Wed Dec 11 17:12:54 UTC 2024 I: starting to build apbs/trixie/i386 on jenkins on '2024-12-11 17:12' Wed Dec 11 17:12:54 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/32967/console.log Wed Dec 11 17:12:54 UTC 2024 I: Downloading source for trixie/apbs=3.4.1-6 --2024-12-11 17:12:55-- http://deb.debian.org/debian/pool/main/a/apbs/apbs_3.4.1-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2698 (2.6K) [text/prs.lines.tag] Saving to: ‘apbs_3.4.1-6.dsc’ 0K .. 100% 357M=0s 2024-12-11 17:12:55 (357 MB/s) - ‘apbs_3.4.1-6.dsc’ saved [2698/2698] Wed Dec 11 17:12:55 UTC 2024 I: apbs_3.4.1-6.dsc -----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 dvyMdc1Vnx7tRnQVcpd5ww+nu+6qjlbeOLro+5hHimbaqOLlEFRWaNnSx6lCk2iD z+8RgCzyTXouNWikvmq7C6MQcu6Q1odTzlfPNq+qpmF0VQvjv3gAgQPuUrE1DXEh wc5hiP6kasL/fiNK1raCob8Fh1iIoL/G6ALrb81WfFyaNq8jnP8aMFhWPLzMWCEH 1vvAsyzQUQzmSKDI5Ueq2tZ/87gErXD5AOKybKlEZTEnYWjVi0QQck1CX5UEdqkP kIFLod8Xlfu+Vmk= =5Vy3 -----END PGP SIGNATURE----- Wed Dec 11 17:12:55 UTC 2024 I: Checking whether the package is not for us Wed Dec 11 17:12:55 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Wed Dec 11 17:12:55 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Wed Dec 11 17:44:51 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 11 05:13:01 -12 2024 I: pbuilder-time-stamp: 1733937181 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [apbs_3.4.1-6.dsc] I: copying [./apbs_3.4.1.orig.tar.gz] I: copying [./apbs_3.4.1-6.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 31 13:25:39 2024 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: issuer "dparsons@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-6.dsc: no acceptable signature found dpkg-source: info: extracting apbs in apbs-3.4.1 dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying 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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/58309/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='7f20c44c09864c8e9da9bc2cd04c3424' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='58309' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/pbuilderrc_GNEP --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/b1 --logfile b1/build.log apbs_3.4.1-6.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/58309/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19952 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libmaloc-dev; however: Package libmaloc-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuitesparse-dev; however: Package libsuitesparse-dev is not installed. pbuilder-satisfydepends-dummy depends on libsuperlu-dev; however: Package libsuperlu-dev is not installed. pbuilder-satisfydepends-dummy depends on libtirpc-dev; however: Package libtirpc-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx | sphinx; however: Package python3-sphinx is not installed. Package sphinx is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-i686-linux-gnu{a} groff-base{a} hwloc-nox{a} intltool-debian{a} libamd3{a} libarchive-zip-perl{a} libarchive13t64{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli1{a} libbtf2{a} libcamd3{a} libccolamd3{a} libcholmod5{a} libcolamd3{a} libcom-err2{a} libcurl4t64{a} libcxsparse4{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc15{a} libicu72{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libklu2{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldl3{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmaloc-dev{a} libmaloc1{a} libmpich-dev{a} libmpich12{a} libnghttp2-14{a} libnsl2{a} libnuma-dev{a} libnuma1{a} libparu1{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} librbio4{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libslurm41t64{a} libspex3{a} libspqr4{a} libssh2-1t64{a} libsuitesparse-dev{a} libsuitesparse-mongoose3{a} libsuitesparseconfig7{a} libsuperlu-dev{a} libsuperlu7{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libumfpack6{a} libuv1t64{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} mpich{a} netbase{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} pybind11-dev{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pybind11{a} python3-pygments{a} python3-pyproject-hooks{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} swig{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libeigen3-dev libgraphblas-dev libhwloc-plugins libjson-xs-perl libldap-common libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-numpy python3-pil wget 0 packages upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 115 MB of archives. After unpacking 459 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.8-1 [815 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.8-1 [2240 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-4 [256 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 13 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.8-1 [1968 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.8-1 [677 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 61 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 67 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 79 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.2.0-1 [731 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20241024 [109 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libgfortran-14-dev i386 14.2.0-8 [800 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 gfortran-14-i686-linux-gnu i386 14.2.0-8 [12.5 MB] Get: 92 http://deb.debian.org/debian trixie/main i386 gfortran-14 i386 14.2.0-8 [12.2 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libhwloc15 i386 2.11.2-1 [177 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 hwloc-nox i386 2.11.2-1 [229 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libsuitesparseconfig7 i386 1:7.8.3+dfsg-2 [24.0 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libamd3 i386 1:7.8.3+dfsg-2 [43.5 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-4 [143 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-4 [2194 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libarpack2t64 i386 3.9.1-4 [102 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-4 [155 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-4 [4452 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libarpack2-dev i386 3.9.1-4 [122 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libbtf2 i386 1:7.8.3+dfsg-2 [25.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libcamd3 i386 1:7.8.3+dfsg-2 [41.1 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libccolamd3 i386 1:7.8.3+dfsg-2 [43.2 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libcolamd3 i386 1:7.8.3+dfsg-2 [35.6 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libcholmod5 i386 1:7.8.3+dfsg-2 [733 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libcxsparse4 i386 1:7.8.3+dfsg-2 [102 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.4-1 [165 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libnuma-dev i386 2.0.18-1+b1 [38.8 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libltdl7 i386 2.4.7-8 [395 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libltdl-dev i386 2.4.7-8 [167 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libhwloc-dev i386 2.11.2-1 [271 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libklu2 i386 1:7.8.3+dfsg-2 [95.5 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libldl3 i386 1:7.8.3+dfsg-2 [25.1 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libmaloc1 i386 1.5-2+b1 [72.9 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libmaloc-dev i386 1.5-2+b1 [1276 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libmpich12 i386 4.2.0-14 [1518 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libslurm41t64 i386 24.05.4-1 [739 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 mpich i386 4.2.0-14 [235 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 libmpich-dev i386 4.2.0-14 [2494 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libumfpack6 i386 1:7.8.3+dfsg-2 [323 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libparu1 i386 1:7.8.3+dfsg-2 [82.2 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 libpython3.12t64 i386 3.12.8-1 [2172 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.8-1 [5295 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.12.6-1 [9956 B] Get: 135 http://deb.debian.org/debian trixie/main i386 librbio4 i386 1:7.8.3+dfsg-2 [45.4 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 libspex3 i386 1:7.8.3+dfsg-2 [70.1 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libspqr4 i386 1:7.8.3+dfsg-2 [167 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 libsuitesparse-mongoose3 i386 1:7.8.3+dfsg-2 [55.0 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 libsuitesparse-dev i386 1:7.8.3+dfsg-2 [1719 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libsuperlu7 i386 7.0.0+dfsg1-2 [175 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 libsuperlu-dev i386 7.0.0+dfsg1-2 [21.9 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libtirpc-dev i386 1.3.4+ds-1.3+b1 [200 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libyaml-0-2 i386 0.2.5-1+b2 [56.0 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 mpi-default-dev i386 1.17 [3144 B] Get: 145 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 pybind11-dev all 2.13.6-1 [204 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.2-1 [55.3 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 python3-toml all 0.10.2-1 [16.2 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 python3-wheel all 0.45.1-1 [56.7 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 python3-build all 1.2.2-1 [36.0 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 pybuild-plugin-pyproject all 6.20241024 [11.4 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.16.0-1 [114 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 159 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.8-1 [505 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.12.6-1 [26.1 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 python3-roman all 4.2-1 [10.4 kB] Get: 165 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.8-2 [41.6 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 168 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 python3-pybind11 all 2.13.6-1 [215 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 172 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 2.2.3-3 [112 kB] Get: 173 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 sphinx-common all 7.4.7-4 [731 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 7.4.7-4 [588 kB] Get: 177 http://deb.debian.org/debian trixie/main i386 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 179 http://deb.debian.org/debian trixie/main i386 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB] Get: 180 http://deb.debian.org/debian trixie/main i386 python3-yaml i386 6.0.2-1+b1 [173 kB] Get: 181 http://deb.debian.org/debian trixie/main i386 swig i386 4.2.1-1 [1499 kB] Fetched 115 MB in 4s (26.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19952 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 libpython3.12-minimal:i386. Preparing to unpack .../libpython3.12-minimal_3.12.8-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_i386.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:i386 (3.12.8-1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20298 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_i386.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_i386.deb ... Unpacking libcom-err2:i386 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.8-1) ... 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Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.5-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:i386 (1.1.0-2+b6) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:i386 (1.47.2~rc1-2) ... Setting up libldl3:i386 (1:7.8.3+dfsg-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 11 17:15:23 UTC 2024. Universal Time is now: Wed Dec 11 17:15:23 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libbtf2:i386 (1:7.8.3+dfsg-2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libexpat1-dev:i386 (2.6.4-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:i386 (1.9.6-3) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up libhwloc15:i386 (2.11.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libltdl7:i386 (2.4.7-8) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:i386 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libmpich12:i386 (4.2.0-14) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libsuitesparseconfig7:i386 (1:7.8.3+dfsg-2) ... Setting up libslurm41t64 (24.05.4-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:i386 (1.4.5-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up libxml2:i386 (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-1) ... Setting up libblas-dev:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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:i386 (14.2.0-8) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libarpack2t64:i386 (3.9.1-4) ... Setting up libamd3:i386 (1:7.8.3+dfsg-2) ... Setting up libtool (2.4.7-8) ... Setting up libcolamd3:i386 (1:7.8.3+dfsg-2) ... Setting up libspex3:i386 (1:7.8.3+dfsg-2) ... Setting up libsuitesparse-mongoose3:i386 (1:7.8.3+dfsg-2) ... Setting up hwloc-nox (2.11.2-1) ... Setting up libcxsparse4:i386 (1:7.8.3+dfsg-2) ... Setting up libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ... Setting up libcamd3:i386 (1:7.8.3+dfsg-2) ... Setting up libsuperlu7:i386 (7.0.0+dfsg1-2) ... Setting up pkgconf:i386 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.18-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-8) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up librbio4:i386 (1:7.8.3+dfsg-2) ... Setting up liblapack-dev:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up gfortran-14-i686-linux-gnu (14.2.0-8) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libccolamd3:i386 (1:7.8.3+dfsg-2) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up libhwloc-dev:i386 (2.11.2-1) ... Setting up gfortran-14 (14.2.0-8) ... Setting up libsuperlu-dev:i386 (7.0.0+dfsg1-2) ... Setting up libarchive13t64:i386 (3.7.4-1.1) ... Setting up libmaloc1:i386 (1.5-2+b1) ... Setting up libcholmod5:i386 (1:7.8.3+dfsg-2) ... Setting up libarpack2-dev:i386 (3.9.1-4) ... Setting up libcurl4t64:i386 (8.11.0-1) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Setting up libspqr4:i386 (1:7.8.3+dfsg-2) ... Setting up mpich (4.2.0-14) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtirpc-dev:i386 (1.3.4+ds-1.3+b1) ... Setting up libklu2:i386 (1:7.8.3+dfsg-2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libmpich-dev:i386 (4.2.0-14) ... update-alternatives: using /usr/include/i386-linux-gnu/mpich to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up libumfpack6:i386 (1:7.8.3+dfsg-2) ... Setting up mpi-default-dev (1.17) ... Setting up libnsl2:i386 (1.3.0-3+b3) ... Setting up cmake (3.30.5-1) ... Setting up libmaloc-dev (1.5-2+b1) ... Setting up libpython3.12-stdlib:i386 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up libparu1:i386 (1:7.8.3+dfsg-2) ... Setting up libpython3.12t64:i386 (3.12.8-1) ... Setting up libpython3-stdlib:i386 (3.12.6-1) ... Setting up libsuitesparse-dev:i386 (1:7.8.3+dfsg-2) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:i386 (3.12.8-1) ... 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 python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pyproject-hooks (1.2.0-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.8-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.2.3-3) ... Setting up python3-build (1.2.2-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:i386 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up pybind11-dev (2.13.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pybind11 (2.13.6-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... 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 python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up dh-python (6.20241024) ... Setting up pybuild-plugin-pyproject (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... 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 (7.4.7-4) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/apbs-3.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../apbs_3.4.1-6_source.changes 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 --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot 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 debian/rules build dh build --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/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-i686-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/i386-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/reproducible-path/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 -- 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 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/i386-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/i386-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/reproducible-path/apbs-3.4.1/obj-i686-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 Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /build/reproducible-path/apbs-3.4.1/obj-i686-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 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/i386-linux-gnu/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/i386-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/i386-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/i386-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/i386-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/i386-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/i386-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/i386-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/i386-linux-gnu/librt.a -- Adding librt: /usr/lib/i386-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/reproducible-path/apbs-3.4.1/obj-i686-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: 2024-10-31T01:24:17 -- ** 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/i386-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/i386-linux-gnu/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/i386-linux-gnu/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/i386-linux-gnu/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/i386-linux-gnu/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/i386-linux-gnu/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/i386-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/i386-linux-gnu/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/i386-linux-gnu/librt.a -- Adding librt: /usr/lib/i386-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/i386-linux-gnu/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so (found version "4.1") -- Found MPI_CXX: /usr/lib/i386-linux-gnu/mpich/lib/libmpichcxx.so (found version "4.1") -- Found MPI: TRUE (found version "4.1") -- 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 -- 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/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 "4.2.1") -- Found Python3: /usr/bin/python3 (found suitable version "3.12.8", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.12 -- ***** Python3 library path is: /usr/lib/i386-linux-gnu/libpython3.12.so -- ***** Python3 library dir is: /usr/lib/i386-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 "3.12.8", minimum required is "3.6") -- Found PythonLibs: /usr/lib/i386-linux-gnu/libpython3.12.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/i386-linux-gnu/libumfpack.so;/usr/lib/i386-linux-gnu/libspqr.so;/usr/lib/i386-linux-gnu/libcholmod.so;/usr/lib/i386-linux-gnu/libccolamd.so;/usr/lib/i386-linux-gnu/libcamd.so;/usr/lib/i386-linux-gnu/libcolamd.so;/usr/lib/i386-linux-gnu/libamd.so;/usr/lib/i386-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/i386-linux-gnu/libblas.so;/usr/lib/i386-linux-gnu/libsuitesparseconfig.so;/usr/lib/i386-linux-gnu/librt.a;/usr/lib/i386-linux-gnu/mpich/lib/libmpich.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 "3.12.8") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/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/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/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/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/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/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/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/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/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/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/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/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /build/reproducible-path/apbs-3.4.1/tests COMMAND /usr/bin/python3 /build/reproducible-path/apbs-3.4.1/tests/apbs_tester.py -e apbs -t solv -- Configuring done (23.0s) -- Generating done (0.7s) 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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' dh_auto_build -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/apbs-3.4.1 -B/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-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 -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake "--color=" 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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake "--color=" make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-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 cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/scr.c.o -MF CMakeFiles/cgcode.dir/scr.c.o.d -o CMakeFiles/cgcode.dir/scr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scr.c Dependee "/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". 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[ 0%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/scgdrv.c.o -MF CMakeFiles/cgcode.dir/scgdrv.c.o.d -o CMakeFiles/cgcode.dir/scgdrv.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scg.c [ 2%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 3%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base/gamer_base.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/scrind.c.o -MF CMakeFiles/cgcode.dir/scrind.c.o.d -o CMakeFiles/cgcode.dir/scrind.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scrind.c [ 3%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcg.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/scgnr.c.o -MF CMakeFiles/cgcode.dir/scgnr.c.o.d -o CMakeFiles/cgcode.dir/scgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgnr.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle/triangle.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/f77vers.c.o -MF CMakeFiles/vf2c.dir/f77vers.c.o.d -o CMakeFiles/vf2c.dir/f77vers.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77vers.c [ 3%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/i77vers.c.o -MF CMakeFiles/vf2c.dir/i77vers.c.o.d -o CMakeFiles/vf2c.dir/i77vers.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i77vers.c Scanning dependencies of target apbslib_swig_compilation make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 4%] Swig compile apbslib.i for python cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python && /usr/bin/cmake -E make_directory /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/_apbslib.dir /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/_apbslib.dir [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_rnge.c.o -MF CMakeFiles/vf2c.dir/s_rnge.c.o.d -o CMakeFiles/vf2c.dir/s_rnge.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgne.c [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgne.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python && /usr/bin/cmake -E touch /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp [ 5%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o [ 6%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/spcgnr.c.o -MF CMakeFiles/cgcode.dir/spcgnr.c.o.d -o CMakeFiles/cgcode.dir/spcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sppcg.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig/4.2.1 /usr/bin/swig -python -outdir /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python -interface _apbslib -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/python3.12 -I/build/reproducible-path/apbs-3.4.1/tools/python -o /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /build/reproducible-path/apbs-3.4.1/tools/python/apbslib.i [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/abort_.c.o -MF CMakeFiles/vf2c.dir/abort_.c.o.d -o CMakeFiles/vf2c.dir/abort_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/abort_.c [ 7%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c [ 7%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scbfix.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/exit_.c.o -MF CMakeFiles/vf2c.dir/exit_.c.o.d -o CMakeFiles/vf2c.dir/exit_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/exit_.c [ 7%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/getarg_.c.o -MF CMakeFiles/vf2c.dir/getarg_.c.o.d -o CMakeFiles/vf2c.dir/getarg_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getarg_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sonest.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/msstop.c [ 9%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/r1mach.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iargc_.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 10%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/getenv_.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/signal_.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcrind.c [ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_stop.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 13%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o [ 13%] Built target apbslib_swig_compilation cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_paus.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'void tetgenmesh::constrainedfacets()': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 *"); | ^~~~~~~~~ [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/dpcgnr.c.o -MF CMakeFiles/cgcode.dir/dpcgnr.c.o.d -o CMakeFiles/cgcode.dir/dpcgnr.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c [ 15%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd 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Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgne.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function 'long int tetgenmesh::reconstructmesh()': /build/reproducible-path/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"); | ^~~~~ [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc 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CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/erf_.c.o -MF CMakeFiles/vf2c.dir/erf_.c.o.d -o CMakeFiles/vf2c.dir/erf_.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/erfc_.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dppcg.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/dpcgca.c.o -MF CMakeFiles/cgcode.dir/dpcgca.c.o.d -o CMakeFiles/cgcode.dir/dpcgca.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uninit.c [ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd 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-Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_dd.c.o -MF CMakeFiles/vf2c.dir/pow_dd.c.o.d -o CMakeFiles/vf2c.dir/pow_dd.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o [ 18%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c /build/reproducible-path/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/reproducible-path/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/reproducible-path/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_abs.c [ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_exp.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/d1mach.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 24%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_exp.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_div.c [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_log.c [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 25%] Linking C shared library libcgcode.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 [ 26%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -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 [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_asin.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-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 [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 28%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_atn2.c.o -MF CMakeFiles/vf2c.dir/r_atn2.c.o.d -o CMakeFiles/vf2c.dir/r_atn2.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 28%] Built target cgcode [ 29%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 29%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cos.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_dim.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'SurfaceMesh* SurfaceMesh_readOFF(char*)': /build/reproducible-path/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/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function 'GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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"); | ^~~~~~~~ [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_exp.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 31%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_int.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 CMakeFiles/vf2c.dir/r_log.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_log.c [ 32%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/triangle -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/tetgen -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/SurfSmooth.C.o -MF CMakeFiles/gamer.dir/biom/SurfSmooth.C.o.d -o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_mod.c.o -MF CMakeFiles/vf2c.dir/r_mod.c.o.d -o CMakeFiles/vf2c.dir/r_mod.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_mod.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sign.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sin.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tan.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_asin.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cos.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_dim.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_imag.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_int.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_nint.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_sin.c.o -MF CMakeFiles/vf2c.dir/d_sin.c.o.d -o CMakeFiles/vf2c.dir/d_sin.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sin.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_sinh.c.o -MF CMakeFiles/vf2c.dir/d_sinh.c.o.d -o CMakeFiles/vf2c.dir/d_sinh.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tan.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dim.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_indx.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_nint.c [ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/i_sign.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/lbitshft.c.o -MF CMakeFiles/vf2c.dir/lbitshft.c.o.d -o CMakeFiles/vf2c.dir/lbitshft.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_abs.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_dim.c.o -MF CMakeFiles/vf2c.dir/h_dim.c.o.d -o CMakeFiles/vf2c.dir/h_dim.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dim.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_indx.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/l_lt.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_le.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -o CMakeFiles/vf2c.dir/f77_aloc.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_cat.c.o -MF CMakeFiles/vf2c.dir/s_cat.c.o.d -o CMakeFiles/vf2c.dir/s_cat.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cat.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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_cmp.c.o -MF CMakeFiles/vf2c.dir/s_cmp.c.o.d -o CMakeFiles/vf2c.dir/s_cmp.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/s_copy.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dtime_.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/close.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dfe.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function 'f_back': /build/reproducible-path/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/dolio.c.o -MF CMakeFiles/vf2c.dir/dolio.c.o.d -o CMakeFiles/vf2c.dir/dolio.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/dolio.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/due.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/endfile.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/err.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmt.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ftell_.c [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o [ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/iio.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/ilnw.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/inquire.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/lread.c.o -MF CMakeFiles/vf2c.dir/lread.c.o.d -o CMakeFiles/vf2c.dir/lread.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lread.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/open.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rewind.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsli.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sfe.c [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/typesize.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/util.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wrtfmt.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsle.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/wsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/main.c [ 60%] Linking C shared library libvf2c.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -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 CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o 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CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o 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/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 60%] Built target vf2c make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -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/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libarpack.so /usr/lib/i386-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 60%] 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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc_base.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mat.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/matcopy.c.o -MF CMakeFiles/mc.dir/bam/matcopy.c.o.d -o CMakeFiles/mc.dir/bam/matcopy.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matcopy.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/matln.c.o -MF CMakeFiles/mc.dir/bam/matln.c.o.d -o CMakeFiles/mc.dir/bam/matln.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/matln.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/mtool.c.o -MF CMakeFiles/mc.dir/bam/mtool.c.o.d -o CMakeFiles/mc.dir/bam/mtool.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mtool.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/slu.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_ctor': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:36: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 2147483646] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 3] 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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function 'sprintf', inlined from 'Bmat_ctor' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17: /usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 4 and 22 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 ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function 'sprintf', inlined from 'Bvec_bcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_bcg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/vec3.c.o -MF CMakeFiles/mc.dir/bam/vec3.c.o.d -o CMakeFiles/mc.dir/bam/vec3.c.o -c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/vec3.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c: In function 'Bmat_galerkin': /build/reproducible-path/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/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In function 'sprintf', inlined from 'Bmat_galerkin' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/zslu.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function 'Bvec_cgnr': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/whb.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c 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/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/rcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/brcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/assem.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function 'sprintf', inlined from 'Bvec_hcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hcg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/bnode.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/estim.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function 'Bvec_ctorPoint': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 1073741823] 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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function 'sprintf', inlined from 'Bvec_ctorPoint' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function 'Bvec_hbcg': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/io.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/node.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/parti.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/re.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/vel.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/ves.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function 'sprintf', inlined from 'Aprx_fe2fd' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c: In function 'Aprx_fe2fd': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemchk.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function 'sprintf', inlined from 'Bvec_sfpcg' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c: In function 'Bvec_submethod': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from 'Bvec_submethod' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemg.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemio.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemref.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function 'Gem_delaunay': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: 'Gem_writeGV' accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: 'Gem_writeGV' accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: 'Gem_writeGV' accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/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, | ^~~~~~~~~~~ [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn 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/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde/pde.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn/svio.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function 'MCsh_builtIn': /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: 'Gem_writeGEOM' accessing 16 bytes in a region of size 12 [-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/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: 'Gem_writeGEOM' accessing 16 bytes in a region of size 12 [-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type 'double *[4]' /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function 'sprintf', inlined from 'Gem_writeTEC' at /build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function 'Gem_writeTEC': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/i386-linux-gnu/libblas.so -lmaloc /usr/lib/i386-linux-gnu/libarpack.so /usr/lib/i386-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/pmgc /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/generic /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 73%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/nosh.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/buildAd.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/mgparm.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/buildGd.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/femparm.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/buildPd.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/pbamparm.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/buildBd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/cgd.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/pbsamparm.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/pbeparm.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/gsd.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/matvecd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/bemparm.c [ 78%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mgcsd.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/geoflowparm.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/apolparm.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/vacc.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/valist.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/vatom.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mgdrvd.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/vpbe.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mgsubd.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mikpckd.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/vcap.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/vclist.c.o -MF CMakeFiles/apbs_generic.dir/vclist.c.o.d -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vclist.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /build/reproducible-path/apbs-3.4.1/src/generic/vstring.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o [ 82%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/vparam.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mlinpckd.c [ 82%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/generic/vgreen.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mypdec.c [ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/newtond.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/newdrvd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/powerd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/smoothd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/pmgc/mgfasd.c [ 84%] Linking C shared library libapbs_generic.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libblas.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 84%] Built target apbs_generic make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/fem /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/fem /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/fem/vcsm.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/fem/vpee.c /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/fem/vfetk.h:67, from /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:57: In function 'sprintf', inlined from 'Bmat_printHB' at /build/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1073:5: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/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/reproducible-path/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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1074:5: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1075:5: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c: In function 'Bmat_printHB': /build/reproducible-path/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/reproducible-path/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/reproducible-path/apbs-3.4.1/src/fem/vfetk.c:1076:5: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Linking C shared library libapbs_fem.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 85%] Built target apbs_fem [ 86%] Linking C shared library libapbs_pmgc.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libblas.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src/mg /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/mg/vgrid.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/mg/vmgrid.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/mg/vpmg.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/mg/vopot.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/mg/vpmgp.c /build/reproducible-path/apbs-3.4.1/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /build/reproducible-path/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/mg/vgrid.h:67, from /build/reproducible-path/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%] Linking C shared library libapbs_mg.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/routines.c /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'initAPOL': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 2 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /build/reproducible-path/apbs-3.4.1/src/routines.c:5046:20: note: referencing argument 3 of type 'char[1024]' In file included from /build/reproducible-path/apbs-3.4.1/src/generic/apolparm.h:73, from /build/reproducible-path/apbs-3.4.1/src/generic/nosh.h:73, from /build/reproducible-path/apbs-3.4.1/src/apbs.h:70, from /build/reproducible-path/apbs-3.4.1/src/routines.h:64, from /build/reproducible-path/apbs-3.4.1/src/routines.c:54: /build/reproducible-path/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/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 2 of type 'char[1024]' /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: warning: 'Vparam_getAtomData' accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /build/reproducible-path/apbs-3.4.1/src/routines.c:5048:24: note: referencing argument 3 of type 'char[1024]' /build/reproducible-path/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, | ^~~~~~~~~~~~~~~~~~ [ 87%] Linking CXX shared library libgamer.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -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/reproducible-path/apbs-3.4.1/obj-i686-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 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 87%] Built target gamer /build/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writematMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/apbs.h:67: In function 'sprintf', inlined from 'writematMG' at /build/reproducible-path/apbs-3.4.1/src/routines.c:2020:9: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2919:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2963:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2954:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2937:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2930:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2944:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataMG': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:2909:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:4887:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:4893:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/src/routines.c: In function 'writedataFE': /build/reproducible-path/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/reproducible-path/apbs-3.4.1/src/routines.c:4880:13: /usr/include/i386-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/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1/obj-i686-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 -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/value.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/multivalue.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/similarity.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/analysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/value.dir/build.make tools/mesh/CMakeFiles/value.dir/build make -f tools/mesh/CMakeFiles/multivalue.dir/build.make tools/mesh/CMakeFiles/multivalue.dir/build make -f tools/mesh/CMakeFiles/benchmark.dir/build.make tools/mesh/CMakeFiles/benchmark.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/similarity.dir/build.make tools/mesh/CMakeFiles/similarity.dir/build make -f tools/mesh/CMakeFiles/analysis.dir/build.make tools/mesh/CMakeFiles/analysis.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 88%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o [ 88%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/dxmath.dir/dxmath.c.o -MF CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dxmath.c [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o [ 89%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/smooth.dir/smooth.c.o -MF CMakeFiles/smooth.dir/smooth.c.o.d -o CMakeFiles/smooth.dir/smooth.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/smooth.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/mergedx.dir/mergedx.c.o -MF CMakeFiles/mergedx.dir/mergedx.c.o.d -o CMakeFiles/mergedx.dir/mergedx.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/mergedx.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/src/main.c [ 89%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o [ 90%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o [ 90%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o [ 90%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam 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CMakeFiles/value.dir/value.c.o.d -o CMakeFiles/value.dir/value.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/value.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde 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-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/reproducible-path/apbs-3.4.1/tools/mesh/analysis.c [ 90%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o [ 91%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/mesh/similarity.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src 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-I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/mesh/mergedx2.c [ 91%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/multivalue.c /build/reproducible-path/apbs-3.4.1/src/main.c: In function 'main': /build/reproducible-path/apbs-3.4.1/src/main.c:319:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /build/reproducible-path/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__); | ^~~~~~~~ [ 91%] Linking C executable ../bin/mgmesh cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 92%] Linking C executable ../bin/benchmark cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 92%] Linking C executable ../bin/value cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 93%] Linking C executable ../bin/multivalue cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 93%] Linking C executable ../bin/smooth cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 [ 93%] Linking C executable ../bin/dxmath cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 93%] Built target mgmesh make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/dx2mol.dir/DependInfo.cmake "--color=" [ 94%] Linking C executable ../bin/analysis cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make tools/mesh/CMakeFiles/dx2mol.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 94%] Linking C executable apbs cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 [ 94%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o [ 94%] Linking C executable ../bin/mergedx make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/dx2mol.dir/dx2mol.c.o -MF CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o CMakeFiles/dx2mol.dir/dx2mol.c.o -c /build/reproducible-path/apbs-3.4.1/tools/mesh/dx2mol.c cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 CMakeFiles/apbs.dir/main.c.o -o apbs -lutil -ldl -lm -lstdc++ /usr/lib/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp libapbs_routines.so.3 mg/libapbs_mg.so.3 pmgc/libapbs_pmgc.so.3 fem/libapbs_fem.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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 94%] Built target benchmark [ 95%] Linking C executable ../bin/similarity make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/depend cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/dx2uhbd.dir/DependInfo.cmake "--color=" [ 95%] Built target value make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/dx2uhbd.dir/build.make tools/mesh/CMakeFiles/dx2uhbd.dir/build /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 95%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/mesh/dx2uhbd.c [ 95%] Built target multivalue make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" [ 95%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 95%] Built target smooth make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake "--color=" make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build [ 95%] Built target dxmath make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/manip /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 96%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c [ 96%] 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-I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF CMakeFiles/coulomb.dir/coulomb.c.o.d -o CMakeFiles/coulomb.dir/coulomb.c.o -c /build/reproducible-path/apbs-3.4.1/tools/manip/coulomb.c make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 97%] Built target analysis make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/manip /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip/CMakeFiles/born.dir/DependInfo.cmake "--color=" /build/reproducible-path/apbs-3.4.1/tools/mesh/del2dx.c: In function 'main': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build [ 97%] Linking C executable ../bin/dx2mol cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [ 97%] Built target apbs [ 97%] Built target similarity make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 97%] Linking C executable ../bin/mergedx2 cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake "--color=" make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/depend [ 97%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/apbs-3.4.1 /build/reproducible-path/apbs-3.4.1/tools/python-pybind /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python-pybind /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python-pybind/CMakeFiles/apbs_pybind.dir/DependInfo.cmake "--color=" [ 97%] Built target mergedx cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip && /usr/bin/cc -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/manip/CMakeFiles/born.dir/born.c.o -MF CMakeFiles/born.dir/born.c.o.d -o CMakeFiles/born.dir/born.c.o -c /build/reproducible-path/apbs-3.4.1/tools/manip/born.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 98%] Linking C executable ../bin/dx2uhbd make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/build /build/reproducible-path/apbs-3.4.1/tools/mesh/tensor2dx.c: In function 'main': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c: In function 'main': /build/reproducible-path/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/reproducible-path/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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/apbs-3.4.1/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[3]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 98%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o [ 98%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/module.cpp.o -MF CMakeFiles/apbs_pybind.dir/module.cpp.o.d -o CMakeFiles/apbs_pybind.dir/module.cpp.o -c /build/reproducible-path/apbs-3.4.1/tools/python-pybind/module.cpp cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_nosh.cpp [ 98%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/python3.12 -I/build/reproducible-path/apbs-3.4.1/tools/python -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c [ 99%] Linking C executable ../bin/del2dx cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 99%] Linking C executable ../bin/tensor2dx cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 [ 99%] Linking C executable ../bin/uhbd_asc2bin make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 99%] Built target dx2mol /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [ 99%] Linking C executable ../bin/coulomb cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_vatom.cpp [100%] Built target mergedx2 make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Built target dx2uhbd [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/apbs-3.4.1/src -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/src -I/build/reproducible-path/apbs-3.4.1/include -I/usr/include/suitesparse -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/mc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/base -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/bam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/whb -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/aprx -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/gem -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/pde -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/nam -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/dyn -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/mc/src/mcsh -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/vf2c/punc -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/_deps/fetk-build/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src -I/build/reproducible-path/apbs-3.4.1/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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/reproducible-path/apbs-3.4.1/tools/python-pybind/bind_valist.cpp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Linking C executable ../bin/born [100%] Built target del2dx cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 CMakeFiles/born.dir/born.c.o -o ../bin/born ../../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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Built target uhbd_asc2bin [100%] Built target tensor2dx make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Built target coulomb make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Built target born [100%] Linking C shared library _apbslib.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -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 -shared -Wl,-soname,_apbslib.so -o _apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lutil -ldl -lm -lstdc++ /usr/lib/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/i386-linux-gnu/libpython3.12.so ../../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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Built target _apbslib [100%] Linking CXX shared module apbs.cpython-312-i386-linux-gnu.so cd /build/reproducible-path/apbs-3.4.1/obj-i686-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/reproducible-path/apbs-3.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-312-i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so /usr/lib/i386-linux-gnu/libblas.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.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/i386-linux-gnu/libarpack.so /usr/lib/i386-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/i386-linux-gnu/libumfpack.so /usr/lib/i386-linux-gnu/libspqr.so /usr/lib/i386-linux-gnu/libcholmod.so /usr/lib/i386-linux-gnu/libccolamd.so /usr/lib/i386-linux-gnu/libcamd.so /usr/lib/i386-linux-gnu/libcolamd.so /usr/lib/i386-linux-gnu/libamd.so -lm -ldl /usr/lib/i386-linux-gnu/libblas.so /usr/lib/i386-linux-gnu/libsuitesparseconfig.so /usr/lib/i386-linux-gnu/librt.a /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so -fopenmp make[3]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' [100%] Built target apbs_pybind make[2]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' PYTHONPATH=/build/reproducible-path/apbs-3.4.1/obj-i386-linux-gnu/tools/python sphinx-build -b html docs /build/reproducible-path/apbs-3.4.1/obj-i386-linux-gnu/docs/_build/html # HTML generator Running Sphinx v7.4.7 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.nonpolar.Nonpolar. 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.finite_element. 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' 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. 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.finite_difference. 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/reproducible-path/apbs-3.4.1/docs/getting/index.rst:41: ERROR: Unexpected indentation. /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow". /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk". /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam". /build/reproducible-path/apbs-3.4.1/docs/releases.rst:3: WARNING: Duplicate explicit target name: "tabi-pb". WARNING: autodoc: failed to import module 'input_file.calculate.boundary_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_difference' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.finite_element' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.calculate.generic' from module 'apbs'; the following exception was raised: No module named 'pyparsing' /build/reproducible-path/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition. /build/reproducible-path/apbs-3.4.1/docs/using/input/new/calculate/index.rst:33: ERROR: Document may not end with a transition. WARNING: autodoc: failed to import module 'input_file.calculate.nonpolar.Nonpolar' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.process' from module 'apbs'; the following exception was raised: No module named 'pyparsing' WARNING: autodoc: failed to import module 'input_file.read' from module 'apbs'; the following exception was raised: No module named 'pyparsing' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/apbs-3.4.1/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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... done copying extra files... done copying assets: done writing output... 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[ 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-i386-linux-gnu/docs/_build/html. make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=cmake dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_installdirs -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/apbs-3.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/apbs-3.4.1 -B/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/punc.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/punc_base.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/punccf.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/punc_base_p.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libpunc.so.1.9.3 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libpunc.so.1.9 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libpunc.so -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/varpack.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vblas.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vcgcode.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vlapack.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vpmg.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/punc/vf2c.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libvf2c.so.1.9.3 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libvf2c.so.1.9 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libvf2c.so -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libcgcode.so.1.9.3 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libcgcode.so.1.9 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu/libcgcode.so -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/gamer_base.h -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/include/gamer/triangle.h -- Installing: 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/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_constants.hpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/module.cpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.hpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/psize.py -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/coulomb.c -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/born.c -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/manip/inputgen.py -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/value -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd make[1]: Leaving directory '/build/reproducible-path/apbs-3.4.1/obj-i686-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/apbs-3.4.1' (cd tests; PATH=/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/lib/i386-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/build/reproducible-path/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/reproducible-path/apbs-3.4.1/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.002556 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/build/reproducible-path/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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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: 24.774053 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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: 20.252869 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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 = 8.142935605695E+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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605695e+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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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 = 1.485246665691E+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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+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, 122.066 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665691e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344953e+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 (5.941003947870e+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: 104.991652 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, 3257.1427835730997, 5941.00394787, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867462003] 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 3257.1427835730997 COMPUTED RESULT 5941.00394787 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867462003 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/build/reproducible-path/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: 61.261 MB total, 61.261 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: 61.261 MB total, 122.066 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: 61.261 MB total, 122.066 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 = 1.485529328300E+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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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: 61.188 MB total, 122.066 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, 122.066 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328300e+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 (5.942108652589e+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: 104.460708 seconds -------------------------------------------------------------------------------- Total elapsed time: 254.481838 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, 5942.108652589, 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 5942.108652589 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/build/reproducible-path/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: 1004.805 MB total, 1004.805 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: 1004.805 MB total, 1995.193 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: 1005.791 MB total, 1995.193 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: 1005.791 MB total, 1997.162 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: 1018.290 MB total, 1997.162 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: 1018.290 MB total, 2013.317 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, 2013.317 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: 402.323255 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/build/reproducible-path/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: 1004.805 MB total, 1004.805 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: 1004.805 MB total, 1995.193 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: 1005.791 MB total, 1995.193 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: 1005.791 MB total, 1997.162 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: 1018.290 MB total, 1997.162 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: 1018.290 MB total, 2013.317 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) = 1.095841077647E+02 kJ/mol Global net ELEC energy = 1.095841077647E+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, 2013.317 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 (1.095841077647e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 267.197034 seconds -------------------------------------------------------------------------------- Total elapsed time: 669.520289 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, 109.5841077647] 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 109.5841077647 Running tests for alkanes section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/build/reproducible-path/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, 2.201 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: 39.348877 seconds -------------------------------------------------------------------------------- Total elapsed time: 39.348877 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/build/reproducible-path/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 0.00e+00 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: 102.611 MB total, 102.611 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: 102.611 MB total, 182.820 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: 102.611 MB total, 182.820 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: 102.611 MB total, 182.820 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: 62.381 MB total, 182.820 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: 62.381 MB total, 182.820 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: 62.381 MB total, 182.820 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: 62.381 MB total, 182.820 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: 102.389 MB total, 182.820 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: 102.389 MB total, 182.820 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: 102.389 MB total, 182.820 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: 102.389 MB total, 182.820 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) = 1.500810086372E+01 kJ/mol Global net ELEC energy = 1.500810086372E+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, 182.820 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 (1.500810086372e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 59.211627 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, 15.00810086372] 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 15.00810086372 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/build/reproducible-path/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 0.00e+00 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: 102.611 MB total, 102.611 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: 102.611 MB total, 182.820 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: 102.611 MB total, 182.820 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: 102.611 MB total, 182.820 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: 62.381 MB total, 182.820 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: 62.381 MB total, 182.820 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: 62.381 MB total, 182.820 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: 62.381 MB total, 182.820 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: 102.389 MB total, 182.820 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: 102.389 MB total, 182.820 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: 102.389 MB total, 182.820 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: 102.389 MB total, 182.820 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) = 1.624454192070E+01 kJ/mol Global net ELEC energy = 1.624454192070E+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, 182.820 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 (1.624454192070e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 56.897793 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, 16.2445419207] 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 16.2445419207 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/build/reproducible-path/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 -7.98e-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: 102.854 MB total, 102.854 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: 102.854 MB total, 183.185 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: 102.854 MB total, 183.185 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: 102.854 MB total, 183.185 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: 62.467 MB total, 183.185 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: 62.467 MB total, 183.185 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: 62.467 MB total, 183.185 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: 62.467 MB total, 183.185 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: 102.552 MB total, 183.185 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: 102.552 MB total, 183.185 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: 102.552 MB total, 183.185 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: 102.552 MB total, 183.185 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) = 1.442499933661E+01 kJ/mol Global net ELEC energy = 1.442499933661E+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, 183.185 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 (1.442499933661e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 58.718971 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, 14.42499933661] 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 14.42499933661 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/build/reproducible-path/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 -7.98e-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: 102.854 MB total, 102.854 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: 102.854 MB total, 183.185 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: 102.854 MB total, 183.185 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: 102.854 MB total, 183.185 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: 62.467 MB total, 183.185 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: 62.467 MB total, 183.185 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: 62.467 MB total, 183.185 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: 62.467 MB total, 183.185 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: 102.552 MB total, 183.185 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: 102.552 MB total, 183.185 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: 102.552 MB total, 183.185 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: 102.552 MB total, 183.185 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) = 1.545150742842E+01 kJ/mol Global net ELEC energy = 1.545150742842E+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, 183.185 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 (1.545150742842e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 44.25756 seconds -------------------------------------------------------------------------------- Total elapsed time: 219.085951 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, 15.45150742842] 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 15.45150742842 Running tests for hca-bind section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/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 -1.99e-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: 62.612 MB total, 62.612 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: 62.612 MB total, 123.493 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: 62.612 MB total, 123.493 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: 127.596 MB total, 127.596 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: 127.596 MB total, 207.283 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: 127.596 MB total, 207.283 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: 127.895 MB total, 207.283 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: 127.895 MB total, 207.693 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: 127.895 MB total, 207.693 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) = -5.246475812678E+01 kJ/mol Global net ELEC energy = -5.246475812678E+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, 207.693 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 (-5.246475812678e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 51.076785 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, -52.46475812678] 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 -52.46475812678 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/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 -1.99e-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: 62.612 MB total, 62.612 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: 62.612 MB total, 123.493 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: 62.612 MB total, 123.493 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: 127.596 MB total, 127.596 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: 127.596 MB total, 207.283 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: 127.596 MB total, 207.283 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: 127.895 MB total, 207.283 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: 127.895 MB total, 207.693 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: 127.895 MB total, 207.693 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) = -5.405979017064E+01 kJ/mol Global net ELEC energy = -5.405979017064E+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, 207.693 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 (-5.405979017064e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 36.262306 seconds -------------------------------------------------------------------------------- Total elapsed time: 87.339091 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, -54.05979017064] 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 -54.05979017064 Running tests for ionize section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/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 0.00e+00 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: 61.580 MB total, 61.580 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: 61.580 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.580 MB total, 122.369 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: 61.580 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.409 MB total, 122.369 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: 61.409 MB total, 122.369 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: 61.369 MB total, 122.369 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: 61.369 MB total, 122.369 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, 122.369 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: 33.753252 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/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 0.00e+00 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: 61.580 MB total, 61.580 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: 61.580 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.580 MB total, 122.369 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: 61.580 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.404 MB total, 122.369 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: 61.409 MB total, 122.369 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: 61.409 MB total, 122.369 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: 61.369 MB total, 122.369 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: 61.369 MB total, 122.369 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) = -4.721246714829E+02 kJ/mol Global net ELEC energy = -4.721246714829E+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, 122.369 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 (-4.721246714829e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 11.699113 seconds -------------------------------------------------------------------------------- Total elapsed time: 45.452365 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, -472.1246714829] 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 -472.1246714829 Running tests for ion-pmf section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/build/reproducible-path/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: 61.094 MB total, 61.094 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: 61.094 MB total, 61.133 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 9.128e-07 9.128e-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 -2.766e-05 -2.766e-05 tot 1 -2.723e-02 9.128e-07 9.128e-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 -2.766e-05 -2.766e-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: -6.909672999302E+00 WCA energy for atom 1: -6.909373990749E+00 Total WCA energy: -13.819 kJ/mol Total non-polar energy = -1.365298695137E+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 8.398642197665E+01 -1.324564430574E-05 -1.613435757406E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416728E-05 -5.378919665050E-05 tot 0 9.013477903583E+01 -3.992081847302E-05 -6.992355422456E-05 qf 1 -8.466423642735E+01 -1.836748314304E-05 -3.062224388545E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352582E-05 -6.291495498104E-05 tot 1 -8.178149719680E+01 -4.986694666886E-05 -9.353719886649E-05 tot all 8.353281839029E+00 -8.978776514188E-05 -1.634607530910E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365298695137E+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 -5.826642849715E-01 -2.765994661276E-05 -2.765994661317E-05 tot 0 -1.158043402830E+01 -2.765994661276E-05 -2.765994661317E-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 5.826650413624E-01 -2.766081309291E-05 -2.766081309331E-05 tot 1 1.170128939726E+01 -2.766081309291E-05 -2.766081309331E-05 tot all 1.208553689549E-01 -5.532075970567E-05 -5.532075970648E-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, 62.228 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: 25.060408 seconds -------------------------------------------------------------------------------- Total elapsed time: 25.060408 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, -13.65298695137] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65298695137 Running tests for pka-lig section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/build/reproducible-path/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 -2.78e-17 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: 203.783 MB total, 203.783 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: 203.783 MB total, 405.012 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: 270.353 MB total, 405.012 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: 270.353 MB total, 491.871 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: 271.031 MB total, 491.871 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: 271.031 MB total, 492.784 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) = 8.083515649209E+00 kJ/mol Global net ELEC energy = 8.083515649209E+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, 492.784 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 (8.083515649209e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 33.333609 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, 8.083515649209] 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 8.083515649209 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/build/reproducible-path/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 -2.78e-17 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: 203.783 MB total, 203.783 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: 203.783 MB total, 405.012 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: 270.353 MB total, 405.012 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: 270.353 MB total, 491.871 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: 271.031 MB total, 491.871 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: 271.031 MB total, 492.784 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) = 2.096300255725E+01 kJ/mol Global net ELEC energy = 2.096300255725E+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, 492.784 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 (2.096300255725e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 33.198069 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, 20.96300255725] 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 20.96300255725 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/build/reproducible-path/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 -2.78e-17 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: 203.369 MB total, 203.369 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: 203.369 MB total, 404.597 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: 230.723 MB total, 404.597 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: 230.723 MB total, 452.241 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: 230.826 MB total, 452.241 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: 230.826 MB total, 452.578 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) = 1.192607686580E+02 kJ/mol Global net ELEC energy = 1.192607686580E+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, 452.578 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 (1.192607686580e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 35.302698 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, 119.260768658] 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 119.260768658 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/build/reproducible-path/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 -2.78e-17 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: 203.369 MB total, 203.369 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: 203.369 MB total, 404.597 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: 230.723 MB total, 404.597 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: 230.723 MB total, 452.241 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: 230.826 MB total, 452.241 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: 230.826 MB total, 452.578 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) = 1.088773280805E+02 kJ/mol Global net ELEC energy = 1.088773280805E+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, 452.578 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 (1.088773280805e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 31.865525 seconds -------------------------------------------------------------------------------- Total elapsed time: 133.699901 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, 108.8773280805] 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 108.8773280805 Running tests for point-pmf section BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/build/reproducible-path/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: 61.058 MB total, 61.058 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: 61.058 MB total, 61.065 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: 61.058 MB total, 61.065 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, 61.065 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: 1.20481 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/build/reproducible-path/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: 61.058 MB total, 61.058 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: 61.058 MB total, 61.065 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: 61.058 MB total, 61.065 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, 61.065 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: 1.203126 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/build/reproducible-path/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: 61.058 MB total, 61.058 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: 61.058 MB total, 61.065 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: 61.058 MB total, 61.065 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, 61.065 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: 1.07812 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/build/reproducible-path/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: 61.058 MB total, 61.058 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: 61.058 MB total, 61.065 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: 61.059 MB total, 61.066 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, 61.066 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: 1.036189 seconds -------------------------------------------------------------------------------- Total elapsed time: 4.522245 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/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/build/reproducible-path/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: 61.246 MB total, 61.246 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: 61.246 MB total, 61.315 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: 61.243 MB total, 61.315 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: 61.243 MB total, 61.315 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) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+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, 61.315 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 (-3.624863488075e+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: 1.679723 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, -36.24863488075, -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 -36.24863488075 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /build/reproducible-path/apbs-3.4.1/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/build/reproducible-path/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: 61.246 MB total, 61.246 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: 61.246 MB total, 61.315 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: 61.243 MB total, 61.315 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: 61.243 MB total, 61.315 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, 61.315 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: 2.237994 seconds -------------------------------------------------------------------------------- Total elapsed time: 3.917717 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/reproducible-path/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-312-i386-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/reproducible-path/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/reproducible-path/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/libapbs3t64/usr/lib/i386-linux-gnu/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 116172 new size 116627 dwz: debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 75333 new size 77556 dwz: debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libmc.so.1.9.3: DWARF compression not beneficial - old size 268033 new size 275565 dwz: debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libgamer.so.1.9.3: DWARF compression not beneficial - old size 706339 new size 709871 dwz: debian/apbs/usr/bin/apbs: DWARF compression not beneficial - old size 25872 new size 26007 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-312-i386-linux-gnu.so: DWARF compression not beneficial - old size 6137795 new size 6150122 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux.so.2.usr-is-merged dpkg-shlibdeps: warning: symbol exp used by debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cosh used by debian/libfetk1.9t64/usr/lib/i386-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/i386-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9t64/usr/lib/i386-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/i386-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sincos used by debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol tan used by debian/libfetk1.9t64/usr/lib/i386-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/i386-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan2 used by debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sinh used by debian/libfetk1.9t64/usr/lib/i386-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 cosh used by debian/libfetk1.9t64/usr/lib/i386-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/i386-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol daxpy_ used by debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol dcopy_ used by debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol saxpy_ used by debian/libfetk1.9t64/usr/lib/i386-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/i386-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol do_fio used by debian/libfetk1.9t64/usr/lib/i386-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol s_wsfe used by debian/libfetk1.9t64/usr/lib/i386-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/i386-linux-gnu/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow_di used by debian/libfetk1.9t64/usr/lib/i386-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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb were not linked against libblas.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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb were not linked against libmpich.so.12 (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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb 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/mergedx debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb were not linked against libamd.so.3 (they use none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake 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 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 dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libapbs3t64-dbgsym' in '../libapbs3t64-dbgsym_3.4.1-6_i386.deb'. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-6_i386.deb'. dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-6_all.deb'. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-6_i386.deb'. dpkg-deb: building package 'libfetk1.9t64' in '../libfetk1.9t64_3.4.1-6_i386.deb'. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-6_i386.deb'. dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-6_all.deb'. dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.4.1-6_i386.deb'. dpkg-deb: building package 'libapbs3t64' in '../libapbs3t64_3.4.1-6_i386.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.4.1-6_i386.deb'. dpkg-deb: building package 'libfetk1.9t64-dbgsym' in '../libfetk1.9t64-dbgsym_3.4.1-6_i386.deb'. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-6_i386.deb'. dpkg-genbuildinfo --build=binary -O../apbs_3.4.1-6_i386.buildinfo dpkg-genchanges --build=binary -O../apbs_3.4.1-6_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/58309 and its subdirectories I: Current time: Wed Dec 11 05:44:49 -12 2024 I: pbuilder-time-stamp: 1733939089 Wed Dec 11 17:44:51 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom08-i386.debian.net. Wed Dec 11 17:44:51 UTC 2024 I: Preparing to do remote build '2' on infom08-i386.debian.net. Wed Dec 11 18:14:52 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. Wed Dec 11 18:14:53 UTC 2024 I: apbs_3.4.1-6_i386.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: all i386 Version: 3.4.1-6 Distribution: unstable 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: 7ebb61da9adb2e6f267edd35bfe941f5db24f868 1489396 apbs-data_3.4.1-6_all.deb 5de327d93bb3c6cd4280bca604613b339c5a77f4 101320 apbs-dbgsym_3.4.1-6_i386.deb 2aa761f4ea078b424484547f32760339ef5f9ae7 5853372 apbs-doc_3.4.1-6_all.deb 99650bca7bf1897930dcb4eb317c26c162e3f90f 12696 apbs_3.4.1-6_i386.buildinfo 61e6c59be767fb56c673f430594e8dfd438cedc2 77872 apbs_3.4.1-6_i386.deb a499f47a9b4636fd5c1e636851ee5ad5eaa12fad 103260 libapbs-dev_3.4.1-6_i386.deb cd2a572d6816b371e74667aa65ae3adf169560cf 492008 libapbs3t64-dbgsym_3.4.1-6_i386.deb 870db6ef20c3376d2dc7b071feab002ffac46b53 258604 libapbs3t64_3.4.1-6_i386.deb cdfcd3ae04007ae92c3fe854833e7ff4e1d4fbcc 148772 libfetk-dev_3.4.1-6_i386.deb 2970bbde0d66962d3e9e9ad96eda186b944c67f3 1464500 libfetk1.9t64-dbgsym_3.4.1-6_i386.deb 3d873c6d6143a276af6a7d65a576f6e6c513b733 571032 libfetk1.9t64_3.4.1-6_i386.deb bc2ff8549e23918f90fdd74b58ed33881a70183f 3523144 python3-apbslib-dbgsym_3.4.1-6_i386.deb a6916c7d94338286c5500b387398414dac898e1c 236280 python3-apbslib_3.4.1-6_i386.deb Checksums-Sha256: baebcbd792f6a3d3c552cca777c6cfe28e46aaa370eedd45a35093ef512d5217 1489396 apbs-data_3.4.1-6_all.deb c3fe7f66106843ef51d133453bfd1b6db44865fb02108dd72eadfdf169eff578 101320 apbs-dbgsym_3.4.1-6_i386.deb a92f639d655269250d71d7e67c0368ac0da81eec3a6ddebce2613091873a54cd 5853372 apbs-doc_3.4.1-6_all.deb 4e9862dc01c02385f748e798f5b1b1c97e5a7329b671570cdd7c3563a5c80f1c 12696 apbs_3.4.1-6_i386.buildinfo f07ec0f1eaea3bf38e08ff7ab728c40d4d2479cf15eae5b98d9d31b99d31f1fe 77872 apbs_3.4.1-6_i386.deb 3202d875ebf0c07a8048c4f43f130e727aa49dfe7126920a97aee06dad42897d 103260 libapbs-dev_3.4.1-6_i386.deb 6894e684259970fbab0392456a600bd0cdd6abd55fcb87bfccd3036cee1f4d80 492008 libapbs3t64-dbgsym_3.4.1-6_i386.deb 2df31e296d0ec019ea4421719a6197390dfe77ea2465cc3f1924dd8708897d50 258604 libapbs3t64_3.4.1-6_i386.deb 2f8ac4af39e548a566ee07b599eab9a4a873e74bd388dd63cb6ef155e5ff56f9 148772 libfetk-dev_3.4.1-6_i386.deb 1f469edb1a38527c69eaacf5583afe1fe56c35a51aff6ec890065309e7ef1852 1464500 libfetk1.9t64-dbgsym_3.4.1-6_i386.deb a4802ed496f9089fb8e059e1f05def25eeb5f9f0734089a47f840b33ef7fcea2 571032 libfetk1.9t64_3.4.1-6_i386.deb dcb9311d3655b244c20b74a51649377a3e540d53fff675a9c77bc7a7a662bbcc 3523144 python3-apbslib-dbgsym_3.4.1-6_i386.deb fbed41084e6762919dfa0db656af1d6ac5df756fd0009c4044243ed7d33b2715 236280 python3-apbslib_3.4.1-6_i386.deb Files: 4269190fa800c80e0bffda44b235b2e2 1489396 science optional apbs-data_3.4.1-6_all.deb 903a0465ad5d94e90dd084e513fa1acb 101320 debug optional apbs-dbgsym_3.4.1-6_i386.deb afa421529aeb394ce0bc5dab62bc121f 5853372 science optional apbs-doc_3.4.1-6_all.deb 9db2c1aac8970a3278944648b5b45cef 12696 science optional apbs_3.4.1-6_i386.buildinfo 6c5d310bddf618122c57bd6e2b147d04 77872 science optional apbs_3.4.1-6_i386.deb 917449e10e3c325f37425878a9989f88 103260 libdevel optional libapbs-dev_3.4.1-6_i386.deb ef62bf6394ac6ca3cada8ddf84b235e3 492008 debug optional libapbs3t64-dbgsym_3.4.1-6_i386.deb 71ee53aa57fc559de7ad4082064016af 258604 libs optional libapbs3t64_3.4.1-6_i386.deb fdeeae50a7112c4ea123d854cf309e0d 148772 libdevel optional libfetk-dev_3.4.1-6_i386.deb cf10829f82d7d2012dc0733de5ad594e 1464500 debug optional libfetk1.9t64-dbgsym_3.4.1-6_i386.deb e68e61b009e14ddba1e09656f5055cec 571032 libs optional libfetk1.9t64_3.4.1-6_i386.deb 85bcc891c067493aa9ea86d000db69c4 3523144 debug optional python3-apbslib-dbgsym_3.4.1-6_i386.deb fb3c0190871089cfa7ae5aae76441c3d 236280 python optional python3-apbslib_3.4.1-6_i386.deb Wed Dec 11 18:14:54 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_12-32967.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/apbs_3.4.1-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/apbs_3.4.1-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/apbs_3.4.1-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/b1/apbs_3.4.1-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.AUnBrMP5/b2/apbs_3.4.1-6_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.474s) 0.474s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.164s) 0.164s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 761ms CPU time consumed: 762ms Wed Dec 11 18:14:55 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 11 18:14:55 UTC 2024 I: apbs from trixie built successfully and reproducibly on i386. Wed Dec 11 18:14:57 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Dec 11 18:14:57 UTC 2024 I: Submitting 16K b1/apbs_3.4.1-6_i386.buildinfo.asc Wed Dec 11 18:14:57 UTC 2024 I: Submitting 16K b2/apbs_3.4.1-6_i386.buildinfo.asc Wed Dec 11 18:14:58 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 11 18:14:58 UTC 2024 I: Done submitting .buildinfo files. Wed Dec 11 18:14:58 UTC 2024 I: Removing signed apbs_3.4.1-6_i386.buildinfo.asc files: removed './b1/apbs_3.4.1-6_i386.buildinfo.asc' removed './b2/apbs_3.4.1-6_i386.buildinfo.asc'