles/mc.dir/bam/zslu.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/zslu.c [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o -MF CMakeFiles/mc.dir/whb/whb.c.o.d -o CMakeFiles/mc.dir/whb/whb.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/whb.c [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o -MF CMakeFiles/mc.dir/whb/bvechb.c.o.d -o CMakeFiles/mc.dir/whb/bvechb.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 267 | sprintf(rn,"Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function ‘sprintf’, inlined from ‘Bvec_hcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 264 | sprintf(rn,"--->Bvec_hcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 474 | sprintf(rn,"Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hbcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 471 | sprintf(rn,"--->Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hbcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function ‘Bvec_ctorPoint’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:28: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483646] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function ‘sprintf’, inlined from ‘Bvec_ctorPoint’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 3 and 21 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o -MF CMakeFiles/mc.dir/whb/rcmat.c.o.d -o CMakeFiles/mc.dir/whb/rcmat.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/rcmat.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o -MF CMakeFiles/mc.dir/whb/brcmat.c.o.d -o CMakeFiles/mc.dir/whb/brcmat.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/brcmat.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o -MF CMakeFiles/mc.dir/whb/subopt.c.o.d -o CMakeFiles/mc.dir/whb/subopt.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:31: warning: ‘%s’ directive writing up to 79 bytes into a region of size 70 [-Wformat-overflow=] 495 | sprintf(rn,"Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function ‘sprintf’, inlined from ‘Bvec_sfpcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from ‘Bvec_submethod’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 11 and 90 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:35: warning: ‘%s’ directive writing up to 79 bytes into a region of size 66 [-Wformat-overflow=] 492 | sprintf(rn,"--->Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from ‘Bvec_submethod’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 15 and 94 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 776 | sprintf(rn,"Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpbcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from ‘Bvec_submethod’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:36: warning: ‘%s’ directive writing up to 79 bytes into a region of size 65 [-Wformat-overflow=] 773 | sprintf(rn,"--->Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpbcg’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from ‘Bvec_submethod’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 16 and 95 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o -MF CMakeFiles/mc.dir/aprx/aprx.c.o.d -o CMakeFiles/mc.dir/aprx/aprx.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o -MF CMakeFiles/mc.dir/aprx/assem.c.o.d -o CMakeFiles/mc.dir/aprx/assem.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/assem.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o -MF CMakeFiles/mc.dir/aprx/bnode.c.o.d -o CMakeFiles/mc.dir/aprx/bnode.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/bnode.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o -MF CMakeFiles/mc.dir/aprx/estim.c.o.d -o CMakeFiles/mc.dir/aprx/estim.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/estim.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o -MF CMakeFiles/mc.dir/aprx/eval.c.o.d -o CMakeFiles/mc.dir/aprx/eval.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 368 | sprintf(filename, "f%dz.dat", block); | ^ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 366 | sprintf(filename, "f%dy.dat", block); | ^ In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 364 | sprintf(filename, "f%dx.dat", block); | ^ In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o -MF CMakeFiles/mc.dir/aprx/io.c.o.d -o CMakeFiles/mc.dir/aprx/io.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/io.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o -MF CMakeFiles/mc.dir/aprx/node.c.o.d -o CMakeFiles/mc.dir/aprx/node.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/node.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o -MF CMakeFiles/mc.dir/aprx/parti.c.o.d -o CMakeFiles/mc.dir/aprx/parti.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/parti.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o -MF CMakeFiles/mc.dir/aprx/re.c.o.d -o CMakeFiles/mc.dir/aprx/re.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/re.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o -MF CMakeFiles/mc.dir/gem/vel.c.o.d -o CMakeFiles/mc.dir/gem/vel.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/vel.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o -MF CMakeFiles/mc.dir/gem/ves.c.o.d -o CMakeFiles/mc.dir/gem/ves.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/ves.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o -MF CMakeFiles/mc.dir/gem/gem.c.o.d -o CMakeFiles/mc.dir/gem/gem.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o -MF CMakeFiles/mc.dir/gem/gemchk.c.o.d -o CMakeFiles/mc.dir/gem/gemchk.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemchk.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o -MF CMakeFiles/mc.dir/gem/gemdisp.c.o.d -o CMakeFiles/mc.dir/gem/gemdisp.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:33: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 1656 | sprintf(str1,"TETRAHEDRA"); | ^ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:33: warning: ‘TETRAHEDRON’ directive writing 11 bytes into a region of size 10 [-Wformat-overflow=] 1657 | sprintf(str2,"TETRAHEDRON"); | ~~~~~~~~~~^ In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o -MF CMakeFiles/mc.dir/gem/gemg.c.o.d -o CMakeFiles/mc.dir/gem/gemg.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemg.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o -MF CMakeFiles/mc.dir/gem/gemgen.c.o.d -o CMakeFiles/mc.dir/gem/gemgen.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function ‘Gem_delaunay’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type ‘double *[4]’ In file included from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type ‘double *[4]’ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type ‘double *[4]’ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o -MF CMakeFiles/mc.dir/gem/gemio.c.o.d -o CMakeFiles/mc.dir/gem/gemio.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemio.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o -MF CMakeFiles/mc.dir/gem/gemref.c.o.d -o CMakeFiles/mc.dir/gem/gemref.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemref.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o -MF CMakeFiles/mc.dir/gem/gemunref.c.o.d -o CMakeFiles/mc.dir/gem/gemunref.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 68%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -MF CMakeFiles/gamer.dir/biom/CorrectNormals.C.o.d -o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemcube.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde/pde.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/am.c [ 69%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -MF CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o.d -o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/lsolv.c [ 69%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o -MF CMakeFiles/gamer.dir/biom/MarchingCube.C.o.d -o CMakeFiles/gamer.dir/biom/MarchingCube.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/nsolv.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/dyn.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o -MF CMakeFiles/mc.dir/dyn/svio.c.o.d -o CMakeFiles/mc.dir/dyn/svio.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/svio.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o -MF CMakeFiles/mc.dir/mcsh/mcsh.c.o.d -o CMakeFiles/mc.dir/mcsh/mcsh.c.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function ‘MCsh_builtIn’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 765 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 766 | sock, | ~~~~~ 767 | defKey, | ~~~~~~~ 768 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 769 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 771 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | defX, | ~~~~~ 773 | "GV"); | ~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type ‘double *[4]’ In file included from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=] 810 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 811 | sock, | ~~~~~ 812 | defKey, | ~~~~~~~ 813 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 816 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 | defX, | ~~~~~ 818 | "MATH"); | ~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type ‘double *[4]’ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ [ 71%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 71%] Linking C shared library libmc.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/mc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/mc.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_symlink_library libmc.so.1.9.3 libmc.so.1.9 libmc.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 71%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/src/generic /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 72%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/nosh.c [ 72%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Volume.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function ‘float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:85:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(fp,"%d\n",&m); | ~~~~~~^~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:88:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fscanf(fp,"%f %f %f %f\n",&x,&y,&z,&radius); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o -MF CMakeFiles/gamer.dir/biom/ReadLattice.C.o.d -o CMakeFiles/gamer.dir/biom/ReadLattice.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C [ 72%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/mgparm.c [ 72%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o -MF CMakeFiles/gamer.dir/biom/ReadPDB.C.o.d -o CMakeFiles/gamer.dir/biom/ReadPDB.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 72%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF CMakeFiles/apbs_generic.dir/femparm.c.o.d -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/femparm.c [ 72%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/pbamparm.c [ 73%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -MF CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o.d -o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘SurfaceMesh* SurfaceMesh_readOFF(char*)’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:401:14: warning: too many arguments for format [-Wformat-extra-args] 401 | printf("Read error. Expected 3 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:494:14: warning: too many arguments for format [-Wformat-extra-args] 494 | printf("Read error. Expected 4 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)’: /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:754:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 754 | in.save_nodes("plc"); | ^~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:755:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 755 | in.save_poly("plc"); | ^~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:761:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 761 | out.save_nodes("result"); | ^~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:762:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 762 | out.save_elements("result"); | ^~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:763:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 763 | out.save_faces("result"); | ^~~~~~~~ [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/pbsamparm.c [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/pbeparm.c [ 74%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/bemparm.c [ 74%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -MF CMakeFiles/gamer.dir/biom/RegionGrowing.C.o.d -o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/geoflowparm.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/apolparm.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF CMakeFiles/apbs_generic.dir/vacc.c.o.d -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vacc.c [ 75%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -MF CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o.d -o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 76%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o -MF CMakeFiles/gamer.dir/biom/SurfExtract.C.o.d -o CMakeFiles/gamer.dir/biom/SurfExtract.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF CMakeFiles/apbs_generic.dir/valist.c.o.d -o CMakeFiles/apbs_generic.dir/valist.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/valist.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF CMakeFiles/apbs_generic.dir/vatom.c.o.d -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vatom.c [ 77%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o -MF CMakeFiles/gamer.dir/biom/SurfRefine.C.o.d -o CMakeFiles/gamer.dir/biom/SurfRefine.C.o -c /build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vpbe.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vcap.c [ 77%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS 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-D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vstring.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF CMakeFiles/apbs_generic.dir/vparam.c.o.d -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vparam.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/generic/vgreen.c [ 78%] Linking CXX shared library libgamer.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 [ 79%] Linking C shared library libapbs_generic.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/apbs_generic.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/generic && /usr/bin/cmake -E cmake_symlink_library libapbs_generic.so.3 libapbs_generic.so.3 libapbs_generic.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 79%] Built target apbs_generic make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/src/pmgc /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/gamer.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_symlink_library libgamer.so.1.9.3 libgamer.so.1.9 libgamer.so [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/buildAd.c make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 80%] Built target gamer make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/src/fem /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 80%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o -MF CMakeFiles/apbs_fem.dir/vcsm.c.o.d -o CMakeFiles/apbs_fem.dir/vcsm.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/fem/vcsm.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/buildBd.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/buildGd.c [ 81%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o -MF CMakeFiles/apbs_fem.dir/vfetk.c.o.d -o CMakeFiles/apbs_fem.dir/vfetk.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c: In function ‘Bmat_printHB’: /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1073:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1073 | sprintf(ptrfmt,"(%dI%d)",nptrline,numZdigits+1); | ^ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.h:67, from /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:57: In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1073:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c: In function ‘Bmat_printHB’: /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1074:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~ /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1074:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c: In function ‘Bmat_printHB’: /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1075:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1075 | sprintf(indfmt,"(%dI%d)",nindline,nrowdigits+1); | ^ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1075:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c: In function ‘Bmat_printHB’: /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1076:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~ /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /build/apbs-PSc155/apbs-3.4.1/src/fem/vfetk.c:1076:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 81%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o -MF CMakeFiles/apbs_fem.dir/vpee.c.o.d -o CMakeFiles/apbs_fem.dir/vpee.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/fem/vpee.c [ 81%] Linking C shared library libapbs_fem.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/apbs_fem.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/fem && /usr/bin/cmake -E cmake_symlink_library libapbs_fem.so.3 libapbs_fem.so.3 libapbs_fem.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 81%] Built target apbs_fem [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/buildPd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/cgd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/gsd.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/matvecd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mgcsd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mgdrvd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mgsubd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mikpckd.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mlinpckd.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mypdec.c [ 84%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/newtond.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/newdrvd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/powerd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/smoothd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/pmgc/mgfasd.c [ 86%] Linking C shared library libapbs_pmgc.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/apbs_pmgc.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/x86_64-linux-gnu/libblas.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/pmgc && /usr/bin/cmake -E cmake_symlink_library libapbs_pmgc.so.3 libapbs_pmgc.so.3 libapbs_pmgc.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 86%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/src/mg /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/mg/vgrid.c [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/mg/vmgrid.c /build/apbs-PSc155/apbs-3.4.1/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /build/apbs-PSc155/apbs-3.4.1/src/mg/vgrid.c:853:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF CMakeFiles/apbs_mg.dir/vopot.c.o.d -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/mg/vopot.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/mg/vpmg.c /build/apbs-PSc155/apbs-3.4.1/src/mg/vgrid.c:831:7: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/src/mg/vgrid.h:67, from /build/apbs-PSc155/apbs-3.4.1/src/mg/vgrid.c:57: /usr/include/stdio.h:184:12: note: in a call to function ‘fclose’ declared ‘nonnull’ 184 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/mg/vpmgp.c [ 87%] Linking C shared library libapbs_mg.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/apbs_mg.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 87%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF CMakeFiles/apbs_routines.dir/routines.c.o.d -o CMakeFiles/apbs_routines.dir/routines.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/routines.c /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘initAPOL’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5046 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type ‘char[1024]’ /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /build/apbs-PSc155/apbs-3.4.1/src/generic/apolparm.h:73, from /build/apbs-PSc155/apbs-3.4.1/src/generic/nosh.h:73, from /build/apbs-PSc155/apbs-3.4.1/src/apbs.h:70, from /build/apbs-PSc155/apbs-3.4.1/src/routines.h:64, from /build/apbs-PSc155/apbs-3.4.1/src/routines.c:54: /build/apbs-PSc155/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5048 | atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type ‘char[1024]’ /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /build/apbs-PSc155/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type ‘char[1024]’ /build/apbs-PSc155/apbs-3.4.1/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writematMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2020:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2020 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /build/apbs-PSc155/apbs-3.4.1/src/apbs.h:67: In function ‘sprintf’, inlined from ‘writematMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2020:9: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2919:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2919 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2919:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2963:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2963 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2963:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2954:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2954 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2954:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2937:34: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2937 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2937:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2930:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2930 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2930:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2944:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2944 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2944:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataMG’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2909:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2909 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:2909:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataFE’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:4887:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4887 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:4887:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataFE’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:4893:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4893 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:4893:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/routines.c: In function ‘writedataFE’: /build/apbs-PSc155/apbs-3.4.1/src/routines.c:4880:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4880 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /build/apbs-PSc155/apbs-3.4.1/src/routines.c:4880:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 88%] Linking C shared library libapbs_routines.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/apbs_routines.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /build/apbs-PSc155/apbs-3.4.1/src/main.c [ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src 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319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/src/main.c:319:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ [ 89%] Linking C executable ../bin/mgmesh cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 [ 89%] Linking C executable apbs cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/mgmesh.dir/link.d CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so 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make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde 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/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 89%] Built target apbs make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 89%] 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CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/dxmath.c [ 89%] Linking C executable ../bin/smooth cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 [ 89%] Linking C executable ../bin/dxmath cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/smooth.dir/link.d CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth 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/build/apbs-PSc155/apbs-3.4.1/tools/mesh/mergedx.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/dxmath.dir/link.d CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 90%] Built target dxmath make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o -MF CMakeFiles/mergedx2.dir/mergedx2.c.o.d -o CMakeFiles/mergedx2.dir/mergedx2.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/mergedx2.c [ 90%] Linking C executable ../bin/mergedx cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/mergedx.dir/link.d CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 90%] Linking C executable ../bin/mergedx2 cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 [ 90%] Built target mergedx make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/value.dir/value.c.o -MF CMakeFiles/value.dir/value.c.o.d -o CMakeFiles/value.dir/value.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/value.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/mergedx2.dir/link.d CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 91%] Linking C executable ../bin/value cd 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tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/multivalue.c [ 92%] Linking C executable ../bin/multivalue cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/value.dir/link.d CMakeFiles/value.dir/value.c.o -o ../bin/value ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 92%] Built target value make -f tools/mesh/CMakeFiles/benchmark.dir/build.make 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-ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/multivalue.dir/link.d CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 92%] Built target multivalue make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/similarity.c [ 93%] Linking C executable ../bin/benchmark cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/benchmark.dir/link.d CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 93%] Built target benchmark make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/analysis.c [ 94%] Linking C executable ../bin/similarity cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/similarity.dir/link.d CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 94%] Built target similarity make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 95%] Linking C executable ../bin/analysis cd 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-D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/dx2mol.c [ 95%] Linking C executable ../bin/dx2mol cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/analysis.dir/link.d CMakeFiles/analysis.dir/analysis.c.o -o ../bin/analysis ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 95%] Built target analysis make -f 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-I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/dx2uhbd.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/dx2mol.dir/link.d CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 95%] Built target dx2mol make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh 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-I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c: In function ‘main’: /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c:76:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c:89:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c:97:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c:103:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/del2dx.c:106:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Linking C executable ../bin/del2dx cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/dx2uhbd.dir/link.d CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 97%] Built target dx2uhbd make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 98%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c: In function ‘main’: /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file=CMakeFiles/del2dx.dir/link.d CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 98%] Built target del2dx make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake "--color=" [ 98%] Linking C executable ../bin/tensor2dx cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 98%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/apbs-PSc155/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | 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CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 98%] Built target tensor2dx make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[3]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/apbs-PSc155/apbs-3.4.1 /build/apbs-PSc155/apbs-3.4.1/tools/manip /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake "--color=" [ 98%] Linking C executable ../bin/uhbd_asc2bin cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make -f 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/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [ 99%] Built target _apbslib [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -c /build/apbs-PSc155/apbs-3.4.1/tools/python-pybind/bind_nosh.cpp [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -c /build/apbs-PSc155/apbs-3.4.1/tools/python-pybind/bind_vatom.cpp [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/apbs-PSc155/apbs-3.4.1/src -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/src -I/build/apbs-PSc155/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/mc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/_deps/fetk-build/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/apbs-PSc155/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -c /build/apbs-PSc155/apbs-3.4.1/tools/python-pybind/bind_valist.cpp [100%] Linking CXX shared module apbs.cpython-313-x86_64-linux-gnu.so cd /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python-pybind && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pybind.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/apbs-PSc155/apbs-3.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/apbs_pybind.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-313-x86_64-linux-gnu.so CMakeFiles/apbs_pybind.dir/module.cpp.o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so /usr/lib/x86_64-linux-gnu/libblas.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/x86_64-linux-gnu/libarpack.so /usr/lib/x86_64-linux-gnu/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/x86_64-linux-gnu/libumfpack.so /usr/lib/x86_64-linux-gnu/libspqr.so /usr/lib/x86_64-linux-gnu/libcholmod.so /usr/lib/x86_64-linux-gnu/libccolamd.so /usr/lib/x86_64-linux-gnu/libcamd.so /usr/lib/x86_64-linux-gnu/libcolamd.so /usr/lib/x86_64-linux-gnu/libamd.so -lm -ldl /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/apbs-PSc155/apbs-3.4.1' PYTHONPATH=/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/tools/python sphinx-build -b html docs /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/docs/_build/html # HTML generator Running Sphinx v8.1.3 loading translations [en]... done WARNING: html_static_path entry '_static' does not exist [autosummary] generating autosummary for: api/index.rst, background.rst, formats/apbs-xml-parm.rst, formats/flat-parm.rst, formats/harwell.rst, formats/index.rst, formats/mcsf.rst, formats/opendx.rst, formats/pdb.rst, formats/pqr.rst, ..., using/input/old/generic/sdens.rst, using/input/old/generic/srad.rst, using/input/old/generic/swin.rst, using/input/old/generic/temp.rst, using/input/old/index.rst, using/input/old/print.rst, using/input/old/read.rst, using/tests.rst, using/tools.rst, using/units.rst WARNING: Failed to import apbs.input_file.calculate.finite_difference. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.finite_element. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.nonpolar.Nonpolar. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.process. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.boundary_element. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.calculate.generic. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' WARNING: Failed to import apbs.input_file.read. Possible hints: * ModuleNotFoundError: No module named 'pyparsing' * AttributeError: module 'apbs' has no attribute 'input_file' loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 127 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 1%] api/index reading sources... [ 2%] background reading sources... [ 2%] formats/apbs-xml-parm reading sources... [ 3%] formats/flat-parm reading sources... [ 4%] formats/harwell reading sources... [ 5%] formats/index reading sources... [ 6%] formats/mcsf reading sources... [ 6%] formats/opendx reading sources... [ 7%] formats/pdb reading sources... [ 8%] formats/pqr reading sources... [ 9%] formats/uhbd reading sources... [ 9%] formats/xml-struct reading sources... [ 10%] getting/index reading sources... [ 11%] getting/source reading sources... [ 12%] help reading sources... [ 13%] index reading sources... [ 13%] reading reading sources... [ 14%] releases reading sources... [ 15%] supporting reading sources... [ 16%] todo reading sources... [ 17%] using/examples/binding-energies reading sources... [ 17%] using/examples/salt-linkage reading sources... [ 18%] using/examples/solvation-energies reading sources... [ 19%] using/examples/visualization-pymol reading sources... [ 20%] using/examples/visualization-unitymol reading sources... [ 20%] using/index reading sources... [ 21%] using/input/new/calculate/boundary_element reading sources... [ 22%] using/input/new/calculate/finite_difference reading sources... [ 23%] using/input/new/calculate/finite_element reading sources... [ 24%] using/input/new/calculate/index reading sources... [ 24%] using/input/new/calculate/nonpolar reading sources... [ 25%] using/input/new/index reading sources... [ 26%] using/input/new/process reading sources... [ 27%] using/input/new/process_api reading sources... [ 28%] using/input/new/read reading sources... [ 28%] using/input/old/apolar/dpos reading sources... [ 29%] using/input/old/apolar/gamma reading sources... [ 30%] using/input/old/apolar/index reading sources... [ 31%] using/input/old/apolar/press reading sources... [ 31%] using/input/old/apolar/srfm reading sources... [ 32%] using/input/old/elec/3dmap reading sources... [ 33%] using/input/old/elec/akeyPRE reading sources... [ 34%] using/input/old/elec/akeySOLVE reading sources... [ 35%] using/input/old/elec/async reading sources... [ 35%] using/input/old/elec/bcfl reading sources... [ 36%] using/input/old/elec/cgcent reading sources... [ 37%] using/input/old/elec/cglen reading sources... [ 38%] using/input/old/elec/chgm reading sources... [ 39%] using/input/old/elec/diff reading sources... [ 39%] using/input/old/elec/dime reading sources... [ 40%] using/input/old/elec/domainLength reading sources... [ 41%] using/input/old/elec/dx reading sources... [ 42%] using/input/old/elec/ekey reading sources... [ 43%] using/input/old/elec/etol reading sources... [ 43%] using/input/old/elec/exp reading sources... [ 44%] using/input/old/elec/fe-manual reading sources... [ 45%] using/input/old/elec/fgcent reading sources... [ 46%] using/input/old/elec/fglen reading sources... [ 46%] using/input/old/elec/gamma-geoflow reading sources... [ 47%] using/input/old/elec/gcent reading sources... [ 48%] using/input/old/elec/geoflow-auto reading sources... [ 49%] using/input/old/elec/glen reading sources... [ 50%] using/input/old/elec/grid2d reading sources... [ 50%] using/input/old/elec/gridpts reading sources... [ 51%] using/input/old/elec/imat reading sources... [ 52%] using/input/old/elec/index reading sources... [ 53%] using/input/old/elec/ion reading sources... [ 54%] using/input/old/elec/lpbe reading sources... [ 54%] using/input/old/elec/lrpbe reading sources... [ 55%] using/input/old/elec/mac reading sources... [ 56%] using/input/old/elec/maxsolve reading sources... [ 57%] using/input/old/elec/maxvert reading sources... [ 57%] using/input/old/elec/mesh reading sources... [ 58%] using/input/old/elec/mg-auto reading sources... [ 59%] using/input/old/elec/mg-dummy reading sources... [ 60%] using/input/old/elec/mg-manual reading sources... [ 61%] using/input/old/elec/mg-para reading sources... [ 61%] using/input/old/elec/nlev reading sources... [ 62%] using/input/old/elec/npbe reading sources... [ 63%] using/input/old/elec/nrpbe reading sources... [ 64%] using/input/old/elec/ntraj reading sources... [ 65%] using/input/old/elec/ofrac reading sources... [ 65%] using/input/old/elec/outdata reading sources... [ 66%] using/input/old/elec/pbam-auto reading sources... [ 67%] using/input/old/elec/pbc reading sources... [ 68%] using/input/old/elec/pbsam-auto reading sources... [ 69%] using/input/old/elec/pdie reading sources... [ 69%] using/input/old/elec/pdime reading sources... [ 70%] using/input/old/elec/press-geoflow reading sources... [ 71%] using/input/old/elec/pygbe reading sources... [ 72%] using/input/old/elec/randorient reading sources... [ 72%] using/input/old/elec/runname reading sources... [ 73%] using/input/old/elec/runtype reading sources... [ 74%] using/input/old/elec/salt reading sources... [ 75%] using/input/old/elec/sdie reading sources... [ 76%] using/input/old/elec/srfm reading sources... [ 76%] using/input/old/elec/surf reading sources... [ 77%] using/input/old/elec/tabi reading sources... [ 78%] using/input/old/elec/targetNum reading sources... [ 79%] using/input/old/elec/targetRes reading sources... [ 80%] using/input/old/elec/term reading sources... [ 80%] using/input/old/elec/termcombine reading sources... [ 81%] using/input/old/elec/tolsp reading sources... [ 82%] using/input/old/elec/tree_n0 reading sources... [ 83%] using/input/old/elec/tree_order reading sources... [ 83%] using/input/old/elec/units reading sources... [ 84%] using/input/old/elec/usemap reading sources... [ 85%] using/input/old/elec/usemesh reading sources... [ 86%] using/input/old/elec/vdwdisp reading sources... [ 87%] using/input/old/elec/write reading sources... [ 87%] using/input/old/elec/writemat reading sources... [ 88%] using/input/old/elec/xyz reading sources... [ 89%] using/input/old/generic/bconc reading sources... [ 90%] using/input/old/generic/calcenergy reading sources... [ 91%] using/input/old/generic/calcforce reading sources... [ 91%] using/input/old/generic/grid reading sources... [ 92%] using/input/old/generic/mol reading sources... [ 93%] using/input/old/generic/sdens reading sources... [ 94%] using/input/old/generic/srad reading sources... [ 94%] using/input/old/generic/swin reading sources... [ 95%] using/input/old/generic/temp reading sources... [ 96%] using/input/old/index reading sources... [ 97%] using/input/old/print reading sources... [ 98%] using/input/old/read reading sources... [ 98%] using/tests reading sources... [ 99%] using/tools reading sources... [100%] using/units /build/apbs-PSc155/apbs-3.4.1/docs/getting/index.rst:41: ERROR: Unexpected indentation. [docutils] /build/apbs-PSc155/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow". [docutils] /build/apbs-PSc155/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk". [docutils] /build/apbs-PSc155/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam". [docutils] /build/apbs-PSc155/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "tabi-pb". [docutils] WARNING: autodoc: failed to import module 'input_file.calculate.boundary_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file.calculate.finite_difference' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file.calculate.finite_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file.calculate' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file.calculate.generic' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] /build/apbs-PSc155/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition. [docutils] /build/apbs-PSc155/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document may not end with a transition. [docutils] WARNING: autodoc: failed to import module 'input_file.calculate.nonpolar.Nonpolar' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file.process' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] WARNING: autodoc: failed to import module 'input_file.read' from module 'apbs'; the following exception was raised: No module named 'pyparsing' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/3dmap.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/3dmap /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/bcfl.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/geoflow-auto', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/bcfl /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/cgcent.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/cgcent /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/cglen.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/cglen /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/chgm.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/chgm /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/diff.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/diff /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/dime.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/dime /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/dx.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/dx /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/etol.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/geoflow-auto', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/etol /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/fgcent.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/fgcent /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/fglen.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/fglen /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/gcent.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual'], selecting: using/input/old/elec/mg-manual <- using/input/old/elec/gcent /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/glen.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual'], selecting: using/input/old/elec/mg-manual <- using/input/old/elec/glen /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/grid2d.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/grid2d /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/ion.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/elec/ion /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/lpbe.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/geoflow-auto', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/lpbe /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/lrpbe.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/lrpbe /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/npbe.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/npbe /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/ntraj.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/ntraj /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/pbc.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/pbc /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/pdie.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/geoflow-auto', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/elec/pdie /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/randorient.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/randorient /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/runname.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/runname /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/runtype.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/runtype /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/salt.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/salt /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/sdie.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/geoflow-auto', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/elec/sdie /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/srfm.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/srfm /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/term.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/term /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/termcombine.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/termcombine /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/units.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/units /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/usemap.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/usemap /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/write.rst: document is referenced in multiple toctrees: ['using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/write /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/writemat.rst: document is referenced in multiple toctrees: ['using/input/old/elec/mg-auto', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/elec/writemat /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/elec/xyz.rst: document is referenced in multiple toctrees: ['using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto'], selecting: using/input/old/elec/pbsam-auto <- using/input/old/elec/xyz /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/bconc.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/geoflow-auto'], selecting: using/input/old/elec/geoflow-auto <- using/input/old/generic/bconc /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/calcenergy.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/generic/calcenergy /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/calcforce.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/generic/calcforce /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/grid.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual'], selecting: using/input/old/elec/mg-manual <- using/input/old/generic/grid /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/mol.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/geoflow-auto', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/pbam-auto', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/generic/mol /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/sdens.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/generic/sdens /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/srad.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/generic/srad /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/swin.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para'], selecting: using/input/old/elec/mg-para <- using/input/old/generic/swin /build/apbs-PSc155/apbs-3.4.1/docs/using/input/old/generic/temp.rst: document is referenced in multiple toctrees: ['using/input/old/apolar/index', 'using/input/old/elec/fe-manual', 'using/input/old/elec/mg-auto', 'using/input/old/elec/mg-dummy', 'using/input/old/elec/mg-manual', 'using/input/old/elec/mg-para', 'using/input/old/elec/pbam-auto', 'using/input/old/elec/pbsam-auto', 'using/input/old/elec/tabi'], selecting: using/input/old/elec/tabi <- using/input/old/generic/temp done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/docs/_build/html/_static/basic.css Writing evaluated template result to /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/docs/_build/html/_static/documentation_options.js Writing evaluated template result to /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/docs/_build/html/_static/language_data.js Writing evaluated template result to /build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu/docs/_build/html/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] api/index writing output... [ 2%] background writing output... [ 2%] formats/apbs-xml-parm writing output... [ 3%] formats/flat-parm writing output... [ 4%] formats/harwell writing output... [ 5%] formats/index writing output... [ 6%] formats/mcsf writing output... [ 6%] formats/opendx writing output... [ 7%] formats/pdb writing output... [ 8%] formats/pqr writing output... [ 9%] formats/uhbd writing output... [ 9%] formats/xml-struct writing output... [ 10%] getting/index writing output... [ 11%] getting/source writing output... [ 12%] help writing output... [ 13%] index writing output... [ 13%] reading writing output... [ 14%] releases writing output... [ 15%] supporting writing output... [ 16%] todo writing output... [ 17%] using/examples/binding-energies writing output... [ 17%] using/examples/salt-linkage writing output... [ 18%] using/examples/solvation-energies writing output... [ 19%] using/examples/visualization-pymol writing output... [ 20%] using/examples/visualization-unitymol writing output... [ 20%] using/index writing output... [ 21%] using/input/new/calculate/boundary_element writing output... [ 22%] using/input/new/calculate/finite_difference writing output... [ 23%] using/input/new/calculate/finite_element writing output... [ 24%] using/input/new/calculate/index writing output... 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[ 96%] using/input/old/index writing output... [ 97%] using/input/old/print writing output... [ 98%] using/input/old/read writing output... [ 98%] using/tests writing output... [ 99%] using/tools writing output... [100%] using/units generating indices... genindex py-modindex done highlighting module code... writing additional pages... search done copying images... [ 10%] media/pb-schematic.png copying images... [ 20%] media/apbs_bind_eng.png copying images... [ 30%] media/rna-qdens-pymol.jpg copying images... [ 40%] media/rna-qdens-vmd.jpg copying images... [ 50%] media/apbs_sol_eng.png copying images... [ 60%] media/fas2-iso-pymol.png copying images... [ 70%] media/fas2-surf-pymol.png copying images... [ 80%] media/1fas_VR.png copying images... [ 90%] media/UI.png copying images... [100%] media/AChE.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 28 warnings. The HTML pages are in obj-x86_64-linux-gnu/docs/_build/html. make[1]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j2 install DESTDIR=/build/apbs-PSc155/apbs-3.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/apbs-PSc155/apbs-3.4.1 -B/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- 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/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx make[1]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/apbs-PSc155/apbs-3.4.1' (cd tests; PATH=/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/build/apbs-PSc155/apbs-3.4.1/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) TESTING WITH BINARY_NAME:apbs START_DIR:/build/apbs-PSc155/apbs-3.4.1/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.000668 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs Testing all sections The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv ================================================================================ Running tests for born section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) *** PASSED *** Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) *** PASSED *** Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) *** PASSED *** Elapsed time: 4.905163 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] COMPUTED RESULT 960.7073836227 COMPUTED RESULT 2200.266567971 COMPUTED RESULT 4732.245131587 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.7735526282 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) *** PASSED *** Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) *** PASSED *** Elapsed time: 4.110576 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 2201.243880085 COMPUTED RESULT 4733.006258977 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.0124252387 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE0.out BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE1.out BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605696E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605696e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE2.out BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344954e+01 Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) *** PASSED *** Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) *** PASSED *** Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) *** PASSED *** Elapsed time: 23.560085 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] COMPUTED RESULT 960.7073836226 COMPUTED RESULT 3257.1427835731997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867463003 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE0.out BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE1.out BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE2.out BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328301e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734462084052e+01 Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) *** PASSED *** Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) *** PASSED *** Elapsed time: 21.206385 seconds -------------------------------------------------------------------------------- Total elapsed time: 53.782877 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermediate energies in input file apbs-smol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 3258.1578983732998 COMPUTED RESULT 5942.108652589999 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -229.38714395599 Running tests for actin-dimer-auto section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058625E+02 kJ/mol Global net ELEC energy = 1.048683058625E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) *** PASSED *** Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) *** PASSED *** Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) *** PASSED *** Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) *** PASSED *** Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) *** PASSED *** Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) *** PASSED *** Testing computed result against expected result (1.048683058625e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 111.561504 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058625] EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] COMPUTED RESULT 152761.7850342 COMPUTED RESULT 291951.0754196 COMPUTED RESULT 152767.184488 COMPUTED RESULT 291546.8859278 COMPUTED RESULT 305631.7807611 COMPUTED RESULT 583602.8296532 COMPUTED RESULT 104.8683058625 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077691E+02 kJ/mol Global net ELEC energy = 1.095841077691E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) *** PASSED *** Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) *** PASSED *** Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) *** PASSED *** Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) *** PASSED *** Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) *** PASSED *** Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) *** PASSED *** Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 84.563137 seconds -------------------------------------------------------------------------------- Total elapsed time: 196.124641 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] COMPUTED RESULT 152863.2421825 COMPUTED RESULT 292061.866232 COMPUTED RESULT 152929.7900572 COMPUTED RESULT 291659.2202835 COMPUTED RESULT 305924.4262535 COMPUTED RESULT 583830.6706232 COMPUTED RESULT 109.5841077691 Running tests for alkanes section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'alkanes.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) *** PASSED *** Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) *** PASSED *** Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) *** PASSED *** Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) *** PASSED *** Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) *** PASSED *** Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) *** PASSED *** Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) *** PASSED *** Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) *** PASSED *** Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) *** PASSED *** Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) *** PASSED *** Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) *** PASSED *** Elapsed time: 13.017623 seconds -------------------------------------------------------------------------------- Total elapsed time: 13.017623 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in Checking for intermediate energies in input file alkanes.out EXPECTED COMPUTED: 11 EXPECTED EXPECTED: 11 COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01'] COMPUTED RESULT 14.39739455792 COMPUTED RESULT 12.08346456826 COMPUTED RESULT 13.54016672221 COMPUTED RESULT 9.363673200142 COMPUTED RESULT 9.422717598546 COMPUTED RESULT 16.40068943201 COMPUTED RESULT 13.23144287435 COMPUTED RESULT 7.894367190329 COMPUTED RESULT 14.49633815052 COMPUTED RESULT 14.47900211546 COMPUTED RESULT 11.92358496286 Running tests for FKBP section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086371E+01 kJ/mol Global net ELEC energy = 1.500810086371E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) *** PASSED *** Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) *** PASSED *** Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) *** PASSED *** Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 15.410997 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermediate energies in input file 1d7h-dmso-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086371] EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01'] COMPUTED RESULT 10608.99690259 COMPUTED RESULT 42765.23673491 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 39.61107503213 COMPUTED RESULT 712.1048606059 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10584.10584089 COMPUTED RESULT 42053.85249581 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3335.429017008 COMPUTED RESULT -21.80527370616 COMPUTED RESULT -3328.631844166 COMPUTED RESULT 15.00810086371 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7h-dmso-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192073E+01 kJ/mol Global net ELEC energy = 1.624454192073E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) *** PASSED *** Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) *** PASSED *** Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) *** PASSED *** Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 14.288466 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermediate energies in input file 1d7h-dmso-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192073] EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01'] COMPUTED RESULT 10749.48704824 COMPUTED RESULT 42894.87256481 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 37.19709905887 COMPUTED RESULT 712.5747080979 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10716.54753674 COMPUTED RESULT 42181.78203716 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3205.793187109 COMPUTED RESULT -21.33542621421 COMPUTED RESULT -3200.702302816 COMPUTED RESULT 16.24454192073 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) *** PASSED *** Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) *** PASSED *** Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) *** PASSED *** Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 18.765452 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermediate energies in input file 1d7i-dss-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933668] EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01'] COMPUTED RESULT 9160.578033846 COMPUTED RESULT 39557.01871716 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 94.31133325426 COMPUTED RESULT 1677.348113184 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9040.108332204 COMPUTED RESULT 37877.47796627 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -3460.997931137 COMPUTED RESULT -20.52167100108 COMPUTED RESULT -3454.901259473 COMPUTED RESULT 14.42499933668 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) *** PASSED *** Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) *** PASSED *** Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) *** PASSED *** Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 14.179213 seconds -------------------------------------------------------------------------------- Total elapsed time: 62.644128 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file 1d7i-dss-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742844] EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01'] COMPUTED RESULT 9634.884642408 COMPUTED RESULT 40031.77540425 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 79.42232645345 COMPUTED RESULT 1677.798535473 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9507.068451372 COMPUTED RESULT 38350.75772299 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -2986.24124404 COMPUTED RESULT -20.07124871262 COMPUTED RESULT -2981.621502756 COMPUTED RESULT 15.45150742844 Running tests for hca-bind section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) *** PASSED *** Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) *** PASSED *** Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) *** PASSED *** Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) *** PASSED *** Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) *** PASSED *** Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) *** PASSED *** Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) *** PASSED *** Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) *** PASSED *** Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) *** PASSED *** Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 16.003001 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01'] COMPUTED RESULT 221.3600726771 COMPUTED RESULT 1825.764811255 COMPUTED RESULT 6458.471211905 COMPUTED RESULT 20936.06095527 COMPUTED RESULT 151543.3544464 COMPUTED RESULT 178636.9323561 COMPUTED RESULT 21053.22784838 COMPUTED RESULT 153330.4996252 COMPUTED RESULT 185042.9388099 COMPUTED RESULT -52.46475812665 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) *** PASSED *** Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) *** PASSED *** Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) *** PASSED *** Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) *** PASSED *** Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) *** PASSED *** Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) *** PASSED *** Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) *** PASSED *** Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) *** PASSED *** Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) *** PASSED *** Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 10.711918 seconds -------------------------------------------------------------------------------- Total elapsed time: 26.714919 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01'] COMPUTED RESULT 188.4888131017 COMPUTED RESULT 1820.045922544 COMPUTED RESULT 6460.002606908 COMPUTED RESULT 21891.61497021 COMPUTED RESULT 152000.0494925 COMPUTED RESULT 179043.619158 COMPUTED RESULT 21958.42512312 COMPUTED RESULT 153777.1604355 COMPUTED RESULT 185449.5619747 COMPUTED RESULT -54.05979017066 Running tests for ionize section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) *** PASSED *** Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) *** PASSED *** Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) *** PASSED *** Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) *** PASSED *** Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) *** PASSED *** Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) *** PASSED *** Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) *** PASSED *** Elapsed time: 9.969676 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398] EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02'] COMPUTED RESULT 5823.898055191 COMPUTED RESULT 9793.274462353 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8219.846763777 COMPUTED RESULT 13927.41988698 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3862.359524598 COMPUTED RESULT 6288.15625161 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.67882018629 COMPUTED RESULT -199.7462636633 COMPUTED RESULT -297.4598403628 COMPUTED RESULT -474.5272838398 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) *** PASSED *** Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) *** PASSED *** Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) *** PASSED *** Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) *** PASSED *** Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) *** PASSED *** Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) *** PASSED *** Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 7.2063 seconds -------------------------------------------------------------------------------- Total elapsed time: 17.175976 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828] EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02'] COMPUTED RESULT 5824.172730822 COMPUTED RESULT 9793.622759239 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8221.328580569 COMPUTED RESULT 13928.67783119 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3863.066835285 COMPUTED RESULT 6289.649216644 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.33052329981 COMPUTED RESULT -198.4883194538 COMPUTED RESULT -295.9668753288 COMPUTED RESULT -472.1246714828 Running tests for ion-pmf section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'ion-pmf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.130e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.767e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) *** PASSED *** Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) *** PASSED *** Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) *** PASSED *** Elapsed time: 8.217168 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.217168 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65308087297 Running tests for pka-lig section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) *** PASSED *** Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) *** PASSED *** Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) *** PASSED *** Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) *** PASSED *** Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) *** PASSED *** Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) *** PASSED *** Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 17.157096 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermediate energies in input file apbs-mol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] COMPUTED RESULT 2224.988750664 COMPUTED RESULT 10496.95084686 COMPUTED RESULT 181845.0789522 COMPUTED RESULT 300825.4338259 COMPUTED RESULT 184091.8409896 COMPUTED RESULT 311330.4681884 COMPUTED RESULT 8.08351564873 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) *** PASSED *** Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) *** PASSED *** Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) *** PASSED *** Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) *** PASSED *** Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) *** PASSED *** Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) *** PASSED *** Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 14.11776 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermediate energies in input file apbs-smol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] COMPUTED RESULT 2226.793167046 COMPUTED RESULT 10505.04485887 COMPUTED RESULT 182797.6621645 COMPUTED RESULT 301722.8546773 COMPUTED RESULT 185081.9075387 COMPUTED RESULT 312248.8625388 COMPUTED RESULT 20.96300255723 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) *** PASSED *** Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) *** PASSED *** Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) *** PASSED *** Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) *** PASSED *** Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) *** PASSED *** Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) *** PASSED *** Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 14.916974 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in Checking for intermediate energies in input file apbs-mol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] COMPUTED RESULT 2244.350164274 COMPUTED RESULT 10521.49475373 COMPUTED RESULT 186261.5690066 COMPUTED RESULT 305181.0884053 COMPUTED RESULT 188662.5455219 COMPUTED RESULT 315821.8439277 COMPUTED RESULT 119.2607686581 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) *** PASSED *** Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) *** PASSED *** Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) *** PASSED *** Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) *** PASSED *** Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) *** PASSED *** Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) *** PASSED *** Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 14.177856 seconds -------------------------------------------------------------------------------- Total elapsed time: 60.369686 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermediate energies in input file apbs-smol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] COMPUTED RESULT 2251.46678942 COMPUTED RESULT 10528.14502873 COMPUTED RESULT 186407.1689626 COMPUTED RESULT 305331.9953673 COMPUTED RESULT 188802.7142979 COMPUTED RESULT 315969.0177241 COMPUTED RESULT 108.8773280806 Running tests for point-pmf section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) *** PASSED *** Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) *** PASSED *** Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) *** PASSED *** Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) *** PASSED *** Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) *** PASSED *** Elapsed time: 2.01227 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermediate energies in input file complex-0_1.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027] EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 89.75920687031 COMPUTED RESULT 205.8277719334 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 89.7592 COMPUTED RESULT 205.828 COMPUTED RESULT 96.5336 COMPUTED RESULT 88.6151 COMPUTED RESULT 201.106 COMPUTED RESULT 18.30820799027 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) *** PASSED *** Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) *** PASSED *** Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 1.602315 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermediate energies in input file complex-0_2.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.90669408675] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 208.4282010393 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 208.428 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.656 COMPUTED RESULT 203.83 COMPUTED RESULT 8.90669408675 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) *** PASSED *** Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) *** PASSED *** Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) *** PASSED *** Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) *** PASSED *** Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) *** PASSED *** Elapsed time: 2.016446 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermediate energies in input file complex-0_3.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984] EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 133.7661883222 COMPUTED RESULT 237.436145212 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 133.766 COMPUTED RESULT 237.436 COMPUTED RESULT 96.5336 COMPUTED RESULT 132.672 COMPUTED RESULT 232.924 COMPUTED RESULT 5.909599816984 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'complex-0_4.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) *** PASSED *** Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) *** PASSED *** Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) *** PASSED *** Elapsed time: 1.18025 seconds -------------------------------------------------------------------------------- Total elapsed time: 6.811281 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file complex-0_4.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 203.9516519 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 203.952 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.654 COMPUTED RESULT 199.493 COMPUTED RESULT 4.430144947418 Running tests for solv section BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) *** PASSED *** Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) *** PASSED *** Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) *** PASSED *** Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) *** PASSED *** Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) *** PASSED *** Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) *** PASSED *** Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) *** PASSED *** Elapsed time: 2.949017 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] COMPUTED RESULT 1847.663548071 COMPUTED RESULT 1883.912182952 COMPUTED RESULT 2732.623683321 COMPUTED RESULT 3123.035854133 COMPUTED RESULT -36.24863488074 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/apbs-PSc155/apbs-3.4.1/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Oct 31 2024 at 13:24:17 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) *** PASSED *** Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) *** PASSED *** Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) *** PASSED *** Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) *** PASSED *** Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) *** PASSED *** Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) *** PASSED *** Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) *** PASSED *** Elapsed time: 1.7269809999999999 seconds -------------------------------------------------------------------------------- Total elapsed time: 4.675998 seconds Test results have been logged -------------------------------------------------------------------------------- Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] COMPUTED RESULT 1847.86044002 COMPUTED RESULT 1885.436377745 COMPUTED RESULT 2734.040568569 COMPUTED RESULT 3125.279428954 COMPUTED RESULT -37.57593772493 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_sphinxdoc -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_python3 -O--buildsystem=cmake I: dh_python3 fs:421: renaming _apbslib.so to _apbslib.cpython-313-x86_64-linux-gnu.so dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/apbs-PSc155/apbs-3.4.1' dh_fixperms for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \ ion-pmf/runme.sh \ point-pmf/runme.sh \ protein-rna/postprocess.sh \ protein-rna/test.sh \ helix/Run_membrane-helix.sh \ protein-rna/run_apdx_files.sh; \ do \ chmod +x debian/apbs-data/usr/share/apbs/examples/${example}; \ done for script in amber2charmm.sh \ param/pdb2pqr/amber2uhbd.sh \ qcd2pqr.awk; \ do \ chmod a+x debian/apbs-data/usr/share/apbs/tools/conversion/${script}; \ done for example in bem-pKa/test_proteins \ pbsam-barn_bars; \ do \ chmod a-x debian/apbs-data/usr/share/apbs/examples/${example}/*.pqr; \ done make[1]: Leaving directory '/build/apbs-PSc155/apbs-3.4.1' dh_fixperms -O--buildsystem=cmake -Napbs-data -Napbs-doc dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/apbs/usr/bin/apbs: DWARF compression not beneficial - old size 29601 new size 29673 dwz: debian/libapbs3t64/usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 143984 new size 144867 dwz: debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 920452 new size 923902 dwz: debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 415188 new size 424493 dwz: debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 91460 new size 93576 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-313-x86_64-linux-gnu.so: DWARF compression not beneficial - old size 6641761 new size 6654703 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol asin used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sin used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erfc used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cos used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol exp used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tanh used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol acos used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol sdot_ used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dnrm2_ used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol e_wsfe used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_dd used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol snrm2_ used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol s_stop used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_ri used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol ddot_ used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol scopy_ used by debian/libfetk1.9t64/usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libcgcode.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libcamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libsuitesparseconfig.so.7 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libcholmod.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libccolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libumfpack.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libvf2c.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libmc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libspqr.so.4 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libarpack.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libcolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libmpi.so.40 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libpunc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libapbs_fem.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libgomp.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libsuperlu.so.7 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/bin/apbs were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: package apbs-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dpkg-gencontrol: warning: Depends field of package libfetk-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libapbs3t64-dbgsym' in '../libapbs3t64-dbgsym_3.4.1-6_amd64.deb'. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-6_amd64.deb'. dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.4.1-6_amd64.deb'. dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-6_all.deb'. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-6_amd64.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.4.1-6_amd64.deb'. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-6_amd64.deb'. dpkg-deb: building package 'libapbs3t64' in '../libapbs3t64_3.4.1-6_amd64.deb'. dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-6_all.deb'. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-6_amd64.deb'. dpkg-deb: building package 'libfetk1.9t64' in '../libfetk1.9t64_3.4.1-6_amd64.deb'. dpkg-deb: building package 'libfetk1.9t64-dbgsym' in '../libfetk1.9t64-dbgsym_3.4.1-6_amd64.deb'. dpkg-genbuildinfo -O../apbs_3.4.1-6_amd64.buildinfo dpkg-genchanges -O../apbs_3.4.1-6_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-01-20T14:44:06Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 20 Jan 2025 14:44:06 +0000 | +------------------------------------------------------------------------------+ apbs_3.4.1-6_amd64.changes: --------------------------- Format: 1.8 Date: Thu, 31 Oct 2024 14:24:17 +0100 Source: apbs Binary: apbs apbs-data apbs-dbgsym apbs-doc libapbs-dev libapbs3t64 libapbs3t64-dbgsym libfetk-dev libfetk1.9t64 libfetk1.9t64-dbgsym python3-apbslib python3-apbslib-dbgsym Architecture: source all amd64 Version: 3.4.1-6 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: apbs - Adaptive Poisson Boltzmann Solver apbs-data - data files for APBS (Adaptive Poisson Boltzmann Solver) apbs-doc - Adaptive Poisson Boltzmann Solver libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs3t64 - Adaptive Poisson Boltzmann Solver libfetk-dev - FETK libraries for APBS (development headers) libfetk1.9t64 - FETK libraries for APBS (shared libraries) python3-apbslib - Adaptive Poisson Boltzmann Solver Closes: 1033528 1077646 Changes: apbs (3.4.1-6) unstable; urgency=medium . * Team upload. . [ Drew Parsons ] * fix build with gcc-14. Closes: #1077646. - patch vf2c in debian/external_deps/fetk - debian patch gcc14.patch reverts an upstream hack in vfetk function definitions that prevent building with gcc-14. * add hashbang to debian/tests/test-apbs. Thanks Simon Chopin. Closes: #1033528. * Build-Depends: pkgconf not pkg-config * mark apbs-doc Multi-Arch: foreign * Standards-Version: 4.7.0 Checksums-Sha1: 63298ef3c4c6e6d9a132760ac064d135ff080183 1787 apbs_3.4.1-6.dsc 2e24495f9172889928680a1f0b142018e2e99baf 20439572 apbs_3.4.1-6.debian.tar.xz 7ebb61da9adb2e6f267edd35bfe941f5db24f868 1489396 apbs-data_3.4.1-6_all.deb c6fa60ba97f83d91ee2023da51b7d544e5a0ee6c 115092 apbs-dbgsym_3.4.1-6_amd64.deb ed89161969196eb197760f08e341d2c1d016c251 5853304 apbs-doc_3.4.1-6_all.deb c74534a604b9339c66954f92bdb631de0344195d 14764 apbs_3.4.1-6_amd64.buildinfo 89104122c29cf81b3f769cedde1811cf01bf5e57 78968 apbs_3.4.1-6_amd64.deb f8192d292141ed7685721db8b90c1d05460f121c 103272 libapbs-dev_3.4.1-6_amd64.deb faaec3e11a5195a37c99323962b1ee06f0a214fe 602124 libapbs3t64-dbgsym_3.4.1-6_amd64.deb 389c804355687160cda622faa87e9cadc2315fbe 260056 libapbs3t64_3.4.1-6_amd64.deb f8b016b55ea466dc6722cf02615c219f52aabea9 148772 libfetk-dev_3.4.1-6_amd64.deb 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556d6aab01c23d878dfe0b6ce2be4e47a7506d309e4ba0c2b53777ef1f62eced 78968 apbs_3.4.1-6_amd64.deb 2a6caf21c1c1c2e3f1a253f9c55bb51cf81224feb4fe94ea783fa6b1e9716082 103272 libapbs-dev_3.4.1-6_amd64.deb a136369cefc7db14a2f0bfa2ea8b90490162ae5b491ae7cfcdf5d7c9aa17f855 602124 libapbs3t64-dbgsym_3.4.1-6_amd64.deb 589af7d6b36f12ffaf40108ce02b38fd5fbe38a523927d2a0929884fce31bfb4 260056 libapbs3t64_3.4.1-6_amd64.deb 822b70347e9abbba9820893e76ade73981525a9c51773e5cf94c476d47f55db2 148772 libfetk-dev_3.4.1-6_amd64.deb 13bafed8fcddfc136b91f31e458cccb37c4abd92736668c34296ded84dfb048b 1785176 libfetk1.9t64-dbgsym_3.4.1-6_amd64.deb e14afab15fea494fbb60306767ab5729aa65dfdf11ea574de2ed13424e556f2c 569728 libfetk1.9t64_3.4.1-6_amd64.deb 241d7e79df3a22d4ea24badac4488058840ec4be5a246c9f6bfe618e18850d5a 3606392 python3-apbslib-dbgsym_3.4.1-6_amd64.deb 3862548b09c283dee29819a27d29f4436fd8536fb5a54c70e64690364a038e75 228960 python3-apbslib_3.4.1-6_amd64.deb Files: 524fd38a59fc426a990f7b27d141c5f7 1787 science optional apbs_3.4.1-6.dsc f833e6215ee1a0c6b64fe6d495f48a3a 20439572 science optional apbs_3.4.1-6.debian.tar.xz 4269190fa800c80e0bffda44b235b2e2 1489396 science optional apbs-data_3.4.1-6_all.deb 42c5502cbdc273fc2dc4b5a0106bfdc5 115092 debug optional apbs-dbgsym_3.4.1-6_amd64.deb fe0dc9381fa9686eda7d1126a697d32b 5853304 science optional apbs-doc_3.4.1-6_all.deb af64a10191039c94b2575c113af0d671 14764 science optional apbs_3.4.1-6_amd64.buildinfo a5993ac9f72d2b5ae46bcb0f498c1638 78968 science optional apbs_3.4.1-6_amd64.deb 5ecbb594f468c3468c7d24552e744d35 103272 libdevel optional libapbs-dev_3.4.1-6_amd64.deb f1d81fe9b853cde56227c3658d350350 602124 debug optional libapbs3t64-dbgsym_3.4.1-6_amd64.deb e25ccc3cc87ae2c7e79537515e56e3a6 260056 libs optional libapbs3t64_3.4.1-6_amd64.deb 28a1496e0829a84843cdf2177c05543e 148772 libdevel optional libfetk-dev_3.4.1-6_amd64.deb 5a20a4390dcfc9feeccce7784c22b546 1785176 debug optional libfetk1.9t64-dbgsym_3.4.1-6_amd64.deb c8d38b203b02d5e6e49d423680b23c4f 569728 libs optional libfetk1.9t64_3.4.1-6_amd64.deb e5e361fe5e72a3713a6bf5fbbe4e0886 3606392 debug optional python3-apbslib-dbgsym_3.4.1-6_amd64.deb 1d9d6381c619cd03a93f06e2b352a8ec 228960 python optional python3-apbslib_3.4.1-6_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 20 Jan 2025 14:44:07 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: apbs Binary: apbs apbs-data apbs-dbgsym apbs-doc libapbs-dev libapbs3t64 libapbs3t64-dbgsym libfetk-dev libfetk1.9t64 libfetk1.9t64-dbgsym python3-apbslib python3-apbslib-dbgsym Architecture: all amd64 source Version: 3.4.1-6 Checksums-Md5: 524fd38a59fc426a990f7b27d141c5f7 1787 apbs_3.4.1-6.dsc 4269190fa800c80e0bffda44b235b2e2 1489396 apbs-data_3.4.1-6_all.deb 42c5502cbdc273fc2dc4b5a0106bfdc5 115092 apbs-dbgsym_3.4.1-6_amd64.deb fe0dc9381fa9686eda7d1126a697d32b 5853304 apbs-doc_3.4.1-6_all.deb 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3862548b09c283dee29819a27d29f4436fd8536fb5a54c70e64690364a038e75 228960 python3-apbslib_3.4.1-6_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 20 Jan 2025 14:44:05 +0000 Build-Path: /build/apbs-PSc155/apbs-3.4.1 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20241223), cmake (= 3.31.4-2), cmake-data (= 3.31.4-2), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-python (= 6.20250108), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-2), docutils-common (= 0.21.2+dfsg-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), fonts-font-awesome (= 5.0.10+really4.7.0~dfsg-4.1), fonts-lato (= 2.015-1), fonts-mathjax (= 2.7.9+dfsg-1), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), gfortran-14 (= 14.2.0-14), gfortran-14-x86-64-linux-gnu (= 14.2.0-14), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), hostname (= 3.25), ibverbs-providers (= 52.0-2+b2), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b2), libamd3 (= 1:7.8.3+dfsg-2), libamdhip64-5 (= 5.7.1-5), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-1.1), libarpack2-dev (= 3.9.1-4), libarpack2t64 (= 3.9.1-4), libasan8 (= 14.2.0-14), libatomic1 (= 14.2.0-14), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libbinutils (= 2.43.50.20250108-1), libblas-dev (= 3.12.0-4), libblas3 (= 3.12.0-4), libblkid1 (= 2.40.4-1), libbrotli1 (= 1.1.0-2+b6), libbsd0 (= 0.12.2-2), libbtf2 (= 1:7.8.3+dfsg-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcamd3 (= 1:7.8.3+dfsg-2), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcbor0.10 (= 0.10.2-2), libcc1-0 (= 14.2.0-14), libccolamd3 (= 1:7.8.3+dfsg-2), libcholmod5 (= 1:7.8.3+dfsg-2), libcolamd3 (= 1:7.8.3+dfsg-2), libcom-err2 (= 1.47.2-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libcurl4t64 (= 8.11.1-1+b1), libcxsparse4 (= 1:7.8.3+dfsg-2), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdpkg-perl (= 1.22.14), libdrm-amdgpu1 (= 2.4.123-1), libdrm-common (= 2.4.123-1), libdrm2 (= 2.4.123-1), libedit2 (= 3.1-20250104-1), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-dev (= 2.1.12-stable-10+b1), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.6.4-1), libexpat1-dev (= 2.6.4-1), libfabric1 (= 1.17.0-3.1), libffi8 (= 3.4.6-1), libfido2-1 (= 1.15.0-1+b1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran-14-dev (= 14.2.0-14), libgfortran5 (= 14.2.0-14), libgmp10 (= 2:6.3.0+dfsg-3), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-14), libgprofng0 (= 2.43.50.20250108-1), libgssapi-krb5-2 (= 1.21.3-4), libhogweed6t64 (= 3.10-1+b1), libhsa-runtime64-1 (= 6.1.2-2), libhsakmt1 (= 6.1.2+ds-1), libhwasan0 (= 14.2.0-14), libhwloc-dev (= 2.11.2-1), libhwloc-plugins (= 2.11.2-1), libhwloc15 (= 2.11.2-1), libibmad5 (= 52.0-2+b2), libibumad3 (= 52.0-2+b2), libibverbs-dev (= 52.0-2+b2), libibverbs1 (= 52.0-2+b2), libicu72 (= 72.1-6), libidn2-0 (= 2.3.7-2+b1), libisl23 (= 0.27-1), libitm1 (= 14.2.0-14), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-mathjax (= 2.7.9+dfsg-1), libjs-sphinxdoc (= 8.1.3-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libjsoncpp26 (= 1.9.6-3), libk5crypto3 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libklu2 (= 1:7.8.3+dfsg-2), libkrb5-3 (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), liblapack-dev (= 3.12.0-4), liblapack3 (= 3.12.0-4), libldap2 (= 2.6.9+dfsg-1), libldl3 (= 1:7.8.3+dfsg-2), libllvm17t64 (= 1:17.0.6-20+b1), liblsan0 (= 14.2.0-14), libltdl-dev (= 2.5.4-2), libltdl7 (= 2.5.4-2), liblz4-1 (= 1.9.4-4), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmaloc-dev (= 1.5-2+b2), libmaloc1 (= 1.5-2+b2), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libmunge2 (= 0.5.15-4+b1), libncursesw6 (= 6.5-2+b1), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnl-3-200 (= 3.7.0-0.3+b1), libnl-3-dev (= 3.7.0-0.3+b1), libnl-route-3-200 (= 3.7.0-0.3+b1), libnl-route-3-dev (= 3.7.0-0.3+b1), libnuma-dev (= 2.0.18-1+b1), libnuma1 (= 2.0.18-1+b1), libopenmpi-dev (= 5.0.6-3), libopenmpi40 (= 5.0.6-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libparu1 (= 1:7.8.3+dfsg-2), libpciaccess0 (= 0.17-3+b3), libpcre2-8-0 (= 10.44-5), libperl5.40 (= 5.40.1-1), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpmix-dev (= 5.0.6-1), libpmix2t64 (= 5.0.6-1), libproc2-0 (= 2:4.0.4-6), libpsl5t64 (= 0.21.2-1.1+b1), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2.1), libpython3-dev (= 3.13.1-2), libpython3-stdlib (= 3.13.1-2), libpython3.13 (= 3.13.1-3), libpython3.13-dev (= 3.13.1-3), libpython3.13-minimal (= 3.13.1-3), libpython3.13-stdlib (= 3.13.1-3), libquadmath0 (= 14.2.0-14), librbio4 (= 1:7.8.3+dfsg-2), librdmacm1t64 (= 52.0-2+b2), libreadline8t64 (= 8.2-6), librhash1 (= 1.4.5-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8+b1), libsasl2-modules-db (= 2.1.28+dfsg1-8+b1), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsemanage-common (= 3.7-2), libsemanage2 (= 3.7-2+b1), libsepol2 (= 3.7-1), libsframe1 (= 2.43.50.20250108-1), libsmartcols1 (= 2.40.4-1), libspex3 (= 1:7.8.3+dfsg-2), libspqr4 (= 1:7.8.3+dfsg-2), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.4.0-2), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libsuitesparse-dev (= 1:7.8.3+dfsg-2), libsuitesparse-mongoose3 (= 1:7.8.3+dfsg-2), libsuitesparseconfig7 (= 1:7.8.3+dfsg-2), libsuperlu-dev (= 7.0.0+dfsg1-2), libsuperlu7 (= 7.0.0+dfsg1-2), libsystemd0 (= 257.2-2), libtasn1-6 (= 4.19.0-3+b3), libtinfo6 (= 6.5-2+b1), libtirpc-common (= 1.3.4+ds-1.3), libtirpc-dev (= 1.3.4+ds-1.3+b1), libtirpc3t64 (= 1.3.4+ds-1.3+b1), libtool (= 2.5.4-2), libtsan2 (= 14.2.0-14), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libucx0 (= 1.17.0+ds-3), libudev1 (= 257.2-2), libumfpack6 (= 1:7.8.3+dfsg-2), libunistring5 (= 1.3-1), libuuid1 (= 2.40.4-1), libuv1t64 (= 1.48.0-7), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libxau6 (= 1:1.0.11-1), libxcb1 (= 1.17.0-2+b1), libxdmcp6 (= 1:1.1.5-1), libxext6 (= 2:1.3.4-1+b3), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxnvctrl0 (= 535.171.04-1+b1), libxxhash0 (= 0.8.3-2), libyaml-0-2 (= 0.2.5-2), libz3-4 (= 4.13.3-1), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), login.defs (= 1:4.16.0-7), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), mpi-default-dev (= 1.18), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1+b2), openmpi-bin (= 5.0.6-3), openmpi-common (= 5.0.6-3), openssh-client (= 1:9.9p1-3), openssl (= 3.4.0-2), openssl-provider-legacy (= 3.4.0-2), passwd (= 1:4.16.0-7), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-6), pybind11-dev (= 2.13.6-1), pybuild-plugin-pyproject (= 6.20250108), python-babel-localedata (= 2.16.0-1), python3 (= 3.13.1-2), python3-alabaster (= 0.7.16-0.1), python3-autocommand (= 2.2.2-3), python3-babel (= 2.16.0-1), python3-build (= 1.2.2-1), python3-certifi (= 2024.12.14+ds-1), python3-chardet (= 5.2.0+dfsg-2), python3-charset-normalizer (= 3.4.0-1+b1), python3-defusedxml (= 0.7.1-3), python3-dev (= 3.13.1-2), python3-docutils (= 0.21.2+dfsg-2), python3-idna (= 3.8-2), python3-imagesize (= 1.4.1-1), python3-inflect (= 7.3.1-2), python3-installer (= 0.7.0+dfsg1-3), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.1.0-1), python3-jaraco.text (= 4.0.0-1), python3-jinja2 (= 3.1.3-2), python3-markupsafe (= 2.1.5-1+b2), python3-minimal (= 3.13.1-2), python3-more-itertools (= 10.6.0-1), python3-packaging (= 24.2-1), python3-pkg-resources (= 75.6.0-1), python3-pybind11 (= 2.13.6-1), python3-pygments (= 2.18.0+dfsg-2), python3-pyproject-hooks (= 1.2.0-1), python3-requests (= 2.32.3+dfsg-1), python3-roman (= 4.2-1), python3-setuptools (= 75.6.0-1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 8.1.3-4), python3-sphinx-rtd-theme (= 3.0.2+dfsg-2), python3-sphinxcontrib.jquery (= 4.1-5), python3-toml (= 0.10.2-1), python3-typeguard (= 4.4.1-1), python3-typing-extensions (= 4.12.2-2), python3-urllib3 (= 2.3.0-1), python3-wheel (= 0.45.1-1), python3-yaml (= 6.0.2-1+b1), python3-zipp (= 3.21.0-1), python3.13 (= 3.13.1-3), python3.13-dev (= 3.13.1-3), python3.13-minimal (= 3.13.1-3), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sgml-base (= 1.31), sphinx-common (= 8.1.3-4), sphinx-rtd-theme-common (= 3.0.2+dfsg-2), swig (= 4.3.0-0.1), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), tzdata (= 2025a-1), util-linux (= 2.40.4-1), xml-core (= 0.19), xz-utils (= 5.6.3-1+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1730381057" +------------------------------------------------------------------------------+ | Package contents Mon, 20 Jan 2025 14:44:07 +0000 | +------------------------------------------------------------------------------+ apbs-data_3.4.1-6_all.deb ------------------------- new Debian package, version 2.0. size 1489396 bytes: control archive=8384 bytes. 698 bytes, 19 lines control 25645 bytes, 313 lines md5sums Package: apbs-data Source: apbs Version: 3.4.1-6 Architecture: all Maintainer: Debichem Team Installed-Size: 15882 Breaks: apbs (<= 1.4-2) Section: science Priority: optional Multi-Arch: foreign Homepage: http://www.poissonboltzmann.org/ Description: data files for APBS (Adaptive Poisson Boltzmann Solver) APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains all data files for apbs package to reduce the redundancy between architectures in Debian. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/ -rw-r--r-- root/root 118791 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -rw-r--r-- root/root 5249 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -rw-r--r-- root/root 5262 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/1d7h-dmso/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/ -rw-r--r-- root/root 103106 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -rw-r--r-- root/root 13309 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -rw-r--r-- root/root 183314 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -rw-r--r-- root/root 183314 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -rw-r--r-- root/root 628 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -rwxr-xr-x root/root 181 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -rw-r--r-- root/root 118073 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-min.pqr -rw-r--r-- root/root 119067 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -rw-r--r-- root/root 5236 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -rw-r--r-- root/root 5248 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss-smol.in drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/1d7i-dss/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/ -rw-r--r-- root/root 103106 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -rw-r--r-- root/root 13305 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -rw-r--r-- root/root 183310 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -rw-r--r-- root/root 868 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -rw-r--r-- root/root 118073 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7i-min.pqr -rw-r--r-- root/root 4384 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/README.md -rw-r--r-- root/root 718 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/dmso-min.pqr -rw-r--r-- root/root 994 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/dss-min.pqr -rw-r--r-- root/root 4276 2022-04-29 18:53 ./usr/share/apbs/examples/README.md drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/actin-dimer/ -rw-r--r-- root/root 5879 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/README.md drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/actin-dimer/UHBD/ -rw-r--r-- root/root 27551 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -rw-r--r-- root/root 24783 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -rw-r--r-- root/root 2156 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -rw-r--r-- root/root 393759 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb -rw-r--r-- root/root 393759 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb -rw-r--r-- root/root 920 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/single.inp -rw-r--r-- root/root 1971182 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot -rw-r--r-- root/root 1639 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -rw-r--r-- root/root 1738 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -rw-r--r-- root/root 1740 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -rw-r--r-- root/root 799272 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/complex.pqr -rw-r--r-- root/root 1808 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/mesh.m -rw-r--r-- root/root 399636 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/mol1.pqr -rw-r--r-- root/root 399636 2022-04-29 18:53 ./usr/share/apbs/examples/actin-dimer/mol2.pqr drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/alkanes/ -rw-r--r-- root/root 1221 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/2-methylbutane.pdb -rw-r--r-- root/root 12664 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/README.md -rw-r--r-- root/root 2976 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/alkanes.in -rw-r--r-- root/root 285 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/apbs-forces.in -rw-r--r-- root/root 1019 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/butane.pdb -rw-r--r-- root/root 1249 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/cyclohexane.pdb -rw-r--r-- root/root 894 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/cyclopentane.pdb -rw-r--r-- root/root 553 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/ethane.pdb -rw-r--r-- root/root 5233 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/force.result -rw-r--r-- root/root 1340 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/hexane.pdb -rw-r--r-- root/root 1007 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/isobutane.pdb -rw-r--r-- root/root 355 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/methane.pdb -rw-r--r-- root/root 781 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/mol.pdb -rw-r--r-- root/root 1208 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/neopentane.pdb -rw-r--r-- root/root 620 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/parm.dat -rw-r--r-- root/root 1143 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/pentane.pdb -rw-r--r-- root/root 781 2022-04-29 18:53 ./usr/share/apbs/examples/alkanes/propane.pdb drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/bem-binding-energy/ -rw-r--r-- root/root 879 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/1d30.in -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -rw-r--r-- root/root 889 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -rw-r--r-- root/root 1024 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/README.md drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/ -rw-r--r-- root/root 43640 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr -rw-r--r-- root/root 41504 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr -rw-r--r-- root/root 2137 2022-04-29 18:53 ./usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/bem-pKa/ -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -rw-r--r-- root/root 891 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -rw-r--r-- root/root 891 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -rw-r--r-- root/root 875 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/ASH66.in -rw-r--r-- root/root 881 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/ASP66.in -rw-r--r-- root/root 1036 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/README.md drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/bem-pKa/test_proteins/ -rw-r--r-- root/root 137270 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -rw-r--r-- root/root 137200 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -rw-r--r-- root/root 137455 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -rw-r--r-- root/root 137385 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -rw-r--r-- root/root 910 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -rw-r--r-- root/root 840 2022-04-29 18:53 ./usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/bem/ -rw-r--r-- root/root 888 2022-04-29 18:53 ./usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -rw-r--r-- root/root 879 2022-04-29 18:53 ./usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -rw-r--r-- root/root 878 2022-04-29 18:53 ./usr/share/apbs/examples/bem/451c_order1.in -rw-r--r-- root/root 878 2022-04-29 18:53 ./usr/share/apbs/examples/bem/451c_order5.in -rw-r--r-- root/root 1381 2022-04-29 18:53 ./usr/share/apbs/examples/bem/README.md drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/bem/test_proteins/ -rw-r--r-- root/root 153780 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/1a63.pqr -rw-r--r-- root/root 38306 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -rw-r--r-- root/root 42524 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -rw-r--r-- root/root 90105 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/451c.pqr -rw-r--r-- root/root 40 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/oneb.pqr -rw-r--r-- root/root 80 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/twob.pqr -rw-r--r-- root/root 82 2022-04-29 18:53 ./usr/share/apbs/examples/bem/test_proteins/twob2.pqr drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/born/ -rw-r--r-- root/root 4410 2022-04-29 18:53 ./usr/share/apbs/examples/born/README.md -rw-r--r-- root/root 719 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-apolar.in -rw-r--r-- root/root 1386 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-forces.in -rw-r--r-- root/root 1151 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-auto.in -rw-r--r-- root/root 1047 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -rw-r--r-- root/root 1160 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-fem.in -rw-r--r-- root/root 1130 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-mol-parallel.in -rw-r--r-- root/root 1126 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-smol-auto.in -rw-r--r-- root/root 668 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-smol-fem.in -rw-r--r-- root/root 1132 2022-04-29 18:53 ./usr/share/apbs/examples/born/apbs-smol-parallel.in -rw-r--r-- root/root 350 2022-04-29 18:53 ./usr/share/apbs/examples/born/apolarforces -rw-r--r-- root/root 66 2022-04-29 18:53 ./usr/share/apbs/examples/born/ion.pqr -rw-r--r-- root/root 1836 2022-04-29 18:53 ./usr/share/apbs/examples/born/mesh.m -rw-r--r-- root/root 524 2022-04-29 18:53 ./usr/share/apbs/examples/born/parm.dat -rw-r--r-- root/root 643 2022-04-29 18:53 ./usr/share/apbs/examples/born/pmf.dat -rw-r--r-- root/root 266 2022-04-29 18:53 ./usr/share/apbs/examples/born/polarforces drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/geoflow/ -rw-r--r-- root/root 686 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/1a63.in -rw-r--r-- root/root 153780 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/1a63.pqr -rw-r--r-- root/root 1130 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/README.md -rw-r--r-- root/root 910 2022-04-29 18:53 ./usr/share/apbs/examples/geoflow/gly.pdb -rw-r--r-- root/root 1613 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./usr/share/doc/apbs-data/copyright apbs-dbgsym_3.4.1-6_amd64.deb ----------------------------- new Debian package, version 2.0. size 115092 bytes: control archive=1408 bytes. 1037 bytes, 12 lines control 1989 bytes, 19 lines md5sums Package: apbs-dbgsym Source: apbs Version: 3.4.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 350 Depends: apbs (= 3.4.1-6) Section: debug Priority: optional Description: debug symbols for apbs Build-Ids: 080ea8e8e3ef4c12735ea28734acd8834368a9d8 1329c1c77764a398cad4d0f264fb8e57902109a3 16978a23f16a9b7cf86dc6615fcb580023371aed 35713237677ebe27b66669d3f8f08fffb8f85e16 5b103e2c0286b9b1b5a444c43995e35d907a7f32 5b43ce263d476e17a072bdeada8f0d6e20367900 65e6da92eb0661450686f999cebf0a750e929f62 7c54e0eed850414cd3511d42df47f329cb78193b 7c9b19a9a76b1d3deb33fa585232996f6f629731 95dd3ca5ec8c588d4001fdf266f219f069c88797 9721365dd0155a277d200317da8b341510d97f70 b3d02ab42b37fbe25dec699e76e8b28a20bd3486 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2024-10-31 13:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/apbs.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/share/doc/apbs-dbgsym -> apbs apbs-doc_3.4.1-6_all.deb ------------------------ new Debian package, version 2.0. size 5853304 bytes: control archive=7876 bytes. 1432 bytes, 33 lines control 26155 bytes, 281 lines md5sums Package: apbs-doc Source: apbs Version: 3.4.1-6 Architecture: all Maintainer: Debichem Team Installed-Size: 7592 Depends: libjs-mathjax, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 8.1), sphinx-rtd-theme-common (>= 3.0.2+dfsg) Recommends: apbs Suggests: python3-apbslib Section: science Priority: optional Multi-Arch: foreign Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . 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control 1618 bytes, 25 lines md5sums Package: apbs Version: 3.4.1-6 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 372 Depends: apbs-data (= 3.4.1-6), libapbs3t64 (= 3.4.1-6), libjs-mathjax, libamd3 (>= 1:7.0.1), libarpack2t64 (>= 2.1), libblas3 | libblas.so.3, libc6 (>= 2.34), libcamd3 (>= 1:7.0.1), libccolamd3 (>= 1:7.0.1), libcholmod5 (>= 1:7.3.1), libcolamd3 (>= 1:7.0.1), libfetk1.9t64 (>= 3.4.1), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi40 (>= 5.0.6), libspqr4 (>= 1:7.8.3+dfsg), libstdc++6 (>= 4.1.1), libsuitesparseconfig7 (>= 1:7.0.1), libsuperlu7 (>= 7.0.0+dfsg1), libumfpack6 (>= 1:7.0.1) Section: science Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . This package contains the apbs program and utilities. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/bin/ -rwxr-xr-x root/root 30800 2024-10-31 13:24 ./usr/bin/apbs drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/apbs/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/apbs/tools/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/ -rwxr-xr-x root/root 18664 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/analysis -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/benchmark -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/born -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/coulomb -rwxr-xr-x root/root 14576 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/del2dx -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/dx2mol -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/dx2uhbd -rwxr-xr-x root/root 18664 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/dxmath -rwxr-xr-x root/root 18664 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/mergedx -rwxr-xr-x root/root 26856 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/mergedx2 -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/mgmesh -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/multivalue -rwxr-xr-x root/root 26856 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/similarity -rwxr-xr-x root/root 18664 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/smooth -rwxr-xr-x root/root 14576 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/tensor2dx -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/uhbd_asc2bin -rwxr-xr-x root/root 14568 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/value drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/apbs/ -rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/apbs/README -rw-r--r-- root/root 294 2024-10-31 13:24 ./usr/share/doc/apbs/README.test -rw-r--r-- root/root 3631 2024-10-31 13:24 ./usr/share/doc/apbs/changelog.Debian.gz -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/apbs/changelog.gz -rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/apbs/copyright -rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/apbs/releases.rst.gz drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/man/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/man/man1/ -rw-r--r-- root/root 835 2024-10-31 13:24 ./usr/share/man/man1/apbs.1.gz libapbs-dev_3.4.1-6_amd64.deb ----------------------------- new Debian package, version 2.0. size 103272 bytes: control archive=2244 bytes. 664 bytes, 19 lines control 4026 bytes, 60 lines md5sums Package: libapbs-dev Source: apbs Version: 3.4.1-6 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 712 Depends: libapbs3t64 (= 3.4.1-6) Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the development headers to build against libapbs_* shared libraries. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/ -rw-r--r-- root/root 3281 2022-04-29 18:53 ./usr/include/apbs/apbs.h drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/fem/ -rw-r--r-- root/root 11331 2022-04-29 18:53 ./usr/include/apbs/fem/vcsm.h -rw-r--r-- root/root 38012 2024-10-31 13:24 ./usr/include/apbs/fem/vfetk.h -rw-r--r-- root/root 10184 2022-04-29 18:53 ./usr/include/apbs/fem/vpee.h drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/generic/ -rw-r--r-- root/root 8229 2022-04-29 18:53 ./usr/include/apbs/generic/apolparm.h -rw-r--r-- root/root 6395 2022-04-29 18:53 ./usr/include/apbs/generic/bemparm.h -rw-r--r-- root/root 8873 2022-04-29 18:53 ./usr/include/apbs/generic/femparm.h -rw-r--r-- root/root 6121 2022-04-29 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libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/cmake/ -rw-r--r-- root/root 949 2024-10-31 13:24 ./usr/share/apbs/cmake/FindAMD.cmake -rw-r--r-- root/root 2501 2024-10-31 13:24 ./usr/share/apbs/cmake/FindARPACK.cmake -rw-r--r-- root/root 22563 2024-10-31 13:24 ./usr/share/apbs/cmake/FindLAPACK.cmake -rw-r--r-- root/root 23393 2024-10-31 13:24 ./usr/share/apbs/cmake/FindSuiteSparse.cmake -rw-r--r-- root/root 2578 2024-10-31 13:24 ./usr/share/apbs/cmake/FindSuperLU.cmake -rw-r--r-- root/root 1153 2024-10-31 13:24 ./usr/share/apbs/cmake/FindUMFPACK.cmake drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libapbs-dev/ -rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/README -rw-r--r-- root/root 3632 2024-10-31 13:24 ./usr/share/doc/libapbs-dev/changelog.Debian.gz -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/changelog.gz -rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libapbs-dev/copyright -rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/releases.rst.gz libapbs3t64-dbgsym_3.4.1-6_amd64.deb ------------------------------------ new Debian package, version 2.0. size 602124 bytes: control archive=812 bytes. 542 bytes, 13 lines control 618 bytes, 6 lines md5sums Package: libapbs3t64-dbgsym Source: apbs Version: 3.4.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 657 Depends: libapbs3t64 (= 3.4.1-6) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libapbs3t64 Build-Ids: 3b120c09e79452ea600659fd23ae69826faea6e2 4c66550683a45e42ac4106ac89b4ca38c9786665 a4086c50339b3fcd8731c6be852849c02d844761 de7f1952fe5496c75d6fdd02fd465d2e958a57ed e0cf8faed93bffb3926f35dc067bfcb01cfee31e drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/3b/ -rw-r--r-- root/root 153880 2024-10-31 13:24 ./usr/lib/debug/.build-id/3b/120c09e79452ea600659fd23ae69826faea6e2.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/4c/ -rw-r--r-- root/root 180936 2024-10-31 13:24 ./usr/lib/debug/.build-id/4c/66550683a45e42ac4106ac89b4ca38c9786665.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/a4/ -rw-r--r-- root/root 160664 2024-10-31 13:24 ./usr/lib/debug/.build-id/a4/086c50339b3fcd8731c6be852849c02d844761.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/de/ -rw-r--r-- root/root 74856 2024-10-31 13:24 ./usr/lib/debug/.build-id/de/7f1952fe5496c75d6fdd02fd465d2e958a57ed.debug drwxr-xr-x 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(>= 2.29), libfetk1.9t64 (>= 3.4.1), libgomp1 (>= 4.9), libmaloc1 (>= 0.2-1) Breaks: libapbs3 (<< 3.4.1-6) Replaces: libapbs3 Provides: libapbs3 (= 3.4.1-6) Section: libs Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the libapbs_* shared libraries. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 65536 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libapbs_fem.so.3 -rw-r--r-- root/root 219128 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libapbs_generic.so.3 -rw-r--r-- root/root 178168 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libapbs_mg.so.3 -rw-r--r-- root/root 235360 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libapbs_pmgc.so.3 -rw-r--r-- root/root 100344 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libapbs3t64/ -rw-r--r-- root/root 3634 2024-10-31 13:24 ./usr/share/doc/libapbs3t64/changelog.Debian.gz -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libapbs3t64/changelog.gz -rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libapbs3t64/copyright drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 164 2024-10-31 13:24 ./usr/share/lintian/overrides/libapbs3t64 libfetk-dev_3.4.1-6_amd64.deb ----------------------------- new Debian package, version 2.0. size 148772 bytes: control archive=2044 bytes. 1256 bytes, 31 lines control 2662 bytes, 42 lines md5sums Package: libfetk-dev Source: apbs Version: 3.4.1-6 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 1507 Depends: libfetk1.9t64 (= 3.4.1-6), libmaloc-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: FETK libraries for APBS (development headers) The Finite Element ToolKit (FETK) is a collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C++, and include a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC) . This package provides a fork of FETK intended for use by APBS (Adaptive Poisson Boltzmann Solver). . The FETK component MALOC (Minimal Abstraction Layer for Object-oriented C/C++ programs) is provided separately by libmaloc-dev. . This package contains the development headers to build against libapbs_* shared libraries. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/gamer/ -rw-r--r-- root/root 11439 2024-10-31 13:24 ./usr/include/fetk/gamer/biom.h -rw-r--r-- root/root 1459 2024-10-31 13:24 ./usr/include/fetk/gamer/gamer.h -rw-r--r-- root/root 2282 2024-10-31 13:24 ./usr/include/fetk/gamer/gamer_base.h -rw-r--r-- root/root 106910 2024-10-31 13:24 ./usr/include/fetk/gamer/tetgen.h -rw-r--r-- root/root 22024 2024-10-31 13:24 ./usr/include/fetk/gamer/triangle.h drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/mc/ -rw-r--r-- root/root 27753 2024-10-31 13:24 ./usr/include/fetk/mc/am.h -rw-r--r-- root/root 49795 2024-10-31 13:24 ./usr/include/fetk/mc/aprx.h -rw-r--r-- root/root 1297 2024-10-31 13:24 ./usr/include/fetk/mc/bam.h -rw-r--r-- root/root 29085 2024-10-31 13:24 ./usr/include/fetk/mc/bmat.h -rw-r--r-- root/root 5029 2024-10-31 13:24 ./usr/include/fetk/mc/bnode.h -rw-r--r-- root/root 32284 2024-10-31 13:24 ./usr/include/fetk/mc/bvec.h -rw-r--r-- root/root 13191 2024-10-31 13:24 ./usr/include/fetk/mc/dyn.h -rw-r--r-- root/root 130602 2024-10-31 13:24 ./usr/include/fetk/mc/gem.h -rw-r--r-- root/root 47965 2024-10-31 13:24 ./usr/include/fetk/mc/mat.h -rw-r--r-- root/root 1457 2024-10-31 13:24 ./usr/include/fetk/mc/mc.h -rw-r--r-- root/root 5705 2024-10-31 13:24 ./usr/include/fetk/mc/mc_base.h -rw-r--r-- root/root 4665 2024-10-31 13:24 ./usr/include/fetk/mc/mcsh.h -rw-r--r-- root/root 14987 2024-10-31 13:24 ./usr/include/fetk/mc/mtool.h -rw-r--r-- root/root 1189 2024-10-31 13:24 ./usr/include/fetk/mc/nam.h -rw-r--r-- root/root 4772 2024-10-31 13:24 ./usr/include/fetk/mc/node.h -rw-r--r-- root/root 17885 2024-10-31 13:24 ./usr/include/fetk/mc/pde.h -rw-r--r-- root/root 17026 2024-10-31 13:24 ./usr/include/fetk/mc/re.h -rw-r--r-- root/root 4823 2024-10-31 13:24 ./usr/include/fetk/mc/slu.h -rw-r--r-- root/root 12682 2024-10-31 13:24 ./usr/include/fetk/mc/vec.h -rw-r--r-- root/root 14016 2024-10-31 13:24 ./usr/include/fetk/mc/vec3.h -rw-r--r-- root/root 26120 2024-10-31 13:24 ./usr/include/fetk/mc/vel.h -rw-r--r-- root/root 68269 2024-10-31 13:24 ./usr/include/fetk/mc/ves.h -rw-r--r-- root/root 50938 2024-10-31 13:24 ./usr/include/fetk/mc/whb.h -rw-r--r-- root/root 7767 2024-10-31 13:24 ./usr/include/fetk/mc/zslu.h drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/punc/ -rw-r--r-- root/root 1569 2024-10-31 13:24 ./usr/include/fetk/punc/punc.h -rw-r--r-- root/root 1272 2024-10-31 13:24 ./usr/include/fetk/punc/punc_base.h -rw-r--r-- root/root 1455 2024-10-31 13:24 ./usr/include/fetk/punc/punc_base_p.h -rw-r--r-- root/root 3987 2024-10-31 13:24 ./usr/include/fetk/punc/punccf.h -rw-r--r-- root/root 46865 2024-10-31 13:24 ./usr/include/fetk/punc/varpack.h -rw-r--r-- root/root 39886 2024-10-31 13:24 ./usr/include/fetk/punc/vblas.h -rw-r--r-- root/root 17098 2024-10-31 13:24 ./usr/include/fetk/punc/vcgcode.h -rw-r--r-- root/root 13077 2024-10-31 13:24 ./usr/include/fetk/punc/vf2c.h -rw-r--r-- root/root 552778 2024-10-31 13:24 ./usr/include/fetk/punc/vlapack.h -rw-r--r-- root/root 82089 2024-10-31 13:24 ./usr/include/fetk/punc/vpmg.h drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libcgcode.so -> libcgcode.so.1.9 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libgamer.so -> libgamer.so.1.9 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libmc.so -> libmc.so.1.9 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libpunc.so -> libpunc.so.1.9 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libvf2c.so -> libvf2c.so.1.9 drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libfetk-dev/ -rw-r--r-- root/root 3632 2024-10-31 13:24 ./usr/share/doc/libfetk-dev/changelog.Debian.gz -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libfetk-dev/changelog.gz -rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libfetk-dev/copyright libfetk1.9t64-dbgsym_3.4.1-6_amd64.deb -------------------------------------- new Debian package, version 2.0. size 1785176 bytes: control archive=816 bytes. 549 bytes, 13 lines control 620 bytes, 6 lines md5sums Package: libfetk1.9t64-dbgsym Source: apbs Version: 3.4.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 1872 Depends: libfetk1.9t64 (= 3.4.1-6) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libfetk1.9t64 Build-Ids: 4efcf95f0512613c8624b2915c3424aacab9e994 5bd73d57d2125601d836e65170458569c4fc8da1 5e68981dd387c48741733502555f2f47ea867f45 be993815105a1dfe024f165fe83d8a9cf0923feb ff85ea3009181f17996527e1d26e599c6a2532aa drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/4e/ -rw-r--r-- root/root 4328 2024-10-31 13:24 ./usr/lib/debug/.build-id/4e/fcf95f0512613c8624b2915c3424aacab9e994.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/5b/ -rw-r--r-- root/root 1230264 2024-10-31 13:24 ./usr/lib/debug/.build-id/5b/d73d57d2125601d836e65170458569c4fc8da1.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/5e/ -rw-r--r-- root/root 82952 2024-10-31 13:24 ./usr/lib/debug/.build-id/5e/68981dd387c48741733502555f2f47ea867f45.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/be/ -rw-r--r-- root/root 115832 2024-10-31 13:24 ./usr/lib/debug/.build-id/be/993815105a1dfe024f165fe83d8a9cf0923feb.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/ff/ -rw-r--r-- root/root 460408 2024-10-31 13:24 ./usr/lib/debug/.build-id/ff/85ea3009181f17996527e1d26e599c6a2532aa.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 2744 2024-10-31 13:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/libfetk1.9t64.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64-dbgsym -> libfetk1.9t64 libfetk1.9t64_3.4.1-6_amd64.deb ------------------------------- new Debian package, version 2.0. size 569728 bytes: control archive=1496 bytes. 1434 bytes, 34 lines control 686 bytes, 9 lines md5sums 186 bytes, 5 lines shlibs 68 bytes, 2 lines triggers Package: libfetk1.9t64 Source: apbs Version: 3.4.1-6 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 1566 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libmaloc1 (>= 0.2-1), libstdc++6 (>= 5), libsuperlu7 (>= 7.0.0+dfsg1), libumfpack6 (>= 1:7.0.1) Breaks: libfetk1.9 (<< 3.4.1-6) Replaces: libfetk1.9 Provides: libfetk1.9 (= 3.4.1-6) Section: libs Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: FETK libraries for APBS (shared libraries) The Finite Element ToolKit (FETK) is a collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C++, and include a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC) . This package provides a fork of FETK intended for use by APBS (Adaptive Poisson Boltzmann Solver). . The FETK component MALOC (Minimal Abstraction Layer for Object-oriented C/C++ programs) is provided separately via libmaloc-dev. . This package contains the libgamer, libmc, libpunc (and libcgcode, libvf2c) shared libraries. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libcgcode.so.1.9 -> libcgcode.so.1.9.3 -rw-r--r-- root/root 126696 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libcgcode.so.1.9.3 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libgamer.so.1.9 -> libgamer.so.1.9.3 -rw-r--r-- root/root 806536 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libgamer.so.1.9.3 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libmc.so.1.9 -> libmc.so.1.9.3 -rw-r--r-- root/root 509880 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libmc.so.1.9.3 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libpunc.so.1.9 -> libpunc.so.1.9.3 -rw-r--r-- root/root 14040 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libpunc.so.1.9.3 lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libvf2c.so.1.9 -> libvf2c.so.1.9.3 -rw-r--r-- root/root 113360 2024-10-31 13:24 ./usr/lib/x86_64-linux-gnu/libvf2c.so.1.9.3 drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64/ -rw-r--r-- root/root 3635 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64/changelog.Debian.gz -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libfetk1.9t64/changelog.gz -rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64/copyright drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 140 2024-10-31 13:24 ./usr/share/lintian/overrides/libfetk1.9t64 python3-apbslib-dbgsym_3.4.1-6_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 3606392 bytes: control archive=644 bytes. 415 bytes, 12 lines control 304 bytes, 3 lines md5sums Package: python3-apbslib-dbgsym Source: apbs Version: 3.4.1-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 3742 Depends: python3-apbslib (= 3.4.1-6) Section: debug Priority: optional Description: debug symbols for python3-apbslib Build-Ids: b4035cfcbc1bbd91dc74164f1e7380c6311ec4ba c68a5e4e151c184d6990855a2597aa71239739a4 drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/b4/ -rw-r--r-- root/root 143872 2024-10-31 13:24 ./usr/lib/debug/.build-id/b4/035cfcbc1bbd91dc74164f1e7380c6311ec4ba.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/c6/ -rw-r--r-- root/root 3661680 2024-10-31 13:24 ./usr/lib/debug/.build-id/c6/8a5e4e151c184d6990855a2597aa71239739a4.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 11896 2024-10-31 13:24 ./usr/lib/debug/.dwz/x86_64-linux-gnu/python3-apbslib.debug drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/share/doc/python3-apbslib-dbgsym -> python3-apbslib python3-apbslib_3.4.1-6_amd64.deb --------------------------------- new Debian package, version 2.0. size 228960 bytes: control archive=2120 bytes. 834 bytes, 18 lines control 3021 bytes, 38 lines md5sums 277 bytes, 12 lines * postinst #!/bin/sh 390 bytes, 12 lines * prerm #!/bin/sh Package: python3-apbslib Source: apbs Version: 3.4.1-6 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 1145 Depends: libapbs3t64 (= 3.4.1-6), python3 (<< 3.14), python3 (>= 3.13~), python3:any, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libmaloc1 (>= 0.2-1), libpython3.13 (>= 3.13.0~rc3), libstdc++6 (>= 14) Section: python Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package provides both the apbs and apbslib modules for Python3 enabling Python applications to access apbs. drwxr-xr-x root/root 0 2024-10-31 13:24 ./ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 428256 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbs.cpython-313-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbslib/ -rw-r--r-- root/root 23 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbslib/__init__.py -rw-r--r-- root/root 134264 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-313-x86_64-linux-gnu.so -rw-r--r-- root/root 14524 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbslib/apbslib.py drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/python-pybind/ -rw-r--r-- root/root 551 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/CMakeLists.txt -rw-r--r-- root/root 812 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_constants.hpp -rw-r--r-- root/root 4224 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.cpp -rw-r--r-- root/root 1906 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.hpp -rw-r--r-- root/root 3131 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.cpp -rw-r--r-- root/root 1018 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.hpp -rw-r--r-- root/root 1601 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.cpp -rw-r--r-- root/root 702 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.hpp -rw-r--r-- root/root 988 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/module.cpp drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/python/ -rw-r--r-- root/root 1896 2024-10-31 13:24 ./usr/share/apbs/tools/python/CMakeLists.txt -rw-r--r-- root/root 20999 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile -rw-r--r-- root/root 898 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile.am -rw-r--r-- root/root 20457 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile.in -rw-r--r-- root/root 1834 2022-04-29 18:53 ./usr/share/apbs/tools/python/README -rw-r--r-- root/root 6111 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbs.in -rw-r--r-- root/root 260435 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.c -rw-r--r-- root/root 14676 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.i -rw-r--r-- root/root 11686 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib_wrap.doc -rw-r--r-- root/root 66 2022-04-29 18:53 ./usr/share/apbs/tools/python/ion.pqr -rw-r--r-- root/root 15725 2022-04-29 18:53 ./usr/share/apbs/tools/python/main.py -rw-r--r-- root/root 19499 2024-10-31 13:24 ./usr/share/apbs/tools/python/noinput.py drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/python/vgrid/ -rw-r--r-- root/root 15551 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile -rw-r--r-- root/root 845 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.am -rw-r--r-- root/root 15036 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.in -rw-r--r-- root/root 1638 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/README -rw-r--r-- root/root 3134 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/average.py -rw-r--r-- root/root 14146 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/mergedx.py -rw-r--r-- root/root 2514 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/read.py -rw-r--r-- root/root 3038 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgrid.i -rw-r--r-- root/root 4711 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgrid.py -rw-r--r-- root/root 97354 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgridlib.c drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/python3-apbslib/ -rw-r--r-- root/root 3632 2024-10-31 13:24 ./usr/share/doc/python3-apbslib/changelog.Debian.gz -rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/python3-apbslib/changelog.gz -rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/python3-apbslib/copyright +------------------------------------------------------------------------------+ | Post Build Mon, 20 Jan 2025 14:44:10 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 20 Jan 2025 14:44:10 +0000 | +------------------------------------------------------------------------------+ Purging /build/apbs-PSc155 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 20 Jan 2025 14:44:13 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 407888 Build-Time: 682 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 69 Job: /srv/debomatic/incoming/apbs_3.4.1-6.dsc Machine Architecture: amd64 Package: apbs Package-Time: 767 Source-Version: 3.4.1-6 Space: 407888 Status: successful Version: 3.4.1-6 -------------------------------------------------------------------------------- Finished at 2025-01-20T14:44:06Z Build needed 00:12:47, 407888k disk space