sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-10.freexian.com
+==============================================================================+
| apbs 3.4.1-6 (arm64) Fri, 15 Nov 2024 18:54:32 +0000 |
+==============================================================================+
Package: apbs
Version: 3.4.1-6
Source Version: 3.4.1-6
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: binary
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/957781/system.tar.xz to /tmp/tmp.sbuild.cmRdZxkyQS...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
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| Chroot Setup Commands |
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rm -f /etc/resolv.conf
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I: Finished running 'rm -f /etc/resolv.conf'.
Finished processing commands.
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Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/dpkg-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/dpkg_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/dselect-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/dselect_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/libdpkg-dev_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/dpkg-dev_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-9l_c1b39/libdpkg-perl_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/apbs-wQ3Qoi/resolver-LJqmlf' with '<<RESOLVERDIR>>'
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| Update chroot |
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Get:1 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ InRelease
Ign:1 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ InRelease
Get:2 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ Release [606 B]
Get:2 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ Release [606 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:4 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ Release.gpg
Ign:4 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ Release.gpg
Get:5 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ Packages [9246 B]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9951 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4911 kB]
Fetched 15.1 MB in 2s (6475 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
apt bsdextrautils bsdutils dpkg dpkg-dev libapt-pkg6.0t64 libaudit-common
libaudit1 libblkid1 libbrotli1 libcap-ng0 libdpkg-perl libglib2.0-0t64
libmount1 libpcre2-8-0 libseccomp2 libselinux1 libsemanage2 libsmartcols1
libuuid1 libxml2 login mount util-linux
24 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 7198 kB/10.7 MB of archives.
After this operation, 602 kB disk space will be freed.
Get:1 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ dpkg 1.22.12~1.gbp82cafd [1513 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 bsdutils arm64 1:2.40.2-11 [104 kB]
Get:3 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ dpkg-dev 1.22.12~1.gbp82cafd [1337 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.11 [921 kB]
Get:5 file:/build/apbs-wQ3Qoi/resolver-0QHEt5/apt_archive ./ libdpkg-perl 1.22.12~1.gbp82cafd [647 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libblkid1 arm64 2.40.2-11 [162 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libmount1 arm64 2.40.2-11 [190 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libsmartcols1 arm64 2.40.2-11 [135 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 mount arm64 2.40.2-11 [153 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libuuid1 arm64 2.40.2-11 [35.7 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 util-linux arm64 2.40.2-11 [1170 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libpcre2-8-0 arm64 10.44-2 [242 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libselinux1 arm64 3.7-3+b1 [72.1 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libseccomp2 arm64 2.5.5-1+b3 [46.8 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.11 [1287 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libcap-ng0 arm64 0.8.5-3+b1 [17.0 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libaudit1 arm64 1:4.0.2-2 [54.2 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 login arm64 1:4.16.0-2+really2.40.2-11 [80.0 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libsemanage2 arm64 3.7-2+b1 [84.5 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
debconf: delaying package configuration, since apt-utils is not installed
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| Fetch source files |
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Local sources
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/tmp/debusine-fetch-exec-upload-9l_c1b39/apbs_3.4.1-6.dsc exists in /tmp/debusine-fetch-exec-upload-9l_c1b39; copying to chroot
I: NOTICE: Log filtering will replace 'build/apbs-wQ3Qoi/apbs-3.4.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/apbs-wQ3Qoi' with '<<BUILDDIR>>'
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkgconf, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, build-essential, fakeroot, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml
Filtered Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkgconf, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx, swig, zlib1g-dev, build-essential, fakeroot, libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml
dpkg-deb: warning: root directory has unusual owner or group 998:999.
Hint: either pass --root-owner-group, see dpkg-build-api(7) or add an explicit 'Rules-Requires-Root: no' in debian/control.
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Get:1 file:/<<BUILDDIR>>/resolver-0QHEt5/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-0QHEt5/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-0QHEt5/apt_archive ./ Release [606 B]
Get:2 file:/<<BUILDDIR>>/resolver-0QHEt5/apt_archive ./ Release [606 B]
Get:3 file:/<<BUILDDIR>>/resolver-0QHEt5/apt_archive ./ Release.gpg
Ign:3 file:/<<BUILDDIR>>/resolver-0QHEt5/apt_archive ./ Release.gpg
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
adduser autoconf automake autopoint autotools-dev build-essential cmake
cmake-data cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
dwz fakeroot fonts-font-awesome fonts-lato fonts-mathjax g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran-14
gfortran-14-aarch64-linux-gnu ibverbs-providers libamd-comgr2 libamd3
libamdhip64-5 libarchive13t64 libarpack2-dev libarpack2t64 libasan8
libblas-dev libblas3 libbtf2 libc-dev-bin libc6-dev libcamd3 libcbor0.10
libcc1-0 libccolamd3 libcholmod5 libcolamd3 libcrypt-dev libcurl4t64
libcxsparse4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2
libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev
libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64
libexpat1 libexpat1-dev libfabric1 libfakeroot libfido2-1
libfile-stripnondeterminism-perl libgcc-14-dev libgfortran-14-dev
libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-dev
libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1
libisl23 libitm1 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc
libjs-underscore libjson-perl libjsoncpp26 libklu2 liblapack-dev liblapack3
libldl3 libllvm17t64 liblsan0 libltdl-dev libltdl7 libmaloc-dev libmaloc1
libmpc3 libmpfr6 libmunge2 libncursesw6 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnsl2 libnuma-dev libnuma1
libopenmpi-dev libopenmpi3t64 libparu1 libpciaccess0 libpkgconf3 libpmix-dev
libpmix2t64 libproc2-0 libpython3-dev libpython3-stdlib libpython3.12-dev
libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librbio4
librdmacm1t64 librhash1 libspex3 libspqr4 libstdc++-14-dev
libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7
libsuperlu-dev libsuperlu7 libtirpc-common libtirpc-dev libtirpc3t64 libtool
libtsan2 libubsan1 libucx0 libumfpack6 libuv1t64 libx11-6 libx11-data
libxau6 libxcb1 libxdmcp6 libxext6 libxnvctrl0 libz3-4 linux-libc-dev m4
media-types mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common
openssh-client pkgconf pkgconf-bin po-debconf procps pybind11-dev
pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster
python3-autocommand python3-babel python3-build python3-certifi
python3-chardet python3-charset-normalizer python3-defusedxml python3-dev
python3-docutils python3-idna python3-imagesize python3-inflect
python3-installer python3-jaraco.context python3-jaraco.functools
python3-jaraco.text python3-jinja2 python3-markupsafe python3-minimal
python3-more-itertools python3-packaging python3-pkg-resources
python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests
python3-roman python3-setuptools python3-snowballstemmer python3-sphinx
python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-toml
python3-typeguard python3-typing-extensions python3-urllib3 python3-wheel
python3-yaml python3-zipp python3.12 python3.12-dev python3.12-minimal
rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common swig xml-core
zlib1g-dev
Suggested packages:
liblocale-gettext-perl cron quota autoconf-archive gnu-standards
autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build cpp-doc
gcc-14-locales cpp-14-doc dh-make flit gcc-14-doc gcc-multilib manpages-dev
flex bison gdb gcc-doc gdb-aarch64-linux-gnu gfortran-14-doc libcoarrays-dev
lrzip liblapack-doc libc-devtools glibc-doc libjs-jquery-ui-docs
fonts-mathjax-extras fonts-stix libjs-mathjax-doc libtool-doc openmpi-doc
pciutils libstdc++-14-doc libsuperlu-doc gcj-jdk m4-doc opencl-icd gfortran
| fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass
libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv
python3-pip python-build-doc python-charset-normalizer-doc docutils-doc
fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-installer-doc
python-jinja2-doc python-pygments-doc ttf-bitstream-vera
python3-cryptography python3-openssl python3-socks python-requests-doc
python-setuptools-doc python3-stemmer dvipng dvisvgm fonts-freefont-otf
imagemagick-6.q16 latexmk sphinx-doc tex-gyre texlive-fonts-extra
texlive-fonts-recommended texlive-latex-extra texlive-plain-generic
python3-brotli python3.12-venv python3.12-doc binfmt-support sgml-base-doc
swig-doc swig-examples
Recommended packages:
manpages manpages-dev libarchive-cpio-perl javascript-common libjson-xs-perl
libgpm2 libcoarrays-openmpi-dev libgraphblas-dev xauth libmail-sendmail-perl
psmisc linux-sysctl-defaults libeigen3-dev libpaper-utils python3-pil
python3-numpy
The following NEW packages will be installed:
adduser autoconf automake autopoint autotools-dev build-essential cmake
cmake-data cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
dwz fakeroot fonts-font-awesome fonts-lato fonts-mathjax g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran-14
gfortran-14-aarch64-linux-gnu ibverbs-providers libamd-comgr2 libamd3
libamdhip64-5 libarchive13t64 libarpack2-dev libarpack2t64 libasan8
libblas-dev libblas3 libbtf2 libc-dev-bin libc6-dev libcamd3 libcbor0.10
libcc1-0 libccolamd3 libcholmod5 libcolamd3 libcrypt-dev libcurl4t64
libcxsparse4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2
libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev
libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64
libexpat1 libexpat1-dev libfabric1 libfakeroot libfido2-1
libfile-stripnondeterminism-perl libgcc-14-dev libgfortran-14-dev
libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-dev
libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1
libisl23 libitm1 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc
libjs-underscore libjson-perl libjsoncpp26 libklu2 liblapack-dev liblapack3
libldl3 libllvm17t64 liblsan0 libltdl-dev libltdl7 libmaloc-dev libmaloc1
libmpc3 libmpfr6 libmunge2 libncursesw6 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnsl2 libnuma-dev libnuma1
libopenmpi-dev libopenmpi3t64 libparu1 libpciaccess0 libpkgconf3 libpmix-dev
libpmix2t64 libproc2-0 libpython3-dev libpython3-stdlib libpython3.12-dev
libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librbio4
librdmacm1t64 librhash1 libspex3 libspqr4 libstdc++-14-dev
libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7
libsuperlu-dev libsuperlu7 libtirpc-common libtirpc-dev libtirpc3t64 libtool
libtsan2 libubsan1 libucx0 libumfpack6 libuv1t64 libx11-6 libx11-data
libxau6 libxcb1 libxdmcp6 libxext6 libxnvctrl0 libz3-4 linux-libc-dev m4
media-types mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common
openssh-client pkgconf pkgconf-bin po-debconf procps pybind11-dev
pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster
python3-autocommand python3-babel python3-build python3-certifi
python3-chardet python3-charset-normalizer python3-defusedxml python3-dev
python3-docutils python3-idna python3-imagesize python3-inflect
python3-installer python3-jaraco.context python3-jaraco.functools
python3-jaraco.text python3-jinja2 python3-markupsafe python3-minimal
python3-more-itertools python3-packaging python3-pkg-resources
python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests
python3-roman python3-setuptools python3-snowballstemmer python3-sphinx
python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-toml
python3-typeguard python3-typing-extensions python3-urllib3 python3-wheel
python3-yaml python3-zipp python3.12 python3.12-dev python3.12-minimal
rpcsvc-proto sbuild-build-depends-main-dummy sgml-base sphinx-common
sphinx-rtd-theme-common swig xml-core zlib1g-dev
0 upgraded, 224 newly installed, 0 to remove and 0 not upgraded.
Need to get 202 MB of archives.
After this operation, 872 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1048 B]
Get:2 http://deb.debian.org/debian sid/main arm64 fonts-lato all 2.015-1 [2780 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2+b1 [125 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-3 [671 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B]
Get:15 http://deb.debian.org/debian sid/main arm64 python3 arm64 3.12.7-1 [27.8 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 adduser all 3.137 [140 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.7-1 [2454 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b2 [680 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b3 [50.5 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8 [9166 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-8 [1284 B]
Get:39 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:40 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:41 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-8 [42.2 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:50 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:52 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:53 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB]
Get:55 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:57 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:58 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:59 http://deb.debian.org/debian sid/main arm64 cmake-data all 3.31.0-1 [2265 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libjsoncpp26 arm64 1.9.6-2 [73.1 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 librhash1 arm64 1.4.5-1 [129 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 cmake arm64 3.31.0-1 [9874 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
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Get:71 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:81 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 75.2.0-1 [731 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20241024 [109 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 xml-core all 0.19 [20.1 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
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Get:93 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB]
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Get:99 http://deb.debian.org/debian sid/main arm64 libibverbs1 arm64 52.0-2+b1 [58.8 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 ibverbs-providers arm64 52.0-2+b1 [321 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 libllvm17t64 arm64 1:17.0.6-18 [21.3 MB]
Get:103 http://deb.debian.org/debian sid/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB]
Get:104 http://deb.debian.org/debian sid/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-2 [23.7 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libamd3 arm64 1:7.8.3+dfsg-2 [38.1 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libdrm-common all 2.4.123-1 [8084 B]
Get:107 http://deb.debian.org/debian sid/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libhsakmt1 arm64 6.1.2+ds-1 [56.9 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libhsa-runtime64-1 arm64 6.1.2-2 [300 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libarpack2t64 arm64 3.9.1-1.1+b2 [81.3 kB]
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Get:117 http://deb.debian.org/debian sid/main arm64 liblapack-dev arm64 3.12.0-3+b1 [3709 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libarpack2-dev arm64 3.9.1-1.1+b2 [98.3 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 libbtf2 arm64 1:7.8.3+dfsg-2 [24.3 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 libcamd3 arm64 1:7.8.3+dfsg-2 [35.2 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 libccolamd3 arm64 1:7.8.3+dfsg-2 [37.7 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-2 [31.5 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 libcholmod5 arm64 1:7.8.3+dfsg-2 [536 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libcxsparse4 arm64 1:7.8.3+dfsg-2 [75.9 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 librdmacm1t64 arm64 52.0-2+b1 [67.4 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libltdl7 arm64 2.4.7-8 [392 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 libltdl-dev arm64 2.4.7-8 [165 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 libpciaccess0 arm64 0.17-3+b2 [51.2 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libxnvctrl0 arm64 535.171.04-1+b1 [14.1 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libibumad3 arm64 52.0-2+b1 [27.1 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 libibmad5 arm64 52.0-2+b1 [41.5 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 libibverbs-dev arm64 52.0-2+b1 [625 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libklu2 arm64 1:7.8.3+dfsg-2 [82.1 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libldl3 arm64 1:7.8.3+dfsg-2 [24.2 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libmaloc1 arm64 1.5-2+b1 [77.8 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libmaloc-dev arm64 1.5-2+b1 [1276 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libmunge2 arm64 0.5.15-4+b1 [19.4 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libpmix2t64 arm64 5.0.3-2+b1 [588 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libopenmpi3t64 arm64 5.0.5-3 [1806 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 openmpi-common all 5.0.5-3 [95.0 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 libpmix-dev arm64 5.0.3-2+b1 [3930 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 openmpi-bin arm64 5.0.5-3 [159 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 libopenmpi-dev arm64 5.0.5-3 [1088 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 libumfpack6 arm64 1:7.8.3+dfsg-2 [228 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 libparu1 arm64 1:7.8.3+dfsg-2 [60.9 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 libpython3-dev arm64 3.12.7-1 [9980 B]
Get:179 http://deb.debian.org/debian sid/main arm64 librbio4 arm64 1:7.8.3+dfsg-2 [38.2 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 libspex3 arm64 1:7.8.3+dfsg-2 [55.4 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 libspqr4 arm64 1:7.8.3+dfsg-2 [127 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 libsuitesparse-mongoose3 arm64 1:7.8.3+dfsg-2 [44.1 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 libsuitesparse-dev arm64 1:7.8.3+dfsg-2 [1306 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 libsuperlu7 arm64 7.0.0+dfsg1-2 [144 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 libsuperlu-dev arm64 7.0.0+dfsg1-2 [21.9 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3+b1 [192 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 mpi-default-dev arm64 1.17 [3148 B]
Get:188 http://deb.debian.org/debian sid/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 pybind11-dev all 2.13.6-1 [204 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-packaging all 24.1-1 [45.8 kB]
Get:192 http://deb.debian.org/debian sid/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB]
Get:193 http://deb.debian.org/debian sid/main arm64 python3-toml all 0.10.2-1 [16.2 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 python3-wheel all 0.45.0-1 [56.7 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 python3-build all 1.2.2-1 [36.0 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB]
Get:197 http://deb.debian.org/debian sid/main arm64 pybuild-plugin-pyproject all 6.20241024 [11.4 kB]
Get:198 http://deb.debian.org/debian sid/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB]
Get:199 http://deb.debian.org/debian sid/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 python3-babel all 2.16.0-1 [114 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get:202 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:203 http://deb.debian.org/debian sid/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB]
Get:204 http://deb.debian.org/debian sid/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB]
Get:205 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB]
Get:206 http://deb.debian.org/debian sid/main arm64 python3-dev arm64 3.12.7-1 [26.1 kB]
Get:207 http://deb.debian.org/debian sid/main arm64 python3-roman all 4.2-1 [10.4 kB]
Get:208 http://deb.debian.org/debian sid/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get:209 http://deb.debian.org/debian sid/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get:210 http://deb.debian.org/debian sid/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get:211 http://deb.debian.org/debian sid/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB]
Get:212 http://deb.debian.org/debian sid/main arm64 python3-jinja2 all 3.1.3-1 [119 kB]
Get:213 http://deb.debian.org/debian sid/main arm64 python3-pybind11 all 2.13.6-1 [215 kB]
Get:214 http://deb.debian.org/debian sid/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get:215 http://deb.debian.org/debian sid/main arm64 python3-urllib3 all 2.0.7-2 [111 kB]
Get:216 http://deb.debian.org/debian sid/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get:217 http://deb.debian.org/debian sid/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get:218 http://deb.debian.org/debian sid/main arm64 sphinx-common all 7.4.7-4 [731 kB]
Get:219 http://deb.debian.org/debian sid/main arm64 python3-sphinx all 7.4.7-4 [588 kB]
Get:220 http://deb.debian.org/debian sid/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB]
Get:221 http://deb.debian.org/debian sid/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get:222 http://deb.debian.org/debian sid/main arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [29.5 kB]
Get:223 http://deb.debian.org/debian sid/main arm64 python3-yaml arm64 6.0.2-1+b1 [148 kB]
Get:224 http://deb.debian.org/debian sid/main arm64 swig arm64 4.2.1-1+b1 [1355 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ...
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Unpacking libexpat1:arm64 (2.6.4-1) ...
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Unpacking python3.12-minimal (3.12.7-3) ...
Setting up libpython3.12-minimal:arm64 (3.12.7-3) ...
Setting up libexpat1:arm64 (2.6.4-1) ...
Setting up python3.12-minimal (3.12.7-3) ...
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Unpacking python3-minimal (3.12.7-1) ...
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Unpacking libncursesw6:arm64 (6.5-2+b1) ...
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Unpacking libtirpc-common (1.3.4+ds-1.3) ...
Selecting previously unselected package libtirpc3t64:arm64.
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ...
Selecting previously unselected package libnsl2:arm64.
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Unpacking libnsl2:arm64 (1.3.0-3+b3) ...
Selecting previously unselected package libpython3.12-stdlib:arm64.
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Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ...
Selecting previously unselected package python3.12.
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Unpacking python3.12 (3.12.7-3) ...
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Unpacking libpython3-stdlib:arm64 (3.12.7-1) ...
Setting up python3-minimal (3.12.7-1) ...
Selecting previously unselected package python3.
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Unpacking python3 (3.12.7-1) ...
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Unpacking sgml-base (1.31) ...
Selecting previously unselected package adduser.
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Unpacking adduser (3.137) ...
Setting up adduser (3.137) ...
Selecting previously unselected package libproc2-0:arm64.
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Unpacking libproc2-0:arm64 (2:4.0.4-6) ...
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Unpacking procps (2:4.0.4-6) ...
Selecting previously unselected package libedit2:arm64.
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Unpacking libedit2:arm64 (3.1-20240808-1) ...
Selecting previously unselected package libcbor0.10:arm64.
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Unpacking libcbor0.10:arm64 (0.10.2-2) ...
Selecting previously unselected package libfido2-1:arm64.
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Unpacking libfido2-1:arm64 (1.15.0-1+b1) ...
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Unpacking openssh-client (1:9.9p1-3) ...
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Unpacking m4 (1.4.19-4) ...
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Unpacking autoconf (2.72-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking automake (1:1.16.5-1.3) ...
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Unpacking libc-dev-bin (2.40-3) ...
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Unpacking linux-libc-dev (6.11.7-1) ...
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Unpacking libcrypt-dev:arm64 (1:4.4.36-5) ...
Selecting previously unselected package rpcsvc-proto.
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Unpacking rpcsvc-proto (1.4.3-1+b1) ...
Selecting previously unselected package libc6-dev:arm64.
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Unpacking libc6-dev:arm64 (2.40-3) ...
Selecting previously unselected package libisl23:arm64.
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Unpacking libisl23:arm64 (0.27-1) ...
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Unpacking libmpfr6:arm64 (4.2.1-1+b2) ...
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Unpacking libmpc3:arm64 (1.3.1-1+b3) ...
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Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8) ...
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Unpacking cpp-14 (14.2.0-8) ...
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Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1) ...
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Unpacking cpp (4:14.2.0-1) ...
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Unpacking libitm1:arm64 (14.2.0-8) ...
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Unpacking libtsan2:arm64 (14.2.0-8) ...
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Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8) ...
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Unpacking gcc-14 (14.2.0-8) ...
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Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1) ...
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Setting up python3-zipp (3.21.0-1) ...
Setting up libibverbs-dev:arm64 (52.0-2+b1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up python3-markupsafe (2.1.5-1+b3) ...
Setting up libparu1:arm64 (1:7.8.3+dfsg-2) ...
Setting up python3-wheel (0.45.0-1) ...
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Setting up python3-pyproject-hooks (1.2.0-1) ...
Setting up python3-certifi (2024.8.30+dfsg-1) ...
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Setting up python3-toml (0.10.2-1) ...
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Setting up python3-urllib3 (2.0.7-2) ...
Setting up libhsa-runtime64-1:arm64 (6.1.2-2) ...
Setting up gfortran-14-aarch64-linux-gnu (14.2.0-8) ...
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Setting up libpython3-dev:arm64 (3.12.7-1) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up libsuitesparse-dev:arm64 (1:7.8.3+dfsg-2) ...
Setting up libtool (2.4.7-8) ...
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Setting up pybind11-dev (2.13.6-1) ...
Setting up gcc (4:14.2.0-1) ...
Setting up dh-autoreconf (20) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up libamdhip64-5 (5.7.1-5) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-dev (3.12.7-1) ...
Setting up g++ (4:14.2.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.12) ...
Setting up python3-pybind11 (2.13.6-1) ...
Setting up python3-pkg-resources (75.2.0-1) ...
Setting up libucx0:arm64 (1.17.0+ds-3) ...
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Setting up python3-babel (2.16.0-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up debhelper (13.20) ...
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 libopenmpi3t64:arm64 (5.0.5-3) ...
Setting up openmpi-bin (5.0.5-3) ...
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Setting up dh-python (6.20241024) ...
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Setting up mpi-default-dev (1.17) ...
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Setting up docutils-common (0.21.2+dfsg-2) ...
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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 (3.0.1+dfsg-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.12~1.gbp82cafd g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.7-1
Package versions: adduser_3.137 appstream_1.0.3-1+b1 apt_2.9.11 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.5 bash_5.2.32-1+b2 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 bsdextrautils_2.40.2-11 bsdutils_1:2.40.2-11 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 cmake_3.31.0-1 cmake-data_3.31.0-1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-aarch64-linux-gnu_14.2.0-8 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9+b1 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20+b1 dh-autoreconf_20 dh-python_6.20241024 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1+b1 diffutils_1:3.10-1+b1 docutils-common_0.21.2+dfsg-2 dpkg_1.22.12~1.gbp82cafd dpkg-dev_1.22.12~1.gbp82cafd dwz_0.15-1+b1 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1 fonts-lato_2.015-1 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libxdmcp6_1:1.1.2-3+b2 libxext6_2:1.3.4-1+b2 libxml-libxml-perl_2.0207+dfsg+really+2.0134-5+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxmlb2_0.3.21-1 libxnvctrl0_535.171.04-1+b1 libxs-parse-keyword-perl_0.46-1+b1 libxxhash0_0.8.2-2+b2 libyaml-0-2_0.2.5-1+b2 libyaml-libyaml-perl_0.902.0+ds-2+b1 libz3-4_4.13.3-1 libzstd1_1.5.6+dfsg-1+b1 lintian_2.120.0 linux-libc-dev_6.11.7-1 login_1:4.16.0-2+really2.40.2-11 login.defs_1:4.16.0-4 logsave_1.47.1-1+b1 lzop_1.04-2+b1 m4_1.4.19-4 make_4.3-4.1+b1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mount_2.40.2-11 mpi-default-dev_1.17 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1+b2 openmpi-bin_5.0.5-3 openmpi-common_5.0.5-3 openssh-client_1:9.9p1-3 openssl_3.3.2-2 openssl-provider-legacy_3.3.2-2 passwd_1:4.16.0-4 patch_2.7.6-7+b1 patchutils_0.4.2-1+b1 perl_5.40.0-7 perl-base_5.40.0-7 perl-modules-5.40_5.40.0-7 perl-openssl-defaults_7+b2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 plzip_1.11-2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 pybind11-dev_2.13.6-1 pybuild-plugin-pyproject_6.20241024 python-babel-localedata_2.16.0-1 python3_3.12.7-1 python3-alabaster_0.7.16-0.1 python3-autocommand_2.2.2-3 python3-babel_2.16.0-1 python3-build_1.2.2-1 python3-certifi_2024.8.30+dfsg-1 python3-chardet_5.2.0+dfsg-1 python3-charset-normalizer_3.4.0-1+b1 python3-defusedxml_0.7.1-2 python3-dev_3.12.7-1 python3-docutils_0.21.2+dfsg-2 python3-idna_3.8-2 python3-imagesize_1.4.1-1 python3-inflect_7.3.1-2 python3-installer_0.7.0+dfsg1-3 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jaraco.text_4.0.0-1 python3-jinja2_3.1.3-1 python3-markupsafe_2.1.5-1+b3 python3-minimal_3.12.7-1 python3-more-itertools_10.5.0-1 python3-packaging_24.1-1 python3-pkg-resources_75.2.0-1 python3-pybind11_2.13.6-1 python3-pygments_2.18.0+dfsg-1 python3-pyproject-hooks_1.2.0-1 python3-requests_2.32.3+dfsg-1 python3-roman_4.2-1 python3-setuptools_75.2.0-1 python3-snowballstemmer_2.2.0-4 python3-sphinx_7.4.7-4 python3-sphinx-rtd-theme_3.0.1+dfsg-1 python3-sphinxcontrib.jquery_4.1-5 python3-toml_0.10.2-1 python3-typeguard_4.4.1-1 python3-typing-extensions_4.12.2-2 python3-urllib3_2.0.7-2 python3-wheel_0.45.0-1 python3-yaml_6.0.2-1+b1 python3-zipp_3.21.0-1 python3.12_3.12.7-3 python3.12-dev_3.12.7-3 python3.12-minimal_3.12.7-3 readline-common_8.2-5 rpcsvc-proto_1.4.3-1+b1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2+b1 sensible-utils_0.0.24 sgml-base_1.31 shared-mime-info_2.4-5+b1 sphinx-common_7.4.7-4 sphinx-rtd-theme-common_3.0.1+dfsg-1 swig_4.2.1-1+b1 sysvinit-utils_3.11-1 t1utils_1.41-4+b1 tar_1.35+dfsg-3+b1 tzdata_2024b-3 ucf_3.0043+nmu1 unzip_6.0-28+b1 util-linux_2.40.2-11 xml-core_0.19 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: apbs
Binary: apbs, python3-apbslib, libapbs-dev, libapbs3t64, apbs-data, apbs-doc, libfetk-dev, libfetk1.9t64
Architecture: any all
Version: 3.4.1-6
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Michael Banck <mbanck@debian.org>
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
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gpgv: Signature made Thu Oct 31 13:25:39 2024 UTC
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 /<<PKGBUILDDIR>>
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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -b -rfakeroot
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 <dparsons@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
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 binary
dh binary --with python3,sphinxdoc --buildsystem=cmake
dh_update_autotools_config -O--buildsystem=cmake
dh_autoreconf -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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=/<<PKGBUILDDIR>>/debian/external_deps/fetk \
-DRPC_CFLAGS=-I/usr/include/tirpc \
-DBUILD_MALOC=Off
cd obj-aarch64-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/aarch64-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=/<<PKGBUILDDIR>>/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Install prefix: /usr
--
-- APBS Static build: Off
-- Building shared libs: ON
-- Find-library suffixes: .so;.so;.a
--
-- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2
CMake Deprecation Warning at debian/external_deps/fetk/CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- FETK set_basic_vars_and_paths: FALSE, FETK
-- Setting project paths
-- Install prefix: /usr
-- FETK static build: OFF
-- Building shared libs: ON
-- Find-library suffixes: .so;.so;.so;.a
CMake Deprecation Warning at debian/external_deps/fetk/punc/CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
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/aarch64-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/aarch64-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: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/punccf.h
-- Type: SOURCES
-- Items: punc_base.c
-- Type: EXTERNAL_HEADERS
-- Items: punc/punc.h;punc/punc_base.h
-- Type: INTERNAL_HEADERS
-- Items: punc_base_p.h
CMake Deprecation Warning at debian/external_deps/fetk/gamer/CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
Configuring build for GAMER
-- FETK set_basic_vars_and_paths: FALSE, gamer
-- Type: INTERNAL_HEADERS
-- Items: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src/gamercf.h
-- Type: SOURCES
-- Items: gamer_base.c
-- Type: EXTERNAL_HEADERS
-- Items: gamer/gamer.h;gamer/gamer_base.h
-- Type: INTERNAL_HEADERS
-- Items: gamer_base_p.h
-- Type: SOURCES
-- Items: triangle.c
-- Type: EXTERNAL_HEADERS
-- Items: gamer/triangle.h
-- Type: INTERNAL_HEADERS
-- Items: triangle_p.h
-- Type: SOURCES
-- Items: predicates.cpp;tetgen.cpp
-- Type: EXTERNAL_HEADERS
-- Items: gamer/tetgen.h
-- Type: INTERNAL_HEADERS
-- Items: tetgen_p.h
-- Type: SOURCES
-- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C
-- Type: EXTERNAL_HEADERS
-- Items: gamer/biom.h
-- Type: INTERNAL_HEADERS
-- Items: MarchingCube.h;PDB2Volume.h
CMake Deprecation Warning at debian/external_deps/fetk/mc/CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
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/aarch64-linux-gnu/libblas.so;-lm;-ldl
-- checking for function cheev_
-- result: TRUE
-- Found LAPACK: /usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl
-- @@@@ finding amd
-- Found AMD headers in: /usr/include/suitesparse
-- Found AMD library: /usr/lib/aarch64-linux-gnu/libamd.so
-- @@@@ finding camd
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so
-- @@@@ finding colamd
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so
-- @@@@ finding ccolamd
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so
-- @@@@ finding cholmod
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so
-- @@@@ finding parseqr
-- Found SUITESPARSEQR headers in: /usr/include/suitesparse
-- Found SUITESPARSEQR library: /usr/lib/aarch64-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/aarch64-linux-gnu/libsuitesparseconfig.so
-- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a
-- Adding librt: /usr/lib/aarch64-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: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/mccf.h
-- Type: SOURCES
-- Items: mc_base.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/mc_base.h;mc/mc.h
-- Type: INTERNAL_HEADERS
-- Items: mc_base_p.h
-- Type: SOURCES
-- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h
-- Type: INTERNAL_HEADERS
-- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h
-- Type: SOURCES
-- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/whb.h
-- Type: INTERNAL_HEADERS
-- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h
-- Type: SOURCES
-- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h
-- Type: INTERNAL_HEADERS
-- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h
-- Type: SOURCES
-- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/gem.h;mc/vel.h;mc/ves.h
-- Type: INTERNAL_HEADERS
-- Items: gem_p.h;vel_p.h;ves_p.h
-- Type: SOURCES
-- Items: pde.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/pde.h
-- Type: INTERNAL_HEADERS
-- Items: pde_p.h
-- Type: SOURCES
-- Items: am.c;lsolv.c;nsolv.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/am.h;mc/nam.h
-- Type: INTERNAL_HEADERS
-- Items: am_p.h;nam_p.h
-- Type: SOURCES
-- Items: dyn.c;svio.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/dyn.h
-- Type: INTERNAL_HEADERS
-- Items: dyn_p.h;svio_p.h
-- Type: SOURCES
-- Items: mcsh.c
-- Type: EXTERNAL_HEADERS
-- Items: mc/mcsh.h
-- Type: INTERNAL_HEADERS
-- Items: mcsh_p.h
-- #############################################################
-- ** PROJECT NAME: APBS
-- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver
-- ** PROJECT URL: http://www.poissonboltzmann.org/
-- ** VERSION_DATA: 3.4.1
-- ** CURRENT_TIME: 2024-10-31T13:24:17
-- ** CURRENT_YEAR: 2024
-- Setting project paths
-- Setting lookup paths for headers and libraries
-- Computing machine epsilon values
-- Floating point epsilon is 2.220446e-16
-- Double precision epsilon is 2.220446e-16
-- Looking for time
-- Looking for time - found
-- Looking for rand
-- Looking for rand - found
-- Looking for srand
-- Looking for srand - found
-- Found Intl: built in to C library
-- Performing Test Iconv_IS_BUILT_IN
-- Performing Test Iconv_IS_BUILT_IN - Success
-- Found Iconv: built in to C library
-- @@@@ finding blas
-- @@@@ finding lapack
-- %%%%% list of libraries:
-- Testing libraries: TRUE
-- CMAKE_REQUIRED_LIBRARIES: /usr/lib/aarch64-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/aarch64-linux-gnu/libamd.so
-- @@@@ finding camd
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib/aarch64-linux-gnu/libcamd.so
-- @@@@ finding colamd
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib/aarch64-linux-gnu/libcolamd.so
-- @@@@ finding ccolamd
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib/aarch64-linux-gnu/libccolamd.so
-- @@@@ finding cholmod
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib/aarch64-linux-gnu/libcholmod.so
-- @@@@ finding parseqr
-- Found SUITESPARSEQR headers in: /usr/include/suitesparse
-- Found SUITESPARSEQR library: /usr/lib/aarch64-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/aarch64-linux-gnu/libsuitesparseconfig.so
-- Found LIBRT library: /usr/lib/aarch64-linux-gnu/librt.a
-- Adding librt: /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so
-- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse
-- SUITESPARSE_LIBRARIES: /usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a
-- Checking for MPI
-- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- MPI support enabled
-- Inline functions enabled
-- Verbose debugging mode enabled
-- Checking for OpenMP
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- OpenMP support enabled
-- Building of iAPBS interface disabled
CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- 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/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp
-- Added apbs_generic
-- Adding apbs_pmgc
-- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c
-- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h
-- With internal header files
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp
-- Added apbs_pmgc
-- Adding apbs_mg
-- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c
-- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h
-- With internal header files
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc
-- Added apbs_mg
-- Adding apbs_fem
-- With source files vcsm.c;vfetk.c;vpee.c
-- With external header files vcsm.h;vfetk.h;vpee.h
-- With internal header files
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic
-- Added apbs_fem
-- Adding apbs_routines
-- With source files routines.c
-- With external header files
-- With internal header files
-- With library dependencies mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem
-- Added apbs_routines
-- External Headers:
--
-- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp
-- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines
--
-- -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 "3.12.7", 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/aarch64-linux-gnu/libpython3.12.so
-- ***** Python3 library dir is: /usr/lib/aarch64-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 "3.12.7", minimum required is "3.6")
-- Found PythonLibs: /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so;/usr/lib/aarch64-linux-gnu/libspqr.so;/usr/lib/aarch64-linux-gnu/libcholmod.so;/usr/lib/aarch64-linux-gnu/libccolamd.so;/usr/lib/aarch64-linux-gnu/libcamd.so;/usr/lib/aarch64-linux-gnu/libcolamd.so;/usr/lib/aarch64-linux-gnu/libamd.so;/usr/lib/aarch64-linux-gnu/libblas.so;-lm;-ldl;/usr/lib/aarch64-linux-gnu/libblas.so;/usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so;/usr/lib/aarch64-linux-gnu/librt.a;/usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so;-fopenmp
-- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines
-- ******* TESTING ADDED *****************
-- Found Python3: /usr/bin/python3 (found suitable exact version "3.12.7") found components: Interpreter
-- ******* FOUND TEST CASE born, born
-- TEST born_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t born
-- ******* FOUND TEST CASE actin, actin-dimer-auto
-- TEST actin-dimer-auto_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t actin-dimer-auto
-- ******* FOUND TEST CASE alkanes, alkanes
-- TEST alkanes_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t alkanes
-- ******* FOUND TEST CASE FKBP, FKBP
-- TEST FKBP_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t FKBP
-- ******* FOUND TEST CASE hca, hca-bind
-- TEST hca-bind_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t hca-bind
-- ******* FOUND TEST CASE ionize, ionize
-- TEST ionize_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t ionize
-- ******* FOUND TEST CASE ion, ion-pmf
-- TEST ion-pmf_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t ion-pmf
-- ******* FOUND TEST CASE pka, pka-lig
-- TEST pka-lig_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t pka-lig
-- ******* FOUND TEST CASE point, point-pmf
-- TEST point-pmf_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t point-pmf
-- ******* FOUND TEST CASE solv, solv
-- TEST solv_test WORKING_DIRECTORY /<<PKGBUILDDIR>>/tests COMMAND /usr/bin/python3 /<<PKGBUILDDIR>>/tests/apbs_tester.py -e apbs -t solv
-- Configuring done (13.7s)
-- Generating done (0.2s)
CMake Warning:
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CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
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[ 6%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o
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[ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o
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[ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/derfc_.c
[ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/erf_.c
[ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/erfc_.c
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cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/scgne.c
[ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o
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[ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o
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cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/pow_di.c
[ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c
[ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c
[ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/spcgne.c
[ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c
[ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/sppcg.c
[ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c
[ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c
[ 12%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/spcgca.c
[ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_abs.c
[ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c
[ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_cos.c
[ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_div.c
[ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/scbfix.c
[ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/sckchb.c
[ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_exp.c
[ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o
[ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/scgchk.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/sonest.c
[ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_log.c
[ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/msstop.c
[ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/r1mach.c
[ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_sin.c
[ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/sratqr.c
[ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c
[ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c
[ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_abs.c
[ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcg.c
[ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_cos.c
[ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcr.c
[ 17%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_div.c
[ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcrind.c
[ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_exp.c
[ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_log.c
[ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dpcg.c
[ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c
[ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_sin.c
[ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcgne.c
[ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c
[ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c
[ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_abs.c
[ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_acos.c
[ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c
[ 21%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dppcg.c
[ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_asin.c
[ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_atan.c
[ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c
[ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c
[ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c
[ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_cos.c
[ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c
[ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dckchb.c
[ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c
[ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c
[ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/donest.c
[ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_dim.c
[ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_exp.c
[ 25%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/mdstop.c
[ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/d1mach.c
[ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_imag.c
[ 27%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o
[ 27%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/dratqr.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp
[ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_int.c
[ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c
[ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_log.c
[ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode/depsln.c
[ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_mod.c
[ 28%] Linking C shared library libcgcode.so
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/cgcode.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-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_nint.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_nint.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 28%] Built target cgcode
[ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_sign.c
[ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_sin.c
[ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c
[ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c
[ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_tan.c
[ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c
[ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_abs.c
[ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_acos.c
[ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_asin.c
[ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_atan.c
[ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c
[ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c
[ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_cos.c
[ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c
[ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_dim.c
[ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_exp.c
[ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_imag.c
[ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_int.c
[ 33%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c
[ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_log.c
[ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_mod.c
[ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_nint.c
[ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_prod.c
[ 35%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o
[ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_sign.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp
[ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_sin.c
[ 35%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c
[ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c
[ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_tan.c
[ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c
[ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_abs.c
[ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_dim.c
[ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘void tetgenmesh::constrainedfacets()’:
/<<PKGBUILDDIR>>/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 *");
| ^~~~~~~~~
/<<PKGBUILDDIR>>/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 *");
| ^~~~~~~~~
/<<PKGBUILDDIR>>/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 *");
| ^~~~~~~~~
/<<PKGBUILDDIR>>/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 *");
| ^~~~~~~~~
[ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_indx.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘long int tetgenmesh::reconstructmesh()’:
/<<PKGBUILDDIR>>/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");
| ^~~~~
[ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_len.c
[ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_mod.c
[ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_nint.c
[ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/i_sign.c
[ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c
[ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c
[ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_abs.c
[ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_dim.c
[ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c
[ 41%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C
[ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_indx.c
[ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_len.c
[ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_mod.c
[ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_nint.c
[ 42%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/h_sign.c
[ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/l_ge.c
[ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/l_gt.c
[ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/l_le.c
[ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/l_lt.c
[ 44%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C
[ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c
[ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c
[ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/hl_le.c
[ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c
[ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c
[ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c
[ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c
[ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/s_cat.c
[ 46%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C
[ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c
[ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/s_copy.c
[ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/dtime_.c
[ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/etime_.c
[ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/backspac.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function ‘f_back’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/close.c
[ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/dfe.c
[ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/dolio.c
[ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/due.c
[ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/endfile.c
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[ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/err.c
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cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/fmt.c
[ 50%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Volume.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C
[ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c
[ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/ftell_.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function ‘float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)’:
/<<PKGBUILDDIR>>/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);
| ~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/iio.c
[ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/ilnw.c
[ 51%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C
[ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/inquire.c
[ 52%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C
[ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/lread.c
[ 53%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C
[ 53%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C
[ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/lwrite.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘SurfaceMesh* SurfaceMesh_readOFF(char*)’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)’:
/<<PKGBUILDDIR>>/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");
| ^~~~~
/<<PKGBUILDDIR>>/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");
| ^~~~~
/<<PKGBUILDDIR>>/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");
| ^~~~~~~~
/<<PKGBUILDDIR>>/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");
| ^~~~~~~~
/<<PKGBUILDDIR>>/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");
| ^~~~~~~~
[ 53%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/open.c
[ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c
[ 54%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C
[ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/rewind.c
[ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/rsfe.c
[ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/rsli.c
[ 56%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C
[ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/rsne.c
[ 56%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C
[ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/sue.c
[ 56%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/gamer/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/triangle -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/tetgen -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C
[ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/main.c
[ 60%] Linking C shared library libvf2c.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/vf2c.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o 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 CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o CMakeFiles/vf2c.dir/z_abs.c.o CMakeFiles/vf2c.dir/z_cos.c.o CMakeFiles/vf2c.dir/z_div.c.o CMakeFiles/vf2c.dir/z_exp.c.o CMakeFiles/vf2c.dir/z_log.c.o CMakeFiles/vf2c.dir/z_sin.c.o CMakeFiles/vf2c.dir/z_sqrt.c.o CMakeFiles/vf2c.dir/r_abs.c.o CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o CMakeFiles/vf2c.dir/d_int.c.o CMakeFiles/vf2c.dir/d_lg10.c.o CMakeFiles/vf2c.dir/d_log.c.o CMakeFiles/vf2c.dir/d_mod.c.o CMakeFiles/vf2c.dir/d_nint.c.o CMakeFiles/vf2c.dir/d_prod.c.o CMakeFiles/vf2c.dir/d_sign.c.o CMakeFiles/vf2c.dir/d_sin.c.o CMakeFiles/vf2c.dir/d_sinh.c.o CMakeFiles/vf2c.dir/d_sqrt.c.o CMakeFiles/vf2c.dir/d_tan.c.o CMakeFiles/vf2c.dir/d_tanh.c.o CMakeFiles/vf2c.dir/i_abs.c.o CMakeFiles/vf2c.dir/i_dim.c.o CMakeFiles/vf2c.dir/i_dnnt.c.o CMakeFiles/vf2c.dir/i_indx.c.o CMakeFiles/vf2c.dir/i_len.c.o CMakeFiles/vf2c.dir/i_mod.c.o CMakeFiles/vf2c.dir/i_nint.c.o CMakeFiles/vf2c.dir/i_sign.c.o CMakeFiles/vf2c.dir/lbitbits.c.o CMakeFiles/vf2c.dir/lbitshft.c.o CMakeFiles/vf2c.dir/h_abs.c.o CMakeFiles/vf2c.dir/h_dim.c.o CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o 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 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cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 60%] Built target vf2c
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color="
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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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base/punc_base.c
[ 60%] Linking C shared library libpunc.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/punc.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color="
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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 '/<<PKGBUILDDIR>>/obj-aarch64-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/bmat.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc_base.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat.c
[ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c
[ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bvec.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_ctor’:
/<<PKGBUILDDIR>>/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);
| ^~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat.c:34:
In function ‘sprintf’,
inlined from ‘Bmat_ctor’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:34:
In function ‘sprintf’,
inlined from ‘Bvec_bcg’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_galerkin’:
/<<PKGBUILDDIR>>/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);
| ^~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/mat.c
[ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o
[ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/matln.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/matcopy.c
[ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/mtool.c
[ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/vec.c
[ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/vec3.c
[ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam/zslu.c
[ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c:34:
In function ‘sprintf’,
inlined from ‘Bvec_hcg’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/hbtools.c
[ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/rcmat.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function ‘Bvec_ctorPoint’:
/<<PKGBUILDDIR>>/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);
| ^~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 2147483646]
291 | sprintf(bname, "%s_%d", thee->name, p);
| ^~~~~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/maloc/maloc_base.h:80,
from /usr/include/maloc/maloc.h:38,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/hbtools.c:34:
In function ‘sprintf’,
inlined from ‘Bvec_ctorPoint’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/aprx.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:39:
In function ‘sprintf’,
inlined from ‘Bvec_sfpcg’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9,
inlined from ‘Bvec_submethod’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9,
inlined from ‘Bvec_submethod’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9,
inlined from ‘Bvec_submethod’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9,
inlined from ‘Bvec_submethod’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/assem.c
[ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/estim.c
[ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c:34:
In function ‘sprintf’,
inlined from ‘Aprx_fe2fd’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/vel.c
[ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o
[ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gem.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/ves.c
[ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemchk.c
[ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function ‘Gem_delaunay’:
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=]
522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type ‘double *[4]’
In file included from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gem_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:34:
/<<PKGBUILDDIR>>/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,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=]
659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type ‘double *[4]’
/<<PKGBUILDDIR>>/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,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: ‘Gem_writeGV’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=]
743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type ‘double *[4]’
/<<PKGBUILDDIR>>/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,
| ^~~~~~~~~~~
[ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemio.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gem_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34:
In function ‘sprintf’,
inlined from ‘Gem_writeTEC’ at /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemref.c
[ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem/gemcube.c
[ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam/am.c
[ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam/lsolv.c
[ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam/nsolv.c
[ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn/dyn.c
[ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_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 /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function ‘MCsh_builtIn’:
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=]
765 | Gem_writeGEOM(thee->gm,
| ^~~~~~~~~~~~~~~~~~~~~~~
766 | sock,
| ~~~~~
767 | defKey,
| ~~~~~~~
768 | Vsh_getenvInt(thee->vsh,"CKEY"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
769 | Vsh_getenvInt(thee->vsh,"DKEY"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
770 | Vsh_getenvReal(thee->vsh,"GVAL"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
771 | Vsh_getenvInt(thee->vsh,"FKEY"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
772 | defX,
| ~~~~~
773 | "GV");
| ~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type ‘double *[4]’
In file included from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam/mc/am.h:43,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37,
from /<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34:
/<<PKGBUILDDIR>>/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,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: ‘Gem_writeGEOM’ accessing 32 bytes in a region of size 24 [-Wstringop-overflow=]
810 | Gem_writeGEOM(thee->gm,
| ^~~~~~~~~~~~~~~~~~~~~~~
811 | sock,
| ~~~~~
812 | defKey,
| ~~~~~~~
813 | Vsh_getenvInt(thee->vsh,"CKEY"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
814 | Vsh_getenvInt(thee->vsh,"DKEY"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
815 | Vsh_getenvReal(thee->vsh,"GVAL"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
816 | Vsh_getenvInt(thee->vsh,"FKEY"),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
817 | defX,
| ~~~~~
818 | "MATH");
| ~~~~~~~
/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type ‘double *[4]’
/<<PKGBUILDDIR>>/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,
| ^~~~~~~~~~~~~
[ 73%] Linking C shared library libmc.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/mc.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/aarch64-linux-gnu/libblas.so -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-linux-gnu/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
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cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/buildAd.c
[ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o
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[ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/buildPd.c
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cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/mgparm.c
[ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/cgd.c
[ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/gsd.c
[ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/femparm.c
[ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/matvecd.c
[ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/pbamparm.c
[ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/pbsamparm.c
[ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/pbeparm.c
[ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/bemparm.c
[ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/geoflowparm.c
[ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/apolparm.c
[ 78%] Linking CXX shared library libgamer.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/gamer.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc
cd /<<PKGBUILDDIR>>/obj-aarch64-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
[ 79%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mgcsd.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 79%] Built target gamer
[ 79%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mgdrvd.c
[ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vacc.c
[ 79%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mgsubd.c
[ 79%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mikpckd.c
[ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mlinpckd.c
[ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mypdec.c
[ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/valist.c
[ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/newtond.c
[ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/newdrvd.c
[ 82%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vatom.c
[ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/powerd.c
[ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/smoothd.c
[ 82%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/pmgc/mgfasd.c
[ 82%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vpbe.c
[ 82%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vcap.c
[ 83%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vclist.c
[ 83%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vstring.c
[ 83%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vparam.c
[ 83%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/generic/vgreen.c
[ 84%] Linking C shared library libapbs_pmgc.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/apbs_pmgc.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 84%] Built target apbs_pmgc
[ 85%] Linking C shared library libapbs_generic.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/apbs_generic.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libblas.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 85%] Built target apbs_generic
make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend
make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/fem /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/fem /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/mg /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 85%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o
[ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o
[ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o
[ 86%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/fem/vcsm.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/mg/vgrid.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/fem/vpee.c
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/fem/vfetk.c
/<<PKGBUILDDIR>>/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/mg/vmgrid.c
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/mg/vgrid.h:67,
from /<<PKGBUILDDIR>>/src/mg/vgrid.c:57:
/usr/include/stdio.h:184:12: note: in a call to function ‘fclose’ declared ‘nonnull’
184 | extern int fclose (FILE *__stream) __nonnull ((1));
| ^~~~~~
[ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/mg/vopot.c
[ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/mg/vpmg.c
[ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/mg/vpmgp.c
/<<PKGBUILDDIR>>/src/fem/vfetk.c: In function ‘Bmat_printHB’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/fem/vfetk.h:67,
from /<<PKGBUILDDIR>>/src/fem/vfetk.c:57:
In function ‘sprintf’,
inlined from ‘Bmat_printHB’ at /<<PKGBUILDDIR>>/src/fem/vfetk.c:1073:5:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/fem/vfetk.c: In function ‘Bmat_printHB’:
/<<PKGBUILDDIR>>/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);
| ^~
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/fem/vfetk.c:1074:5:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/fem/vfetk.c: In function ‘Bmat_printHB’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/fem/vfetk.c:1075:5:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/fem/vfetk.c: In function ‘Bmat_printHB’:
/<<PKGBUILDDIR>>/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);
| ^~
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/fem/vfetk.c:1076:5:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
[ 87%] Linking C shared library libapbs_fem.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/apbs_fem.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 87%] Built target apbs_fem
[ 87%] Linking C shared library libapbs_mg.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/apbs_mg.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/src/routines.c
/<<PKGBUILDDIR>>/src/routines.c: In function ‘initAPOL’:
/<<PKGBUILDDIR>>/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c:5046:20: note: referencing argument 2 of type ‘char[1024]’
/<<PKGBUILDDIR>>/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=]
/<<PKGBUILDDIR>>/src/routines.c:5046:20: note: referencing argument 3 of type ‘char[1024]’
In file included from /<<PKGBUILDDIR>>/src/generic/apolparm.h:73,
from /<<PKGBUILDDIR>>/src/generic/nosh.h:73,
from /<<PKGBUILDDIR>>/src/apbs.h:70,
from /<<PKGBUILDDIR>>/src/routines.h:64,
from /<<PKGBUILDDIR>>/src/routines.c:54:
/<<PKGBUILDDIR>>/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’
304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c:5048:24: note: referencing argument 2 of type ‘char[1024]’
/<<PKGBUILDDIR>>/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=]
/<<PKGBUILDDIR>>/src/routines.c:5048:24: note: referencing argument 3 of type ‘char[1024]’
/<<PKGBUILDDIR>>/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’
304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writematMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/apbs.h:67:
In function ‘sprintf’,
inlined from ‘writematMG’ at /<<PKGBUILDDIR>>/src/routines.c:2020:9:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2937:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2963:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2919:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2954:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2944:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2930:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataMG’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:2909:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataFE’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:4893:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataFE’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:4887:13:
/usr/include/aarch64-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 ());
| ~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/routines.c: In function ‘writedataFE’:
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/routines.c:4880:13:
/usr/include/aarch64-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 /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/apbs_routines.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so
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/<<PKGBUILDDIR>>/src/main.c: In function ‘main’:
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319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__);
| ^~~~~~~~
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319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__);
| ^~~~~~~~
[ 89%] Linking C executable ../bin/mgmesh
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/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file,CMakeFiles/mgmesh.dir/link.d CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
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cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/tools/mesh/mergedx.c
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/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file,CMakeFiles/mergedx.dir/link.d CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
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/<<PKGBUILDDIR>>/tools/mesh/del2dx.c: In function ‘main’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed -Wl,--dependency-file,CMakeFiles/dx2uhbd.dir/link.d CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/tools/mesh && /usr/bin/cc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fcommon -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /<<PKGBUILDDIR>>/tools/mesh/uhbd_asc2bin.c
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/<<PKGBUILDDIR>>/tools/mesh/tensor2dx.c: In function ‘main’:
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/<<PKGBUILDDIR>>/tools/mesh/uhbd_asc2bin.c: In function ‘main’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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[100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src -I/<<PKGBUILDDIR>>/include -I/usr/include/suitesparse -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/mc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/base -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/bam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/whb -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/aprx -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/gem -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/pde -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/nam -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/dyn -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/mc/src/mcsh -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/_deps/fetk-build/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src -I/<<PKGBUILDDIR>>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/tools/python-pybind/bind_valist.cpp
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,--dependency-file,CMakeFiles/apbs_pybind.dir/link.d -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-312-aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so /usr/lib/aarch64-linux-gnu/libblas.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/aarch64-linux-gnu/libarpack.so /usr/lib/aarch64-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/aarch64-linux-gnu/libumfpack.so /usr/lib/aarch64-linux-gnu/libspqr.so /usr/lib/aarch64-linux-gnu/libcholmod.so /usr/lib/aarch64-linux-gnu/libccolamd.so /usr/lib/aarch64-linux-gnu/libcamd.so /usr/lib/aarch64-linux-gnu/libcolamd.so /usr/lib/aarch64-linux-gnu/libamd.so -lm -ldl /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libsuitesparseconfig.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -fopenmp
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PYTHONPATH=/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/tools/python sphinx-build -b html docs /<<PKGBUILDDIR>>/obj-aarch64-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.boundary_element.
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.read.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
WARNING: Failed to import apbs.input_file.calculate.finite_element.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
WARNING: Failed to import apbs.input_file.calculate.
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.calculate.finite_difference.
Possible hints:
* ModuleNotFoundError: No module named 'pyparsing'
* AttributeError: module 'apbs' has no attribute 'input_file'
WARNING: Failed to import apbs.input_file.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.
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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xffff8d0236b0>: Failed to establish a new connection: [Errno 111] Connection refused')))
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building [html]: targets for 127 source files that are out of date
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/<<PKGBUILDDIR>>/docs/getting/index.rst:41: ERROR: Unexpected indentation.
/<<PKGBUILDDIR>>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "geometric flow".
/<<PKGBUILDDIR>>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "fetk".
/<<PKGBUILDDIR>>/docs/releases.rst:3: WARNING: Duplicate explicit target name: "pbam/pbsam".
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/docs/using/input/new/calculate/index.rst:33: ERROR: Document or section may not begin with a transition.
/<<PKGBUILDDIR>>/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... /<<PKGBUILDDIR>>/docs/using/input/old/elec/pygbe.rst: WARNING: document isn't included in any toctree
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
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-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/generic/vstring.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/generic/vparam.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/generic/vgreen.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/generic/vmatrix.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/generic/vhal.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/generic/vunit.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_generic.so.3
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_generic.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/buildAd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/buildBd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/buildGd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/buildPd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/cgd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/gsd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/matvecd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mgcsd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mgdrvd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mgsubd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mikpckd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mlinpckd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mypdec.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/newtond.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/newdrvd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/powerd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/smoothd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pmgc/mgfasd.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so.3
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_pmgc.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mg/vgrid.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mg/vmgrid.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mg/vopot.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mg/vpmg.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/mg/vpmgp.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_mg.so.3
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_mg.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/fem/vcsm.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/fem/vfetk.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/fem/vpee.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_fem.so.3
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libapbs_fem.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/apbs.cpython-312-aarch64-linux-gnu.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.param
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.face
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.vert
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.face
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.face
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.vert
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.vert
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.face
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.face
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.vert
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.config
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pygbe/lys.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/mol1.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/mol2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/apbs.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/force.result
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.inp.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.dat.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/proton.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/run_apdx_files.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNB.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/postprocess.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs_dx.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/test.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/run_selected_examples.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/fas2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/param.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/apbs.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/misc/mache.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/neg_2.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/pos_1.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbam/1a63.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/mesh.m
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/polarforces
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/pmf.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/parm.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/ion.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apolarforces
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/UHBD
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.dat.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/examples/run_examples.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/apbs_logger.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/test_cases.cfg
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/apbs_check_results.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/apbs_tester.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/smooth.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/analysis.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/similarity.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/mesh/value.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/README.md
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/apbslib.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/Makefile.am
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/main.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/Makefile
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/ion.pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/README
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/Makefile.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/README
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/apbslib.i
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/apbs.in
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/noinput.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/CMakeLists.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/manip
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/manip/coulomb.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/manip/psize.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/manip/born.c
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/manip/inputgen.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/module.cpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_constants.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/github
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/github/release-data.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/github/getReleases.sh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/coulomb
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/analysis
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/smooth
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/value
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/dxmath
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/mergedx2
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/del2dx
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/dx2mol
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/similarity
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/tensor2dx
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/mergedx
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/born
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/multivalue
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/mgmesh
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/apbs/tools/bin/benchmark
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
debian/rules execute_after_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
(cd tests; PATH=/<<PKGBUILDDIR>>/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/<<PKGBUILDDIR>>/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__)
TESTING WITH BINARY_NAME:apbs
START_DIR:/<<PKGBUILDDIR>>/build
--------------------------------------------------------------------------------
Testing forces from apbs-forces.in
Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.002003 seconds
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file apbs-mol-auto.in
CHECKING:/<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
NOTE: Using apbs binary:/<<PKGBUILDDIR>>/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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-auto.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-auto.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.607073836227E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.383 x 0.383 x 0.383
Grid lengths: 24.495 x 24.495 x 24.495
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.200266567971E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Potential to be written to potential.dx.gz
Total electrostatic energy = 4.732245131587E+03 kJ/mol
Calculating forces...
Writing potential to potential-PE0.dx.gz
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.190871482831E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.383 x 0.383 x 0.383
Grid lengths: 24.495 x 24.495 x 24.495
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.430874049735E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.962018684215E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -2.297735526282E+02 kJ/mol
Global net ELEC energy = -2.297735526282E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02)
*** PASSED ***
Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03)
*** PASSED ***
Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03)
*** PASSED ***
Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
*** PASSED ***
Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03)
*** PASSED ***
Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03)
*** PASSED ***
Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02)
*** PASSED ***
Elapsed time: 1.7911510000000002 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-auto.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-auto.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.532928767450E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.383 x 0.383 x 0.383
Grid lengths: 24.495 x 24.495 x 24.495
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.201243880085E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.733006258977E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.190871482831E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.383 x 0.383 x 0.383
Grid lengths: 24.495 x 24.495 x 24.495
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.430874049735E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.962018684215E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -2.290124252387E+02 kJ/mol
Global net ELEC energy = -2.290124252387E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02)
*** PASSED ***
Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03)
*** PASSED ***
Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03)
*** PASSED ***
Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
*** PASSED ***
Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03)
*** PASSED ***
Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03)
*** PASSED ***
Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02)
*** PASSED ***
Elapsed time: 1.671395 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-parallel-PE0.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-parallel-PE0.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.401768459022E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.142935592471E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485255308186E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707009E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557588E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949131E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.761864094552E+01 kJ/mol
Global net ELEC energy = -5.761864094552E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 0 results:
2.401768459022e+02
8.142935592471e+02
1.485255308186e+03
2.977178707009e+02
8.799304557588e+02
1.542873949131e+03
-5.761864094552e+01
Checking for intermediate energies in input file apbs-mol-parallel-PE0.out
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-parallel-PE1.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-parallel-PE1.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.401768459022E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.142778312125E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485246667424E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707009E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557588E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949131E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.762728170718E+01 kJ/mol
Global net ELEC energy = -5.762728170718E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 1 results:
2.401768459022e+02
8.142778312125e+02
1.485246667424e+03
2.977178707009e+02
8.799304557588e+02
1.542873949131e+03
-5.762728170718e+01
Checking for intermediate energies in input file apbs-mol-parallel-PE1.out
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-parallel-PE2.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-parallel-PE2.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.401768459091E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.142935605695E+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: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485255306569E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707146E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557596E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949141E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.761864257239E+01 kJ/mol
Global net ELEC energy = -5.761864257239E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 2 results:
2.401768459091e+02
8.142935605695e+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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-parallel-PE3.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-parallel-PE3.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.401768459091E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.142778325440E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485246665692E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707146E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557596E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949141E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.762728344953E+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, 122.102 MB high water
Thanks for using APBS!
Processor 3 results:
2.401768459091e+02
8.142778325440e+02
1.485246665692e+03
2.977178707146e+02
8.799304557596e+02
1.542873949141e+03
-5.762728344953e+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 (5.941003947871e+03, 5.941003947871e+03)
*** PASSED ***
Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
*** PASSED ***
Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03)
*** PASSED ***
Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03)
*** PASSED ***
Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02)
*** PASSED ***
Elapsed time: 7.941632 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, 5941.0039478710005, 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 5941.0039478710005
COMPUTED RESULT 1190.8714828309999
COMPUTED RESULT 3519.7218230368003
COMPUTED RESULT 6171.495796544
COMPUTED RESULT -230.49184867462003
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-parallel-PE0.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-parallel-PE0.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.383232191816E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.145369591602E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485524998001E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707009E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557588E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949131E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.734895113069E+01 kJ/mol
Global net ELEC energy = -5.734895113069E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 0 results:
2.383232191816e+02
8.145369591602e+02
1.485524998001e+03
2.977178707009e+02
8.799304557588e+02
1.542873949131e+03
-5.734895113069e+01
Checking for intermediate energies in input file apbs-smol-parallel-PE0.out
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-parallel-PE1.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-parallel-PE1.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.383232191816E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.145419898332E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485529328612E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707009E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557588E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, -2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949131E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.734462051928E+01 kJ/mol
Global net ELEC energy = -5.734462051928E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 1 results:
2.383232191816e+02
8.145419898332e+02
1.485529328612e+03
2.977178707009e+02
8.799304557588e+02
1.542873949131e+03
-5.734462051928e+01
Checking for intermediate energies in input file apbs-smol-parallel-PE1.out
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-parallel-PE2.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-parallel-PE2.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.383232191909E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.145369593489E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485524997676E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707146E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557596E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (-2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949141E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.734895146550E+01 kJ/mol
Global net ELEC energy = -5.734895146550E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 2 results:
2.383232191909e+02
8.145369593489e+02
1.485524997676e+03
2.977178707146e+02
8.799304557596e+02
1.542873949141e+03
-5.734895146550e+01
Checking for intermediate energies in input file apbs-smol-parallel-PE2.out
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-parallel-PE3.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-parallel-PE3.in...
rank 0 size 1...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from ion.pqr.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 61.280 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.383232191909E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.145419900310E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #3 (solvated): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.280 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.485529328301E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.781 x 0.781 x 0.781
Grid lengths: 50.000 x 50.000 x 50.000
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.977178707146E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.296 x 0.296 x 0.383
Grid lengths: 18.944 x 18.944 x 24.495
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.799304557596E+02 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (reference): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.207 MB total, 122.102 MB high water
Using cubic spline charge discretization.
Partition overlap fraction = 0.1
Processor array = 2 x 2 x 1
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.112 x 0.112 x 0.188
Grid lengths: 7.178 x 7.178 x 12.000
Grid center: (2.411, 2.411, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.542873949141E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (solvated) - 2 (reference) end
Local net energy (PE 0) = -5.734462084052E+01 kJ/mol
Global net ELEC energy = -5.734462084052E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 0.001 MB total, 122.102 MB high water
Thanks for using APBS!
Processor 3 results:
2.383232191909e+02
8.145419900310e+02
1.485529328301e+03
2.977178707146e+02
8.799304557596e+02
1.542873949141e+03
-5.734462084052e+01
Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02)
*** PASSED ***
Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03)
*** PASSED ***
Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03)
*** PASSED ***
Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03)
*** PASSED ***
Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03)
*** PASSED ***
Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03)
*** PASSED ***
Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02)
*** PASSED ***
Elapsed time: 7.527007 seconds
--------------------------------------------------------------------------------
Total elapsed time: 18.933188 seconds
Test results have been logged
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file apbs-mol-auto.in
Checking for intermediate energies in input file apbs-smol-parallel-PE3.out
EXPECTED COMPUTED: 7
EXPECTED EXPECTED: 7
COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599]
EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02']
COMPUTED RESULT 953.292876745
COMPUTED RESULT 3258.1578983732998
COMPUTED RESULT 5942.108652589999
COMPUTED RESULT 1190.8714828309999
COMPUTED RESULT 3519.7218230368003
COMPUTED RESULT 6171.495796544
COMPUTED RESULT -229.38714395599
Running tests for actin-dimer-auto section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-auto.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-auto.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mol1.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
5877 atoms
Centered at (1.535e+01, -3.100e-02, 2.993e+00)
Net charge -1.20e+01 e
Reading PQR-format atom data from mol2.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
5877 atoms
Centered at (-1.404e+01, -3.356e+00, 3.049e+01)
Net charge -1.20e+01 e
Reading PQR-format atom data from complex.pqr.
11754 atoms
Centered at (2.518e+00, -2.465e+00, 1.674e+01)
Net charge -2.40e+01 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (mol1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1028.322 MB total, 1028.322 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.975 x 0.756 x 1.012
Grid lengths: 156.000 x 121.000 x 162.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 1
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.527617850342E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (mol1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1028.322 MB total, 2042.113 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.700 x 0.569 x 0.725
Grid lengths: 112.000 x 91.000 x 116.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 1
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.919510754196E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1030.291 MB total, 2042.113 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.975 x 0.756 x 1.012
Grid lengths: 156.000 x 121.000 x 162.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 2
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.527671844880E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1030.291 MB total, 2046.048 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.700 x 0.569 x 0.725
Grid lengths: 112.000 x 91.000 x 116.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 2
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.915468859278E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1046.446 MB total, 2046.048 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.975 x 0.756 x 1.012
Grid lengths: 156.000 x 121.000 x 162.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 3
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.056317807611E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1046.446 MB total, 2069.492 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.700 x 0.569 x 0.725
Grid lengths: 112.000 x 91.000 x 116.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 3
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 5.836028296532E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 2 (mol2) - 1 (mol1) end
Local net energy (PE 0) = 1.048683058621E+02 kJ/mol
Global net ELEC energy = 1.048683058621E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 2069.492 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05)
*** PASSED ***
Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05)
*** PASSED ***
Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05)
*** PASSED ***
Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05)
*** PASSED ***
Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05)
*** PASSED ***
Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05)
*** PASSED ***
Testing computed result against expected result (1.048683058621e+02, 1.048683060915e+02)
*** PASSED ***
Elapsed time: 84.064021 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, 104.8683058621]
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 104.8683058621
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-auto.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-auto.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mol1.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
5877 atoms
Centered at (1.535e+01, -3.100e-02, 2.993e+00)
Net charge -1.20e+01 e
Reading PQR-format atom data from mol2.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
5877 atoms
Centered at (-1.404e+01, -3.356e+00, 3.049e+01)
Net charge -1.20e+01 e
Reading PQR-format atom data from complex.pqr.
11754 atoms
Centered at (2.518e+00, -2.465e+00, 1.674e+01)
Net charge -2.40e+01 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (mol1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1028.322 MB total, 1028.322 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.975 x 0.756 x 1.012
Grid lengths: 156.000 x 121.000 x 162.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 1
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.528632421825E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (mol1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1028.322 MB total, 2042.113 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.700 x 0.569 x 0.725
Grid lengths: 112.000 x 91.000 x 116.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 1
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.920618662320E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1030.291 MB total, 2042.113 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.975 x 0.756 x 1.012
Grid lengths: 156.000 x 121.000 x 162.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 2
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.529297900572E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (mol2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1030.291 MB total, 2046.048 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.700 x 0.569 x 0.725
Grid lengths: 112.000 x 91.000 x 116.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 2
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.916592202835E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1046.446 MB total, 2046.048 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.975 x 0.756 x 1.012
Grid lengths: 156.000 x 121.000 x 162.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 3
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.059244262535E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 13.5959 A
Current memory usage: 1046.446 MB total, 2069.492 MB high water
Using linear spline charge discretization.
Grid dimensions: 161 x 161 x 161
Grid spacings: 0.700 x 0.569 x 0.725
Grid lengths: 112.000 x 91.000 x 116.000
Grid center: (2.518, -2.465, 16.742)
Multigrid levels: 4
Molecule ID: 3
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.050 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.050 M concentration
2.000 A-radius, -1.000 e-charge, 0.050 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.400
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 5.838306706232E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 2 (mol2) - 1 (mol1) end
Local net energy (PE 0) = 1.095841077688E+02 kJ/mol
Global net ELEC energy = 1.095841077688E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 2069.492 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05)
*** PASSED ***
Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05)
*** PASSED ***
Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05)
*** PASSED ***
Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05)
*** PASSED ***
Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05)
*** PASSED ***
Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05)
*** PASSED ***
Testing computed result against expected result (1.095841077688e+02, 1.095841074454e+02)
*** PASSED ***
Elapsed time: 60.681835 seconds
--------------------------------------------------------------------------------
Total elapsed time: 144.745856 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, 109.5841077688]
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 109.5841077688
Running tests for alkanes section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: alkanes.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file alkanes.in...
rank 0 size 1...
Parsed input file.
Reading parameter data from parm.dat.
Got paths for 11 molecules
Reading PDB-format atom data from 2-methylbutane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
17 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 4.33e+00 e
Reading PDB-format atom data from butane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
14 atoms
Centered at (3.917e+00, 7.025e-01, -8.575e+00)
Net charge 3.51e+00 e
Reading PDB-format atom data from cyclohexane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
18 atoms
Centered at (1.123e+00, 5.880e-01, 7.680e-01)
Net charge 4.93e+00 e
Reading PDB-format atom data from cyclopentane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
13 atoms
Centered at (1.320e+00, 5.255e-01, 1.289e+00)
Net charge 3.88e+00 e
Reading PDB-format atom data from ethane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
8 atoms
Centered at (2.210e-01, -2.100e-02, 7.650e-01)
Net charge 1.87e+00 e
Reading PDB-format atom data from hexane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
20 atoms
Centered at (4.951e+00, -9.500e-03, -8.406e+00)
Net charge 5.16e+00 e
Reading PDB-format atom data from isobutane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
14 atoms
Centered at (1.859e+01, 1.864e+01, 1.921e+01)
Net charge 3.51e+00 e
Reading PDB-format atom data from methane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
5 atoms
Centered at (1.803e+01, 1.779e+01, 1.782e+01)
Net charge 1.05e+00 e
Reading PDB-format atom data from neopentane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
17 atoms
Centered at (1.867e+01, 1.894e+01, 1.920e+01)
Net charge 4.33e+00 e
Reading PDB-format atom data from pentane.pdb.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
17 atoms
Centered at (4.460e+00, 1.615e-01, -8.566e+00)
Net charge 4.33e+00 e
Reading PDB-format atom data from propane.pdb.
11 atoms
Centered at (1.836e+01, 1.896e+01, 1.861e+01)
Net charge 2.69e+00 e
Preparing to run 11 PBE calculations.
----------------------------------------
CALCULATION #1 (solvated-2-methylbutane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 3.815624614267E+00
SASA for atom 1: 0.000000000000E+00
SASA for atom 2: 6.122920124655E-01
SASA for atom 3: 3.957497153740E+00
SASA for atom 4: 4.308445014544E+00
SASA for atom 5: 1.843264951960E+01
SASA for atom 6: 1.837011296483E+01
SASA for atom 7: 1.666599184724E+01
SASA for atom 8: 1.480031796315E+01
SASA for atom 9: 1.603020354037E+01
SASA for atom 10: 1.473778140838E+01
SASA for atom 11: 1.611879699297E+01
SASA for atom 12: 1.810954398660E+01
SASA for atom 13: 1.420100931324E+01
SASA for atom 14: 1.437298483886E+01
SASA for atom 15: 1.814081226399E+01
SASA for atom 16: 2.152820898091E+01
Total solvent accessible surface area: 214.202 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 3.243280922127E-02
Surface tension*area energy for atom 1: 0.000000000000E+00
Surface tension*area energy for atom 2: 5.204482105957E-03
Surface tension*area energy for atom 3: 3.363872580679E-02
Surface tension*area energy for atom 4: 3.662178262362E-02
Surface tension*area energy for atom 5: 1.566775209166E-01
Surface tension*area energy for atom 6: 1.561459602010E-01
Surface tension*area energy for atom 7: 1.416609307015E-01
Surface tension*area energy for atom 8: 1.258027026868E-01
Surface tension*area energy for atom 9: 1.362567300932E-01
Surface tension*area energy for atom 10: 1.252711419712E-01
Surface tension*area energy for atom 11: 1.370097744402E-01
Surface tension*area energy for atom 12: 1.539311238861E-01
Surface tension*area energy for atom 13: 1.207085791625E-01
Surface tension*area energy for atom 14: 1.221703711303E-01
Surface tension*area energy for atom 15: 1.541969042439E-01
Surface tension*area energy for atom 16: 1.829897763377E-01
Total surface tension energy: 1.82072 kJ/mol
Total solvent accessible volume: 253.665 A^3
Total pressure*volume energy: 60.7274 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.271287875274E+00
WCA energy for atom 1: -5.600872869478E+00
WCA energy for atom 2: -5.773775123943E+00
WCA energy for atom 3: -6.072801488986E+00
WCA energy for atom 4: -6.378470721845E+00
WCA energy for atom 5: -1.573474558351E+00
WCA energy for atom 6: -1.582338715648E+00
WCA energy for atom 7: -1.504044838266E+00
WCA energy for atom 8: -1.351002262819E+00
WCA energy for atom 9: -1.437367175239E+00
WCA energy for atom 10: -1.384626257493E+00
WCA energy for atom 11: -1.468867560891E+00
WCA energy for atom 12: -1.557005662832E+00
WCA energy for atom 13: -1.473759654043E+00
WCA energy for atom 14: -1.502261431335E+00
WCA energy for atom 15: -1.550940901474E+00
WCA energy for atom 16: -1.667828659696E+00
Total WCA energy: -48.1507 kJ/mol
Total non-polar energy = 1.439739455792E+01 kJ/mol
----------------------------------------
CALCULATION #2 (solvated-butane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 4.405515699447E+00
SASA for atom 1: 8.213673337951E-01
SASA for atom 2: 8.064333822716E-01
SASA for atom 3: 4.375647796400E+00
SASA for atom 4: 1.855251124959E+01
SASA for atom 5: 2.147609518526E+01
SASA for atom 6: 1.852645435176E+01
SASA for atom 7: 1.660345529247E+01
SASA for atom 8: 1.658782115377E+01
SASA for atom 9: 1.658260977421E+01
SASA for atom 10: 1.658260977421E+01
SASA for atom 11: 2.145003828744E+01
SASA for atom 12: 1.852124297220E+01
SASA for atom 13: 1.856293400871E+01
Total solvent accessible surface area: 193.855 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 3.744688344530E-02
Surface tension*area energy for atom 1: 6.981622337259E-03
Surface tension*area energy for atom 2: 6.854683749309E-03
Surface tension*area energy for atom 3: 3.719300626940E-02
Surface tension*area energy for atom 4: 1.576963456215E-01
Surface tension*area energy for atom 5: 1.825468090747E-01
Surface tension*area energy for atom 6: 1.574748619900E-01
Surface tension*area energy for atom 7: 1.411293699860E-01
Surface tension*area energy for atom 8: 1.409964798071E-01
Surface tension*area energy for atom 9: 1.409521830808E-01
Surface tension*area energy for atom 10: 1.409521830808E-01
Surface tension*area energy for atom 11: 1.823253254433E-01
Surface tension*area energy for atom 12: 1.574305652637E-01
Surface tension*area energy for atom 13: 1.577849390741E-01
Total surface tension energy: 1.64777 kJ/mol
Total solvent accessible volume: 217.863 A^3
Total pressure*volume energy: 52.1564 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.728858147814E+00
WCA energy for atom 1: -6.204037472587E+00
WCA energy for atom 2: -6.202937735018E+00
WCA energy for atom 3: -6.728762249931E+00
WCA energy for atom 4: -1.623549989062E+00
WCA energy for atom 5: -1.709092300778E+00
WCA energy for atom 6: -1.625196457114E+00
WCA energy for atom 7: -1.484289341167E+00
WCA energy for atom 8: -1.485410538626E+00
WCA energy for atom 9: -1.485593139015E+00
WCA energy for atom 10: -1.484878734279E+00
WCA energy for atom 11: -1.708585062695E+00
WCA energy for atom 12: -1.625094916482E+00
WCA energy for atom 13: -1.624416805392E+00
Total WCA energy: -41.7207 kJ/mol
Total non-polar energy = 1.208346456826E+01 kJ/mol
----------------------------------------
CALCULATION #3 (solvated-cyclohexane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 7.840324549863E-01
SASA for atom 1: 8.064333822716E-01
SASA for atom 2: 8.288343095569E-01
SASA for atom 3: 7.840324549863E-01
SASA for atom 4: 7.989664065098E-01
SASA for atom 5: 8.363012853187E-01
SASA for atom 6: 2.001169752764E+01
SASA for atom 7: 1.616048802948E+01
SASA for atom 8: 2.001169752764E+01
SASA for atom 9: 1.619175630687E+01
SASA for atom 10: 1.616048802948E+01
SASA for atom 11: 1.993352683418E+01
SASA for atom 12: 2.001169752764E+01
SASA for atom 13: 1.618133354774E+01
SASA for atom 14: 1.617091078861E+01
SASA for atom 15: 2.001690890721E+01
SASA for atom 16: 1.993873821374E+01
SASA for atom 17: 1.617091078861E+01
Total solvent accessible surface area: 221.799 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 6.664275867383E-03
Surface tension*area energy for atom 1: 6.854683749309E-03
Surface tension*area energy for atom 2: 7.045091631234E-03
Surface tension*area energy for atom 3: 6.664275867383E-03
Surface tension*area energy for atom 4: 6.791214455333E-03
Surface tension*area energy for atom 5: 7.108560925209E-03
Surface tension*area energy for atom 6: 1.700994289850E-01
Surface tension*area energy for atom 7: 1.373641482506E-01
Surface tension*area energy for atom 8: 1.700994289850E-01
Surface tension*area energy for atom 9: 1.376299286084E-01
Surface tension*area energy for atom 10: 1.373641482506E-01
Surface tension*area energy for atom 11: 1.694349780905E-01
Surface tension*area energy for atom 12: 1.700994289850E-01
Surface tension*area energy for atom 13: 1.375413351558E-01
Surface tension*area energy for atom 14: 1.374527417032E-01
Surface tension*area energy for atom 15: 1.701437257113E-01
Surface tension*area energy for atom 16: 1.694792748168E-01
Surface tension*area energy for atom 17: 1.374527417032E-01
Total surface tension energy: 1.88529 kJ/mol
Total solvent accessible volume: 267.435 A^3
Total pressure*volume energy: 64.0239 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -5.793234697241E+00
WCA energy for atom 1: -5.784370526583E+00
WCA energy for atom 2: -5.791799130412E+00
WCA energy for atom 3: -5.788504399087E+00
WCA energy for atom 4: -5.797319672490E+00
WCA energy for atom 5: -5.787358035342E+00
WCA energy for atom 6: -1.523887929614E+00
WCA energy for atom 7: -1.413678912317E+00
WCA energy for atom 8: -1.521751604392E+00
WCA energy for atom 9: -1.414741802525E+00
WCA energy for atom 10: -1.413367854344E+00
WCA energy for atom 11: -1.523407238081E+00
WCA energy for atom 12: -1.523000623583E+00
WCA energy for atom 13: -1.413922068538E+00
WCA energy for atom 14: -1.416316744211E+00
WCA energy for atom 15: -1.524577474659E+00
WCA energy for atom 16: -1.523300410052E+00
WCA energy for atom 17: -1.414522566061E+00
Total WCA energy: -52.3691 kJ/mol
Total non-polar energy = 1.354016672221E+01 kJ/mol
----------------------------------------
CALCULATION #4 (solvated-cyclopentane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 9.490526193215E+00
SASA for atom 1: 9.512927120500E+00
SASA for atom 2: 2.299828534626E+00
SASA for atom 3: 1.919012770776E+00
SASA for atom 4: 2.307295510388E+00
SASA for atom 5: 2.325838699632E+01
SASA for atom 6: 2.325838699632E+01
SASA for atom 7: 2.045987617019E+01
SASA for atom 8: 2.067875411190E+01
SASA for atom 9: 2.028790064456E+01
SASA for atom 10: 1.897463299431E+01
SASA for atom 11: 2.048593306801E+01
SASA for atom 12: 2.070481100972E+01
Total solvent accessible surface area: 193.638 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 8.066947264233E-02
Surface tension*area energy for atom 1: 8.085988052425E-02
Surface tension*area energy for atom 2: 1.954854254432E-02
Surface tension*area energy for atom 3: 1.631160855160E-02
Surface tension*area energy for atom 4: 1.961201183830E-02
Surface tension*area energy for atom 5: 1.976962894687E-01
Surface tension*area energy for atom 6: 1.976962894687E-01
Surface tension*area energy for atom 7: 1.739089474466E-01
Surface tension*area energy for atom 8: 1.757694099511E-01
Surface tension*area energy for atom 9: 1.724471554788E-01
Surface tension*area energy for atom 10: 1.612843804516E-01
Surface tension*area energy for atom 11: 1.741304310781E-01
Surface tension*area energy for atom 12: 1.759908935826E-01
Total surface tension energy: 1.64593 kJ/mol
Total solvent accessible volume: 217.998 A^3
Total pressure*volume energy: 52.1887 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.343496616804E+00
WCA energy for atom 1: -6.327869601807E+00
WCA energy for atom 2: -6.334858040579E+00
WCA energy for atom 3: -6.296075406417E+00
WCA energy for atom 4: -6.345600816761E+00
WCA energy for atom 5: -1.663697465126E+00
WCA energy for atom 6: -1.662444032853E+00
WCA energy for atom 7: -1.572325104493E+00
WCA energy for atom 8: -1.604626551065E+00
WCA energy for atom 9: -1.586431484963E+00
WCA energy for atom 10: -1.554291291374E+00
WCA energy for atom 11: -1.574315220751E+00
WCA energy for atom 12: -1.604941679892E+00
Total WCA energy: -44.471 kJ/mol
Total non-polar energy = 9.363673200142E+00 kJ/mol
----------------------------------------
CALCULATION #5 (solvated-ethane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 5.995981536705E+00
SASA for atom 1: 5.966113633657E+00
SASA for atom 2: 2.121552620704E+01
SASA for atom 3: 2.124158310486E+01
SASA for atom 4: 2.125200586399E+01
SASA for atom 5: 2.123116034573E+01
SASA for atom 6: 2.125200586399E+01
SASA for atom 7: 2.127285138225E+01
Total solvent accessible surface area: 139.427 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 5.096584306199E-02
Surface tension*area energy for atom 1: 5.071196588609E-02
Surface tension*area energy for atom 2: 1.803319727598E-01
Surface tension*area energy for atom 3: 1.805534563913E-01
Surface tension*area energy for atom 4: 1.806420498439E-01
Surface tension*area energy for atom 5: 1.804648629387E-01
Surface tension*area energy for atom 6: 1.806420498439E-01
Surface tension*area energy for atom 7: 1.808192367491E-01
Total surface tension energy: 1.18513 kJ/mol
Total solvent accessible volume: 140.346 A^3
Total pressure*volume energy: 33.5988 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -7.360066353115E+00
WCA energy for atom 1: -7.355483516201E+00
WCA energy for atom 2: -1.776106201066E+00
WCA energy for atom 3: -1.773973940651E+00
WCA energy for atom 4: -1.775401936843E+00
WCA energy for atom 5: -1.773464835521E+00
WCA energy for atom 6: -1.774382856097E+00
WCA energy for atom 7: -1.772366599434E+00
Total WCA energy: -25.3612 kJ/mol
Total non-polar energy = 9.422717598546E+00 kJ/mol
----------------------------------------
CALCULATION #6 (solvated-hexane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 4.405515699447E+00
SASA for atom 1: 8.213673337951E-01
SASA for atom 2: 3.285469335181E-01
SASA for atom 3: 2.986790304710E-01
SASA for atom 4: 1.855251124959E+01
SASA for atom 5: 2.147609518526E+01
SASA for atom 6: 1.852645435176E+01
SASA for atom 7: 1.655655287639E+01
SASA for atom 8: 1.655134149682E+01
SASA for atom 9: 1.360170066332E+01
SASA for atom 10: 1.357043238593E+01
SASA for atom 11: 1.381536722546E+01
SASA for atom 12: 1.384142412329E+01
SASA for atom 13: 7.765654792245E-01
SASA for atom 14: 1.684839013200E+01
SASA for atom 15: 1.682233323417E+01
SASA for atom 16: 4.166572475070E+00
SASA for atom 17: 2.179398933870E+01
SASA for atom 18: 1.877660057086E+01
SASA for atom 19: 1.876096643216E+01
Total solvent accessible surface area: 250.291 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 3.744688344530E-02
Surface tension*area energy for atom 1: 6.981622337259E-03
Surface tension*area energy for atom 2: 2.792648934903E-03
Surface tension*area energy for atom 3: 2.538771759003E-03
Surface tension*area energy for atom 4: 1.576963456215E-01
Surface tension*area energy for atom 5: 1.825468090747E-01
Surface tension*area energy for atom 6: 1.574748619900E-01
Surface tension*area energy for atom 7: 1.407306994493E-01
Surface tension*area energy for atom 8: 1.406864027230E-01
Surface tension*area energy for atom 9: 1.156144556382E-01
Surface tension*area energy for atom 10: 1.153486752804E-01
Surface tension*area energy for atom 11: 1.174306214164E-01
Surface tension*area energy for atom 12: 1.176521050479E-01
Surface tension*area energy for atom 13: 6.600806573408E-03
Surface tension*area energy for atom 14: 1.432113161220E-01
Surface tension*area energy for atom 15: 1.429898324905E-01
Surface tension*area energy for atom 16: 3.541586603809E-02
Surface tension*area energy for atom 17: 1.852489093789E-01
Surface tension*area energy for atom 18: 1.596011048523E-01
Surface tension*area energy for atom 19: 1.594682146734E-01
Total surface tension energy: 2.12748 kJ/mol
Total solvent accessible volume: 298.053 A^3
Total pressure*volume energy: 71.3539 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.635406071935E+00
WCA energy for atom 1: -5.957247427848E+00
WCA energy for atom 2: -5.524801144538E+00
WCA energy for atom 3: -5.522294168859E+00
WCA energy for atom 4: -1.605314409440E+00
WCA energy for atom 5: -1.701051761776E+00
WCA energy for atom 6: -1.606669162773E+00
WCA energy for atom 7: -1.442505934938E+00
WCA energy for atom 8: -1.443059002759E+00
WCA energy for atom 9: -1.328947132810E+00
WCA energy for atom 10: -1.328906972440E+00
WCA energy for atom 11: -1.331566344214E+00
WCA energy for atom 12: -1.328041776815E+00
WCA energy for atom 13: -5.937562025661E+00
WCA energy for atom 14: -1.442277774427E+00
WCA energy for atom 15: -1.442777091510E+00
WCA energy for atom 16: -6.602262542378E+00
WCA energy for atom 17: -1.698172146664E+00
WCA energy for atom 18: -1.600970858835E+00
WCA energy for atom 19: -1.600841970217E+00
Total WCA energy: -57.0807 kJ/mol
Total non-polar energy = 1.640068943201E+01 kJ/mol
----------------------------------------
CALCULATION #7 (solvated-isobutane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 3.464676753463E+00
SASA for atom 1: 1.984493338158E+01
SASA for atom 2: 1.778643845361E+01
SASA for atom 3: 1.671289426332E+01
SASA for atom 4: 0.000000000000E+00
SASA for atom 5: 3.531879535319E+00
SASA for atom 6: 1.673895116114E+01
SASA for atom 7: 1.793756846098E+01
SASA for atom 8: 1.973549441072E+01
SASA for atom 9: 1.710895911022E+01
SASA for atom 10: 4.599657069253E+00
SASA for atom 11: 1.937069784121E+01
SASA for atom 12: 1.654613011726E+01
SASA for atom 13: 1.936548646165E+01
Total solvent accessible surface area: 192.744 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 2.944975240444E-02
Surface tension*area energy for atom 1: 1.686819337434E-01
Surface tension*area energy for atom 2: 1.511847268556E-01
Surface tension*area energy for atom 3: 1.420596012382E-01
Surface tension*area energy for atom 4: 0.000000000000E+00
Surface tension*area energy for atom 5: 3.002097605021E-02
Surface tension*area energy for atom 6: 1.422810848697E-01
Surface tension*area energy for atom 7: 1.524693319183E-01
Surface tension*area energy for atom 8: 1.677517024912E-01
Surface tension*area energy for atom 9: 1.454261524369E-01
Surface tension*area energy for atom 10: 3.909708508865E-02
Surface tension*area energy for atom 11: 1.646509316503E-01
Surface tension*area energy for atom 12: 1.406421059967E-01
Surface tension*area energy for atom 13: 1.646066349240E-01
Total surface tension energy: 1.63832 kJ/mol
Total solvent accessible volume: 218.943 A^3
Total pressure*volume energy: 52.415 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.381016335247E+00
WCA energy for atom 1: -1.612317964554E+00
WCA energy for atom 2: -1.588013719598E+00
WCA energy for atom 3: -1.532162371190E+00
WCA energy for atom 4: -5.987950445279E+00
WCA energy for atom 5: -6.393089030861E+00
WCA energy for atom 6: -1.533454887042E+00
WCA energy for atom 7: -1.587650918485E+00
WCA energy for atom 8: -1.614083521570E+00
WCA energy for atom 9: -1.442402031577E+00
WCA energy for atom 10: -6.408813541353E+00
WCA energy for atom 11: -1.605830214390E+00
WCA energy for atom 12: -1.529385873788E+00
WCA energy for atom 13: -1.605662490385E+00
Total WCA energy: -40.8218 kJ/mol
Total non-polar energy = 1.323144287435E+01 kJ/mol
----------------------------------------
CALCULATION #8 (solvated-methane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 1.231304303117E+01
SASA for atom 1: 2.323233009850E+01
SASA for atom 2: 2.345641941977E+01
SASA for atom 3: 2.377431357320E+01
SASA for atom 4: 2.264344420771E+01
Total solvent accessible surface area: 105.42 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 1.046608657649E-01
Surface tension*area energy for atom 1: 1.974748058372E-01
Surface tension*area energy for atom 2: 1.993795650680E-01
Surface tension*area energy for atom 3: 2.020816653722E-01
Surface tension*area energy for atom 4: 1.924692757655E-01
Total surface tension energy: 0.896066 kJ/mol
Total solvent accessible volume: 95.985 A^3
Total pressure*volume energy: 22.9788 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -8.133807570805E+00
WCA energy for atom 1: -1.962181541765E+00
WCA energy for atom 2: -1.964078319162E+00
WCA energy for atom 3: -1.963015006647E+00
WCA energy for atom 4: -1.957425549100E+00
Total WCA energy: -15.9805 kJ/mol
Total non-polar energy = 7.894367190329E+00 kJ/mol
----------------------------------------
CALCULATION #9 (solvated-neopentane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 2.441701074100E+00
SASA for atom 1: 1.663993494942E+01
SASA for atom 2: 1.715586152630E+01
SASA for atom 3: 1.645753666466E+01
SASA for atom 4: 0.000000000000E+00
SASA for atom 5: 2.389432243768E+00
SASA for atom 6: 1.638457735076E+01
SASA for atom 7: 1.667641460637E+01
SASA for atom 8: 1.721839808108E+01
SASA for atom 9: 2.419300146815E+00
SASA for atom 10: 1.640021148945E+01
SASA for atom 11: 1.666599184724E+01
SASA for atom 12: 1.719234118325E+01
SASA for atom 13: 2.449168049862E+00
SASA for atom 14: 1.723403221977E+01
SASA for atom 15: 1.639500010989E+01
SASA for atom 16: 1.663472356985E+01
Total solvent accessible surface area: 210.755 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 2.075445912985E-02
Surface tension*area energy for atom 1: 1.414394470700E-01
Surface tension*area energy for atom 2: 1.458248229736E-01
Surface tension*area energy for atom 3: 1.398890616496E-01
Surface tension*area energy for atom 4: 0.000000000000E+00
Surface tension*area energy for atom 5: 2.031017407203E-02
Surface tension*area energy for atom 6: 1.392689074814E-01
Surface tension*area energy for atom 7: 1.417495241541E-01
Surface tension*area energy for atom 8: 1.463563836891E-01
Surface tension*area energy for atom 9: 2.056405124793E-02
Surface tension*area energy for atom 10: 1.394017976603E-01
Surface tension*area energy for atom 11: 1.416609307015E-01
Surface tension*area energy for atom 12: 1.461349000577E-01
Surface tension*area energy for atom 13: 2.081792842383E-02
Surface tension*area energy for atom 14: 1.464892738680E-01
Surface tension*area energy for atom 15: 1.393575009340E-01
Surface tension*area energy for atom 16: 1.413951503437E-01
Total surface tension energy: 1.79141 kJ/mol
Total solvent accessible volume: 251.127 A^3
Total pressure*volume energy: 60.1198 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.011082520236E+00
WCA energy for atom 1: -1.497367782613E+00
WCA energy for atom 2: -1.498546483218E+00
WCA energy for atom 3: -1.492562171495E+00
WCA energy for atom 4: -5.447325863939E+00
WCA energy for atom 5: -6.004516149175E+00
WCA energy for atom 6: -1.492776531092E+00
WCA energy for atom 7: -1.496078170066E+00
WCA energy for atom 8: -1.501529655270E+00
WCA energy for atom 9: -5.996267554365E+00
WCA energy for atom 10: -1.492194267752E+00
WCA energy for atom 11: -1.496027211216E+00
WCA energy for atom 12: -1.500561393960E+00
WCA energy for atom 13: -6.000218612907E+00
WCA energy for atom 14: -1.500859921426E+00
WCA energy for atom 15: -1.492908499790E+00
WCA energy for atom 16: -1.494057174414E+00
Total WCA energy: -47.4149 kJ/mol
Total non-polar energy = 1.449633815052E+01 kJ/mol
----------------------------------------
CALCULATION #10 (solvated-pentane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 4.405515699447E+00
SASA for atom 1: 8.213673337951E-01
SASA for atom 2: 3.285469335181E-01
SASA for atom 3: 7.466975761774E-01
SASA for atom 4: 1.855251124959E+01
SASA for atom 5: 2.147609518526E+01
SASA for atom 6: 1.852645435176E+01
SASA for atom 7: 1.655655287639E+01
SASA for atom 8: 1.655134149682E+01
SASA for atom 9: 1.360170066332E+01
SASA for atom 10: 1.357043238593E+01
SASA for atom 11: 1.685881289113E+01
SASA for atom 12: 1.687444702982E+01
SASA for atom 13: 4.196440378117E+00
SASA for atom 14: 1.881308022781E+01
SASA for atom 15: 1.882350298694E+01
SASA for atom 16: 2.182004623652E+01
Total solvent accessible surface area: 222.524 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 3.744688344530E-02
Surface tension*area energy for atom 1: 6.981622337259E-03
Surface tension*area energy for atom 2: 2.792648934903E-03
Surface tension*area energy for atom 3: 6.346929397508E-03
Surface tension*area energy for atom 4: 1.576963456215E-01
Surface tension*area energy for atom 5: 1.825468090747E-01
Surface tension*area energy for atom 6: 1.574748619900E-01
Surface tension*area energy for atom 7: 1.407306994493E-01
Surface tension*area energy for atom 8: 1.406864027230E-01
Surface tension*area energy for atom 9: 1.156144556382E-01
Surface tension*area energy for atom 10: 1.153486752804E-01
Surface tension*area energy for atom 11: 1.432999095746E-01
Surface tension*area energy for atom 12: 1.434327997535E-01
Surface tension*area energy for atom 13: 3.566974321399E-02
Surface tension*area energy for atom 14: 1.599111819364E-01
Surface tension*area energy for atom 15: 1.599997753890E-01
Surface tension*area energy for atom 16: 1.854703930104E-01
Total surface tension energy: 1.89145 kJ/mol
Total solvent accessible volume: 258.93 A^3
Total pressure*volume energy: 61.9878 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.655804319869E+00
WCA energy for atom 1: -6.027315962813E+00
WCA energy for atom 2: -5.696430965386E+00
WCA energy for atom 3: -6.016749084714E+00
WCA energy for atom 4: -1.608595384643E+00
WCA energy for atom 5: -1.703300955380E+00
WCA energy for atom 6: -1.609931495887E+00
WCA energy for atom 7: -1.457107525189E+00
WCA energy for atom 8: -1.457741620594E+00
WCA energy for atom 9: -1.354235498709E+00
WCA energy for atom 10: -1.354106470090E+00
WCA energy for atom 11: -1.456736412636E+00
WCA energy for atom 12: -1.455995435596E+00
WCA energy for atom 13: -6.633650611186E+00
WCA energy for atom 14: -1.605996088477E+00
WCA energy for atom 15: -1.606549890103E+00
WCA energy for atom 16: -1.700042300035E+00
Total WCA energy: -49.4003 kJ/mol
Total non-polar energy = 1.447900211546E+01 kJ/mol
----------------------------------------
CALCULATION #11 (solvated-propane): APOLAR
Solvent Accessible Surface Area (SASA) for each atom:
SASA for atom 0: 3.173464698754E+00
SASA for atom 1: 1.931858404557E+01
SASA for atom 2: 2.014198201675E+01
SASA for atom 3: 2.149694070352E+01
SASA for atom 4: 1.904078819252E+00
SASA for atom 5: 2.067354273233E+01
SASA for atom 6: 1.937590922077E+01
SASA for atom 7: 3.098794941136E+00
SASA for atom 8: 1.942802301642E+01
SASA for atom 9: 1.973028303116E+01
SASA for atom 10: 2.204934693736E+01
Total solvent accessible surface area: 170.391 A^2
Surface tension*area energies (gamma * SASA) for each atom:
Surface tension*area energy for atom 0: 2.697444993941E-02
Surface tension*area energy for atom 1: 1.642079643873E-01
Surface tension*area energy for atom 2: 1.712068471424E-01
Surface tension*area energy for atom 3: 1.827239959799E-01
Surface tension*area energy for atom 4: 1.618466996365E-02
Surface tension*area energy for atom 5: 1.757251132248E-01
Surface tension*area energy for atom 6: 1.646952283766E-01
Surface tension*area energy for atom 7: 2.633975699966E-02
Surface tension*area energy for atom 8: 1.651381956396E-01
Surface tension*area energy for atom 9: 1.677074057649E-01
Surface tension*area energy for atom 10: 1.874194489675E-01
Total surface tension energy: 1.44832 kJ/mol
Total solvent accessible volume: 183.573 A^3
Total pressure*volume energy: 43.9474 kJ/mol
WCA dispersion Energies for each atom:
WCA energy for atom 0: -6.818670105515E+00
WCA energy for atom 1: -1.641297645338E+00
WCA energy for atom 2: -1.649584120441E+00
WCA energy for atom 3: -1.711408141255E+00
WCA energy for atom 4: -6.624720142882E+00
WCA energy for atom 5: -1.610117050515E+00
WCA energy for atom 6: -1.596858009746E+00
WCA energy for atom 7: -6.816460624835E+00
WCA energy for atom 8: -1.642782751806E+00
WCA energy for atom 9: -1.645779566650E+00
WCA energy for atom 10: -1.714436154542E+00
Total WCA energy: -33.4721 kJ/mol
Total non-polar energy = 1.192358496286E+01 kJ/mol
----------------------------------------
PRINT STATEMENTS
print APOL energy 1 (solvated-2-methylbutane) end
Global net APOL energy = 1.439739455792E+01 kJ/mol
print APOL energy 2 (solvated-butane) end
Global net APOL energy = 1.208346456826E+01 kJ/mol
print APOL energy 3 (solvated-cyclohexane) end
Global net APOL energy = 1.354016672221E+01 kJ/mol
print APOL energy 4 (solvated-cyclopentane) end
Global net APOL energy = 9.363673200142E+00 kJ/mol
print APOL energy 5 (solvated-ethane) end
Global net APOL energy = 9.422717598546E+00 kJ/mol
print APOL energy 6 (solvated-hexane) end
Global net APOL energy = 1.640068943201E+01 kJ/mol
print APOL energy 7 (solvated-isobutane) end
Global net APOL energy = 1.323144287435E+01 kJ/mol
print APOL energy 8 (solvated-methane) end
Global net APOL energy = 7.894367190329E+00 kJ/mol
print APOL energy 9 (solvated-neopentane) end
Global net APOL energy = 1.449633815052E+01 kJ/mol
print APOL energy 10 (solvated-pentane) end
Global net APOL energy = 1.447900211546E+01 kJ/mol
print APOL energy 11 (solvated-propane) end
Global net APOL energy = 1.192358496286E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 11 molecules
Final memory usage: 0.001 MB total, 2.267 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01)
*** PASSED ***
Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01)
*** PASSED ***
Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01)
*** PASSED ***
Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00)
*** PASSED ***
Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00)
*** PASSED ***
Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01)
*** PASSED ***
Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01)
*** PASSED ***
Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00)
*** PASSED ***
Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01)
*** PASSED ***
Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01)
*** PASSED ***
Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01)
*** PASSED ***
Elapsed time: 10.144193 seconds
--------------------------------------------------------------------------------
Total elapsed time: 10.144193 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: 1d7h-dmso-mol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file 1d7h-dmso-mol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from 1d7h-dmso-complex.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1673 atoms
Centered at (2.587e+01, 1.835e+01, 1.911e+01)
Net charge 9.91e-01 e
Reading PQR-format atom data from dmso-min.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
10 atoms
Centered at (1.775e+01, 1.777e+01, 2.049e+01)
Net charge 2.78e-17 e
Reading PQR-format atom data from 1d7h-min.pqr.
1663 atoms
Centered at (2.587e+01, 1.835e+01, 1.911e+01)
Net charge 9.91e-01 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (complex-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.059 MB total, 122.059 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.060899690259E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #2 (complex-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.059 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.276523673491E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.059 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.399234956777E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (complex-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.059 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.610066575192E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (dmso-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.961107503213E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (dmso-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 7.121048606059E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (dmso-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.751571424823E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #8 (dmso-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 7.339101343121E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #9 (1d7h-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.058410584089E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #10 (1d7h-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.205385249581E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #11 (1d7h-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.395961902233E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #12 (1d7h-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.538248433997E+04 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
Local net energy (PE 0) = -3.335429017008E+03 kJ/mol
Global net ELEC energy = -3.335429017008E+03 kJ/mol
print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end
Local net energy (PE 0) = -2.180527370616E+01 kJ/mol
Global net ELEC energy = -2.180527370616E+01 kJ/mol
print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end
Local net energy (PE 0) = -3.328631844166E+03 kJ/mol
Global net ELEC energy = -3.328631844166E+03 kJ/mol
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end
Local net energy (PE 0) = 1.500810086373E+01 kJ/mol
Global net ELEC energy = 1.500810086373E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 221.696 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04)
*** PASSED ***
Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04)
*** PASSED ***
Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04)
*** PASSED ***
Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04)
*** PASSED ***
Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01)
*** PASSED ***
Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02)
*** PASSED ***
Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01)
*** PASSED ***
Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02)
*** PASSED ***
Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04)
*** PASSED ***
Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04)
*** PASSED ***
Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04)
*** PASSED ***
Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04)
*** PASSED ***
Testing computed result against expected result (1.500810086373e+01, 1.500810086371e+01)
*** PASSED ***
Elapsed time: 9.153531 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, 15.00810086373]
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 15.00810086373
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: 1d7h-dmso-smol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file 1d7h-dmso-smol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from 1d7h-dmso-complex.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1673 atoms
Centered at (2.587e+01, 1.835e+01, 1.911e+01)
Net charge 9.91e-01 e
Reading PQR-format atom data from dmso-min.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
10 atoms
Centered at (1.775e+01, 1.777e+01, 2.049e+01)
Net charge 2.78e-17 e
Reading PQR-format atom data from 1d7h-min.pqr.
1663 atoms
Centered at (2.587e+01, 1.835e+01, 1.911e+01)
Net charge 9.91e-01 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (complex-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.059 MB total, 122.059 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.074948704824E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #2 (complex-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.059 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.289487256481E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.059 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.399234956777E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (complex-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.059 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.610066575192E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (dmso-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.719709905887E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (dmso-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 7.125747080979E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (dmso-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.751571424823E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #8 (dmso-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.428 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 7.339101343121E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #9 (1d7h-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.071654753674E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #10 (1d7h-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.218178203716E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #11 (1d7h-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.875, 18.349, 19.112)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.395961902233E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #12 (1d7h-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.736 MB total, 221.696 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.751, 17.770, 20.492)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.538248433997E+04 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
Local net energy (PE 0) = -3.205793187109E+03 kJ/mol
Global net ELEC energy = -3.205793187109E+03 kJ/mol
print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end
Local net energy (PE 0) = -2.133542621421E+01 kJ/mol
Global net ELEC energy = -2.133542621421E+01 kJ/mol
print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end
Local net energy (PE 0) = -3.200702302816E+03 kJ/mol
Global net ELEC energy = -3.200702302816E+03 kJ/mol
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end
Local net energy (PE 0) = 1.624454192074E+01 kJ/mol
Global net ELEC energy = 1.624454192074E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 221.696 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04)
*** PASSED ***
Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04)
*** PASSED ***
Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04)
*** PASSED ***
Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04)
*** PASSED ***
Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01)
*** PASSED ***
Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02)
*** PASSED ***
Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01)
*** PASSED ***
Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02)
*** PASSED ***
Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04)
*** PASSED ***
Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04)
*** PASSED ***
Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04)
*** PASSED ***
Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04)
*** PASSED ***
Testing computed result against expected result (1.624454192074e+01, 1.624454192072e+01)
*** PASSED ***
Elapsed time: 7.915477 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, 16.24454192074]
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 16.24454192074
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: 1d7i-dss-mol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file 1d7i-dss-mol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from 1d7i-dss-complex.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1677 atoms
Centered at (2.526e+01, 1.899e+01, 1.912e+01)
Net charge 9.91e-01 e
Reading PQR-format atom data from dss-min.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
14 atoms
Centered at (1.734e+01, 1.921e+01, 2.050e+01)
Net charge -8.33e-17 e
Reading PQR-format atom data from 1d7i-min.pqr.
1663 atoms
Centered at (2.526e+01, 1.899e+01, 1.912e+01)
Net charge 9.91e-01 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (complex-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.425 MB total, 122.425 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.160578033846E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #2 (complex-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.425 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.955701871716E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.425 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.264965939588E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (complex-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.425 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.301801664829E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (dss-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.431133325426E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (dss-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.677348113184E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (dss-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.171079106781E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #8 (dss-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.697869784185E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #9 (1d7i-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.040108332204E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #10 (1d7i-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.787747796627E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #11 (1d7i-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.252495566243E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #12 (1d7i-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.133237922574E+04 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
Local net energy (PE 0) = -3.460997931137E+03 kJ/mol
Global net ELEC energy = -3.460997931137E+03 kJ/mol
print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end
Local net energy (PE 0) = -2.052167100108E+01 kJ/mol
Global net ELEC energy = -2.052167100108E+01 kJ/mol
print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end
Local net energy (PE 0) = -3.454901259473E+03 kJ/mol
Global net ELEC energy = -3.454901259473E+03 kJ/mol
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end
Local net energy (PE 0) = 1.442499933664E+01 kJ/mol
Global net ELEC energy = 1.442499933664E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 222.305 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03)
*** PASSED ***
Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04)
*** PASSED ***
Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04)
*** PASSED ***
Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04)
*** PASSED ***
Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01)
*** PASSED ***
Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03)
*** PASSED ***
Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02)
*** PASSED ***
Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03)
*** PASSED ***
Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03)
*** PASSED ***
Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04)
*** PASSED ***
Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04)
*** PASSED ***
Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04)
*** PASSED ***
Testing computed result against expected result (1.442499933664e+01, 1.442500529301e+01)
*** PASSED ***
Elapsed time: 8.980205 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, 14.42499933664]
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 14.42499933664
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: 1d7i-dss-smol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file 1d7i-dss-smol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from 1d7i-dss-complex.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1677 atoms
Centered at (2.526e+01, 1.899e+01, 1.912e+01)
Net charge 9.91e-01 e
Reading PQR-format atom data from dss-min.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
14 atoms
Centered at (1.734e+01, 1.921e+01, 2.050e+01)
Net charge -8.33e-17 e
Reading PQR-format atom data from 1d7i-min.pqr.
1663 atoms
Centered at (2.526e+01, 1.899e+01, 1.912e+01)
Net charge 9.91e-01 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (complex-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.425 MB total, 122.425 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.634884642408E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #2 (complex-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 122.425 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.003177540425E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.425 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.264965939588E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (complex-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 122.425 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.301801664829E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (dss-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 7.942232645345E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (dss-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.677798535473E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (dss-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.171079106781E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #8 (dss-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 62.528 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.697869784185E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #9 (1d7i-solv-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.507068451372E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #10 (1d7i-solv-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 30.4176 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.835075772299E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #11 (1d7i-ref-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (25.264, 18.988, 19.122)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.252495566243E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #12 (1d7i-ref-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 4.87072 A
Current memory usage: 121.977 MB total, 222.305 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (17.340, 19.211, 20.503)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.010 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.010 M concentration
2.000 A-radius, -1.000 e-charge, 0.010 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.133237922574E+04 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end
Local net energy (PE 0) = -2.986241244040E+03 kJ/mol
Global net ELEC energy = -2.986241244040E+03 kJ/mol
print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end
Local net energy (PE 0) = -2.007124871262E+01 kJ/mol
Global net ELEC energy = -2.007124871262E+01 kJ/mol
print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end
Local net energy (PE 0) = -2.981621502756E+03 kJ/mol
Global net ELEC energy = -2.981621502756E+03 kJ/mol
print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end
Local net energy (PE 0) = 1.545150742843E+01 kJ/mol
Global net ELEC energy = 1.545150742843E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 222.305 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03)
*** PASSED ***
Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04)
*** PASSED ***
Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04)
*** PASSED ***
Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04)
*** PASSED ***
Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01)
*** PASSED ***
Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03)
*** PASSED ***
Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02)
*** PASSED ***
Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03)
*** PASSED ***
Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03)
*** PASSED ***
Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04)
*** PASSED ***
Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04)
*** PASSED ***
Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04)
*** PASSED ***
Testing computed result against expected result (1.545150742843e+01, 1.545150009785e+01)
*** PASSED ***
Elapsed time: 7.877545 seconds
--------------------------------------------------------------------------------
Total elapsed time: 33.926758 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, 15.45150742843]
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 15.45150742843
Running tests for hca-bind section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from acet.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
18 atoms
Centered at (-6.028e+00, 3.898e+00, 1.518e+01)
Net charge -1.00e+00 e
Reading PQR-format atom data from hca.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
2482 atoms
Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
Net charge 1.00e+00 e
Reading PQR-format atom data from complex.pqr.
2500 atoms
Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
Net charge -1.02e-14 e
Preparing to run 9 PBE calculations.
----------------------------------------
CALCULATION #1 (acet): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 62.727 MB total, 62.727 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.213600726771E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (acet): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 62.727 MB total, 123.701 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.581 x 0.581 x 0.581
Grid lengths: 37.181 x 37.181 x 37.181
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.825764811255E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (acet): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 62.727 MB total, 123.701 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.458471211905E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (hca): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.516 MB total, 146.516 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.093606095527E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #5 (hca): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.516 MB total, 245.092 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.581 x 0.581 x 0.581
Grid lengths: 37.181 x 37.181 x 37.181
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.515433544464E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (hca): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.516 MB total, 245.092 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.786369323561E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.926 MB total, 245.092 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.105322784838E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #8 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.926 MB total, 245.725 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.581 x 0.581 x 0.581
Grid lengths: 37.181 x 37.181 x 37.181
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.533304996252E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #9 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.926 MB total, 245.725 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.850429388099E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 1 (acet) - 2 (hca) end
Local net energy (PE 0) = -5.246475812684E+01 kJ/mol
Global net ELEC energy = -5.246475812684E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 245.725 MB high water
Thanks for using APBS!
Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02)
*** PASSED ***
Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03)
*** PASSED ***
Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03)
*** PASSED ***
Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04)
*** PASSED ***
Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05)
*** PASSED ***
Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05)
*** PASSED ***
Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04)
*** PASSED ***
Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05)
*** PASSED ***
Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05)
*** PASSED ***
Testing computed result against expected result (-5.246475812684e+01, -5.246475812665e+01)
*** PASSED ***
Elapsed time: 7.924429 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, -52.46475812684]
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 -52.46475812684
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from acet.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
18 atoms
Centered at (-6.028e+00, 3.898e+00, 1.518e+01)
Net charge -1.00e+00 e
Reading PQR-format atom data from hca.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
2482 atoms
Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
Net charge 1.00e+00 e
Reading PQR-format atom data from complex.pqr.
2500 atoms
Centered at (-7.196e+00, 4.070e-01, 1.704e+01)
Net charge -1.02e-14 e
Preparing to run 9 PBE calculations.
----------------------------------------
CALCULATION #1 (acet): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 62.727 MB total, 62.727 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.884888131017E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (acet): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 62.727 MB total, 123.701 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.581 x 0.581 x 0.581
Grid lengths: 37.181 x 37.181 x 37.181
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.820045922544E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (acet): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 62.727 MB total, 123.701 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.460002606908E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (hca): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.516 MB total, 146.516 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.189161497021E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #5 (hca): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.516 MB total, 245.092 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.581 x 0.581 x 0.581
Grid lengths: 37.181 x 37.181 x 37.181
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.520000494925E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (hca): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.516 MB total, 245.092 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.790436191580E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.926 MB total, 245.092 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 1.500 x 1.500 x 1.500
Grid lengths: 96.000 x 96.000 x 96.000
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.195842512312E+04 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #8 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.926 MB total, 245.725 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.581 x 0.581 x 0.581
Grid lengths: 37.181 x 37.181 x 37.181
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.537771604355E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #9 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 146.926 MB total, 245.725 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.225 x 0.225 x 0.225
Grid lengths: 14.400 x 14.400 x 14.400
Grid center: (-6.028, 3.898, 15.179)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.854495619747E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 1 (acet) - 2 (hca) end
Local net energy (PE 0) = -5.405979017059E+01 kJ/mol
Global net ELEC energy = -5.405979017059E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 245.725 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02)
*** PASSED ***
Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03)
*** PASSED ***
Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03)
*** PASSED ***
Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04)
*** PASSED ***
Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05)
*** PASSED ***
Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05)
*** PASSED ***
Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04)
*** PASSED ***
Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05)
*** PASSED ***
Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05)
*** PASSED ***
Testing computed result against expected result (-5.405979017059e+01, -5.405977880082e+01)
*** PASSED ***
Elapsed time: 6.9116610000000005 seconds
--------------------------------------------------------------------------------
Total elapsed time: 14.83609 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, -54.05979017059]
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 -54.05979017059
Running tests for ionize section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from acetic-acid.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
8 atoms
Centered at (0.000e+00, -1.535e-01, 1.287e+00)
Net charge -1.67e-16 e
Reading PQR-format atom data from acetate.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
8 atoms
Centered at (0.000e+00, -1.535e-01, 1.287e+00)
Net charge -1.00e+00 e
Reading PQR-format atom data from proton.pqr.
1 atoms
Centered at (1.780e-01, -1.286e+00, 2.937e+00)
Net charge 1.00e+00 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (acetic-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 61.598 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 5.823898055191E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (acetic-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.793274462353E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (acetic-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 5.846917564309E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (acetic-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.815953282539E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (acetate-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.219846763777E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (acetate-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.392741988698E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (acetate-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.420373979905E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #8 (acetate-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.412716615065E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #9 (proton-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.412 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.862359524598E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #10 (proton-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.412 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.288156251610E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #11 (proton-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.373 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.162533113906E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #12 (proton-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.373 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.585616091973E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (acetic-solv) - 2 (acetic-ref) end
Local net energy (PE 0) = -2.267882018629E+01 kJ/mol
Global net ELEC energy = -2.267882018629E+01 kJ/mol
print energy 3 (acetate-solv) - 4 (acetate-ref) end
Local net energy (PE 0) = -1.997462636633E+02 kJ/mol
Global net ELEC energy = -1.997462636633E+02 kJ/mol
print energy 5 (proton-solv) - 6 (proton-ref) end
Local net energy (PE 0) = -2.974598403628E+02 kJ/mol
Global net ELEC energy = -2.974598403628E+02 kJ/mol
print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end
Local net energy (PE 0) = -4.745272838398E+02 kJ/mol
Global net ELEC energy = -4.745272838398E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 122.404 MB high water
Thanks for using APBS!
Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03)
*** PASSED ***
Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03)
*** PASSED ***
Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03)
*** PASSED ***
Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03)
*** PASSED ***
Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03)
*** PASSED ***
Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04)
*** PASSED ***
Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03)
*** PASSED ***
Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04)
*** PASSED ***
Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03)
*** PASSED ***
Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03)
*** PASSED ***
Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03)
*** PASSED ***
Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03)
*** PASSED ***
Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01)
*** PASSED ***
Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02)
*** PASSED ***
Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02)
*** PASSED ***
Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02)
*** PASSED ***
Elapsed time: 3.211452 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from acetic-acid.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
8 atoms
Centered at (0.000e+00, -1.535e-01, 1.287e+00)
Net charge -1.67e-16 e
Reading PQR-format atom data from acetate.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
8 atoms
Centered at (0.000e+00, -1.535e-01, 1.287e+00)
Net charge -1.00e+00 e
Reading PQR-format atom data from proton.pqr.
1 atoms
Centered at (1.780e-01, -1.286e+00, 2.937e+00)
Net charge 1.00e+00 e
Preparing to run 12 PBE calculations.
----------------------------------------
CALCULATION #1 (acetic-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 61.598 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 5.824172730822E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (acetic-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.793622759239E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (acetic-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 5.846917564309E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (acetic-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.815953282539E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (acetate-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.221328580569E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (acetate-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.598 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.392867783119E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #7 (acetate-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.420373979905E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #8 (acetate-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.422 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.412716615065E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #9 (proton-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.412 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.863066835285E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #10 (proton-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 7.76163 A
Current memory usage: 61.412 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.150 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.150 M concentration
2.000 A-radius, -1.000 e-charge, 0.150 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.289649216644E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #11 (proton-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.373 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.188 x 0.188 x 0.188
Grid lengths: 12.000 x 12.000 x 12.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 4.162533113906E+03 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #12 (proton-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.373 MB total, 122.404 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.094 x 0.094 x 0.094
Grid lengths: 6.000 x 6.000 x 6.000
Grid center: (0.000, -0.154, 1.287)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 2.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 293.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 6.585616091973E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (acetic-solv) - 2 (acetic-ref) end
Local net energy (PE 0) = -2.233052329981E+01 kJ/mol
Global net ELEC energy = -2.233052329981E+01 kJ/mol
print energy 3 (acetate-solv) - 4 (acetate-ref) end
Local net energy (PE 0) = -1.984883194538E+02 kJ/mol
Global net ELEC energy = -1.984883194538E+02 kJ/mol
print energy 5 (proton-solv) - 6 (proton-ref) end
Local net energy (PE 0) = -2.959668753288E+02 kJ/mol
Global net ELEC energy = -2.959668753288E+02 kJ/mol
print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end
Local net energy (PE 0) = -4.721246714828E+02 kJ/mol
Global net ELEC energy = -4.721246714828E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 122.404 MB high water
Thanks for using APBS!
Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03)
*** PASSED ***
Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03)
*** PASSED ***
Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03)
*** PASSED ***
Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03)
*** PASSED ***
Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03)
*** PASSED ***
Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04)
*** PASSED ***
Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03)
*** PASSED ***
Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04)
*** PASSED ***
Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03)
*** PASSED ***
Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03)
*** PASSED ***
Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03)
*** PASSED ***
Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03)
*** PASSED ***
Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01)
*** PASSED ***
Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02)
*** PASSED ***
Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02)
*** PASSED ***
Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02)
*** PASSED ***
Elapsed time: 2.741475 seconds
--------------------------------------------------------------------------------
Total elapsed time: 5.952927 seconds
Test results have been logged
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file ion-pmf.in
Checking for intermediate energies in input file apbs-smol.out
EXPECTED COMPUTED: 16
EXPECTED EXPECTED: 16
COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828]
EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02']
COMPUTED RESULT 5824.172730822
COMPUTED RESULT 9793.622759239
COMPUTED RESULT 5846.917564309
COMPUTED RESULT 9815.953282539
COMPUTED RESULT 8221.328580569
COMPUTED RESULT 13928.67783119
COMPUTED RESULT 8420.373979905
COMPUTED RESULT 14127.16615065
COMPUTED RESULT 3863.066835285
COMPUTED RESULT 6289.649216644
COMPUTED RESULT 4162.533113906
COMPUTED RESULT 6585.616091973
COMPUTED RESULT -22.33052329981
COMPUTED RESULT -198.4883194538
COMPUTED RESULT -295.9668753288
COMPUTED RESULT -472.1246714828
Running tests for ion-pmf section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: ion-pmf.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file ion-pmf.in...
rank 0 size 1...
Parsed input file.
Reading parameter data from parm.dat.
Got paths for 1 molecules
Reading PDB-format atom data from ion-pmf.pdb.
Vpmg_ibForce: No force for zero ionic strength!
Vpmg_ibForce: No force for zero ionic strength!
2 atoms
Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
Net charge 2.00e+00 e
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.106 MB total, 61.106 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
All-atom solvent forces will be calculated
Total electrostatic energy = 7.839535983197E+03 kJ/mol
Calculating forces...
Printing per-atom forces for molecule 1 (kJ/mol/A)
Legend:
tot n -- total force for atom n
qf n -- fixed charge force for atom n
db n -- dielectric boundary force for atom n
ib n -- ionic boundary force for atom n
mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05
mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05
mgF ib 0 0.000e+00 0.000e+00 0.000e+00
mgF db 0 6.148e+00 -2.668e-05 -5.379e-05
mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04
mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05
mgF ib 1 0.000e+00 0.000e+00 0.000e+00
mgF db 1 2.883e+00 -3.150e-05 -6.291e-05
Vpmg_ibForce: No force for zero ionic strength!
Vpmg_ibForce: No force for zero ionic strength!
----------------------------------------
CALCULATION #2 (ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.106 MB total, 61.155 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 1.000
Solvent dielectric: 1.000
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
All-atom solvent forces will be calculated
Total electrostatic energy = 8.964727588811E+03 kJ/mol
Calculating forces...
Printing per-atom forces for molecule 1 (kJ/mol/A)
Legend:
tot n -- total force for atom n
qf n -- fixed charge force for atom n
db n -- dielectric boundary force for atom n
ib n -- ionic boundary force for atom n
mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06
mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06
mgF ib 0 0.000e+00 0.000e+00 0.000e+00
mgF db 0 0.000e+00 0.000e+00 0.000e+00
mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06
mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06
mgF ib 1 0.000e+00 0.000e+00 0.000e+00
mgF db 1 0.000e+00 0.000e+00 0.000e+00
----------------------------------------
CALCULATION #3 (asolv): APOLAR
Printing per atom forces (kJ/mol/A)
Legend:
tot n -- Total force for atom n
sasa n -- SASA force for atom n
sav n -- SAV force for atom n
wca n -- WCA force for atom n
gamma 0.000720
pressure 0.000000
bconc 0.033000
tot 0 2.715e-02 9.130e-07 9.128e-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 -2.767e-05 -2.766e-05
tot 1 -2.723e-02 9.131e-07 9.134e-07
sasa 1 1.112e+01 0.000e+00 0.000e+00
sav 1 0.000e+00 0.000e+00 0.000e+00
wca 1 5.827e-01 -2.767e-05 -2.768e-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: -6.909718345777E+00
WCA energy for atom 1: -6.909411348230E+00
Total WCA energy: -13.8191 kJ/mol
Total non-polar energy = -1.365306965532E+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 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05
ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05
tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05
qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05
ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05
tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05
tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04
print APOL energy 1 (asolv) end
Global net APOL energy = -1.365306965532E+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 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05
tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-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 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05
tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05
tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 1 molecules
Final memory usage: 60.711 MB total, 62.250 MB high water
Thanks for using APBS!
Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03)
*** PASSED ***
Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03)
*** PASSED ***
Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03)
*** PASSED ***
Elapsed time: 6.2396139999999995 seconds
--------------------------------------------------------------------------------
Total elapsed time: 6.2396139999999995 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, -13.65306965532]
EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*']
COMPUTED RESULT 7839.535983197
COMPUTED RESULT 8964.727588811
COMPUTED RESULT -1125.191605614
COMPUTED RESULT -13.65306965532
Running tests for pka-lig section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-vdw.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-vdw.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
47 atoms
Centered at (2.482e+01, -3.315e+01, 2.154e+01)
Net charge 1.11e-16 e
Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
3423 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
3470 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (lig-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 204.292 MB total, 204.292 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.224988750664E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (lig-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 204.292 MB total, 406.001 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.049695084686E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (pka-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 291.151 MB total, 406.001 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.818450789522E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (pka-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 291.151 MB total, 533.426 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.008254338259E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (complex-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 292.063 MB total, 533.426 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.840918409896E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (complex-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 292.063 MB total, 534.806 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.113304681884E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
Local net energy (PE 0) = 8.083515648803E+00 kJ/mol
Global net ELEC energy = 8.083515648803E+00 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 534.806 MB high water
Thanks for using APBS!
Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03)
*** PASSED ***
Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04)
*** PASSED ***
Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05)
*** PASSED ***
Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05)
*** PASSED ***
Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05)
*** PASSED ***
Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05)
*** PASSED ***
Testing computed result against expected result (8.083515648803e+00, 8.083515648730e+00)
*** PASSED ***
Elapsed time: 14.622565999999999 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, 8.083515648803]
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 8.083515648803
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-vdw.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-vdw.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
47 atoms
Centered at (2.482e+01, -3.315e+01, 2.154e+01)
Net charge 1.11e-16 e
Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
3423 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
3470 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (lig-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 204.292 MB total, 204.292 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.226793167046E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (lig-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 204.292 MB total, 406.001 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.050504485887E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (pka-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 291.151 MB total, 406.001 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.827976621645E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (pka-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 291.151 MB total, 533.426 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.017228546773E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (complex-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 292.063 MB total, 533.426 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.850819075387E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (complex-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 292.063 MB total, 534.806 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.122488625388E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
Local net energy (PE 0) = 2.096300255720E+01 kJ/mol
Global net ELEC energy = 2.096300255720E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 534.806 MB high water
Thanks for using APBS!
Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03)
*** PASSED ***
Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04)
*** PASSED ***
Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05)
*** PASSED ***
Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05)
*** PASSED ***
Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05)
*** PASSED ***
Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05)
*** PASSED ***
Testing computed result against expected result (2.096300255720e+01, 2.096296139195e+01)
*** PASSED ***
Elapsed time: 10.450363 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, 20.9630025572]
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 20.9630025572
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol-surf.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol-surf.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
47 atoms
Centered at (2.482e+01, -3.315e+01, 2.154e+01)
Net charge 1.11e-16 e
Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
3423 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
3470 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (lig-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 203.877 MB total, 203.877 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.244350164274E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (lig-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 203.877 MB total, 405.586 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.052149475373E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (pka-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.521 MB total, 405.586 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.862615690066E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (pka-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.521 MB total, 493.795 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.051810884053E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (complex-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.858 MB total, 493.795 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.886625455219E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (complex-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.858 MB total, 494.601 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.158218439277E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
Local net energy (PE 0) = 1.192607686582E+02 kJ/mol
Global net ELEC energy = 1.192607686582E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 494.601 MB high water
Thanks for using APBS!
Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03)
*** PASSED ***
Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04)
*** PASSED ***
Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05)
*** PASSED ***
Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05)
*** PASSED ***
Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05)
*** PASSED ***
Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05)
*** PASSED ***
Testing computed result against expected result (1.192607686582e+02, 1.192608095265e+02)
*** PASSED ***
Elapsed time: 11.459585 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, 119.2607686582]
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 119.2607686582
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol-surf.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol-surf.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from bx6_7_lig_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
47 atoms
Centered at (2.482e+01, -3.315e+01, 2.154e+01)
Net charge 1.11e-16 e
Reading PQR-format atom data from bx6_7_apo_apbs.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
3423 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Reading PQR-format atom data from bx6_7_bin_apbs.pqr.
3470 atoms
Centered at (2.897e+01, -3.251e+01, 2.702e+01)
Net charge 1.00e+00 e
Preparing to run 6 PBE calculations.
----------------------------------------
CALCULATION #1 (lig-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 203.877 MB total, 203.877 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.251466789420E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (lig-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 203.877 MB total, 405.586 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.052814502873E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (pka-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.521 MB total, 405.586 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.864071689626E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #4 (pka-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.521 MB total, 493.795 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 2
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.053319953673E+05 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #5 (complex-coarse): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.858 MB total, 493.795 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.729 x 0.729 x 0.729
Grid lengths: 70.000 x 70.000 x 70.000
Grid center: (28.969, -32.507, 27.022)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.888027142979E+05 kJ/mol
Calculating forces...
[focusFillBound()]: WARNING:
Unusually large potential values
detected on the focusing boundary!
Convergence not guaranteed for NPBE/NRPBE calculations!
----------------------------------------
CALCULATION #6 (complex-fine): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 251.858 MB total, 494.601 MB high water
Using linear spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 24.000 x 24.000 x 24.000
Grid center: (24.822, -33.153, 21.545)
Multigrid levels: 4
Molecule ID: 3
Linearized traditional PBE
Boundary conditions from focusing
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.159690177241E+05 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end
Local net energy (PE 0) = 1.088773280806E+02 kJ/mol
Global net ELEC energy = 1.088773280806E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 494.601 MB high water
Thanks for using APBS!
Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03)
*** PASSED ***
Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04)
*** PASSED ***
Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05)
*** PASSED ***
Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05)
*** PASSED ***
Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05)
*** PASSED ***
Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05)
*** PASSED ***
Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02)
*** PASSED ***
Elapsed time: 9.590712 seconds
--------------------------------------------------------------------------------
Total elapsed time: 46.123226 seconds
Test results have been logged
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Testing input file complex-0_1.in
Checking for intermediate energies in input file apbs-smol-surf.out
EXPECTED COMPUTED: 7
EXPECTED EXPECTED: 7
COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806]
EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02']
COMPUTED RESULT 2251.46678942
COMPUTED RESULT 10528.14502873
COMPUTED RESULT 186407.1689626
COMPUTED RESULT 305331.9953673
COMPUTED RESULT 188802.7142979
COMPUTED RESULT 315969.0177241
COMPUTED RESULT 108.8773280806
Running tests for point-pmf section
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: complex-0_1.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file complex-0_1.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mol0.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from mol1.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (-2.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from complex-0_1.pqr.
2 atoms
Centered at (-2.500e+00, 0.000e+00, 0.000e+00)
Net charge 2.00e+00 e
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (point1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.060 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.776035707281E+01 kJ/mol
Fixed charge energy = 97.7604 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 96.5336 kJ/mol
Per-atom energies:
Atom 0: 9.776035707281E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (point2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.067 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 8.975920687031E+01 kJ/mol
Fixed charge energy = 89.7592 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 88.6151 kJ/mol
Per-atom energies:
Atom 0: 8.975920687031E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.067 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.058277719334E+02 kJ/mol
Fixed charge energy = 205.828 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 201.106 kJ/mol
Per-atom energies:
Atom 0: 1.069144350786E+02 kJ/mol
Atom 1: 9.891333685475E+01 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 1 (point1) - 2 (point2) end
Local net energy (PE 0) = 1.830820799027E+01 kJ/mol
Global net ELEC energy = 1.830820799027E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 61.067 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
*** PASSED ***
Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01)
*** PASSED ***
Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02)
*** PASSED ***
Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
*** PASSED ***
Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01)
*** PASSED ***
Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02)
*** PASSED ***
Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
*** PASSED ***
Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01)
*** PASSED ***
Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02)
*** PASSED ***
Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01)
*** PASSED ***
Elapsed time: 0.65469 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: complex-0_2.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file complex-0_2.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mol0.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from mol2.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from complex-0_2.pqr.
2 atoms
Centered at (-2.000e+00, 0.000e+00, 0.000e+00)
Net charge 2.00e+00 e
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (point1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.060 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.776035707281E+01 kJ/mol
Fixed charge energy = 97.7604 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 96.5336 kJ/mol
Per-atom energies:
Atom 0: 9.776035707281E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (point2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.067 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.017611498797E+02 kJ/mol
Fixed charge energy = 101.761 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 100.656 kJ/mol
Per-atom energies:
Atom 0: 1.017611498797E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.068 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.084282010393E+02 kJ/mol
Fixed charge energy = 208.428 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 203.83 kJ/mol
Per-atom energies:
Atom 0: 1.022136878480E+02 kJ/mol
Atom 1: 1.062145131913E+02 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 1 (point1) - 2 (point2) end
Local net energy (PE 0) = 8.906694086751E+00 kJ/mol
Global net ELEC energy = 8.906694086751E+00 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 61.068 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
*** PASSED ***
Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02)
*** PASSED ***
Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02)
*** PASSED ***
Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
*** PASSED ***
Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02)
*** PASSED ***
Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02)
*** PASSED ***
Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
*** PASSED ***
Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02)
*** PASSED ***
Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02)
*** PASSED ***
Testing computed result against expected result (8.906694086751e+00, 8.906694086750e+00)
*** PASSED ***
Elapsed time: 0.706883 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, 8.906694086751]
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 8.906694086751
BINARY: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: complex-0_3.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file complex-0_3.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mol0.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from mol3.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (0.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from complex-0_3.pqr.
2 atoms
Centered at (-1.500e+00, 0.000e+00, 0.000e+00)
Net charge 2.00e+00 e
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (point1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.060 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.776035707281E+01 kJ/mol
Fixed charge energy = 97.7604 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 96.5336 kJ/mol
Per-atom energies:
Atom 0: 9.776035707281E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (point2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.067 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.337661883222E+02 kJ/mol
Fixed charge energy = 133.766 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 132.672 kJ/mol
Per-atom energies:
Atom 0: 1.337661883222E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.068 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.374361452120E+02 kJ/mol
Fixed charge energy = 237.436 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 232.924 kJ/mol
Per-atom energies:
Atom 0: 1.007151570480E+02 kJ/mol
Atom 1: 1.367209881640E+02 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 1 (point1) - 2 (point2) end
Local net energy (PE 0) = 5.909599816984E+00 kJ/mol
Global net ELEC energy = 5.909599816984E+00 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 61.068 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
*** PASSED ***
Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02)
*** PASSED ***
Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02)
*** PASSED ***
Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
*** PASSED ***
Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02)
*** PASSED ***
Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02)
*** PASSED ***
Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
*** PASSED ***
Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02)
*** PASSED ***
Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02)
*** PASSED ***
Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00)
*** PASSED ***
Elapsed time: 0.673134 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: complex-0_4.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file complex-0_4.in...
rank 0 size 1...
Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mol0.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (-3.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from mol4.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1 atoms
Centered at (1.000e+00, 0.000e+00, 0.000e+00)
Net charge 1.00e+00 e
Reading PQR-format atom data from complex-0_4.pqr.
2 atoms
Centered at (-1.000e+00, 0.000e+00, 0.000e+00)
Net charge 2.00e+00 e
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (point1): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.060 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 9.776035707281E+01 kJ/mol
Fixed charge energy = 97.7604 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 96.5336 kJ/mol
Per-atom energies:
Atom 0: 9.776035707281E+01 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (point2): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.060 MB total, 61.067 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.017611498797E+02 kJ/mol
Fixed charge energy = 101.761 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 100.654 kJ/mol
Per-atom energies:
Atom 0: 1.017611498797E+02 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (complex): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.061 MB total, 61.068 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.210 x 0.210 x 0.210
Grid lengths: 13.440 x 13.440 x 13.440
Grid center: (0.000, 0.000, 0.000)
Multigrid levels: 5
Molecule ID: 3
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 78.540
Solvent dielectric: 78.540
Using spline-based surface definition;window = 0.300
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.039516519000E+02 kJ/mol
Fixed charge energy = 203.952 kJ/mol
Mobile charge energy = 0 kJ/mol
Dielectric energy = 199.493 kJ/mol
Per-atom energies:
Atom 0: 9.997541697022E+01 kJ/mol
Atom 1: 1.039762349297E+02 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 3 (complex) - 1 (point1) - 2 (point2) end
Local net energy (PE 0) = 4.430144947418E+00 kJ/mol
Global net ELEC energy = 4.430144947418E+00 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 61.068 MB high water
Thanks for using APBS!
Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01)
*** PASSED ***
Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02)
*** PASSED ***
Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02)
*** PASSED ***
Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01)
*** PASSED ***
Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02)
*** PASSED ***
Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02)
*** PASSED ***
Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01)
*** PASSED ***
Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02)
*** PASSED ***
Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02)
*** PASSED ***
Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00)
*** PASSED ***
Elapsed time: 0.672674 seconds
--------------------------------------------------------------------------------
Total elapsed time: 2.707381 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-mol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-mol.in...
rank 0 size 1...
Parsed input file.
Got paths for 2 molecules
Reading PQR-format atom data from methanol.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
3 atoms
Centered at (3.086e-01, 0.000e+00, -2.417e-01)
Net charge 5.55e-17 e
Reading PQR-format atom data from methoxide.pqr.
2 atoms
Centered at (0.000e+00, 0.000e+00, -1.279e-01)
Net charge -1.00e+00 e
Preparing to run 4 PBE calculations.
----------------------------------------
CALCULATION #1 (methanol-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.253 MB total, 61.253 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.309, 0.000, -0.242)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.847663548071E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (methanol-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.253 MB total, 61.328 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.309, 0.000, -0.242)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.883912182952E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (methoxide-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.250 MB total, 61.328 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.000, 0.000, -0.128)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.732623683321E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (methoxide-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.250 MB total, 61.328 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.000, 0.000, -0.128)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.123035854133E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (methanol-solv) - 2 (methanol-ref) end
Local net energy (PE 0) = -3.624863488075E+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, 61.328 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03)
*** PASSED ***
Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03)
*** PASSED ***
Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03)
*** PASSED ***
Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03)
*** PASSED ***
Testing computed result against expected result (-3.624863488075e+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: 1.030249 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: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/apbs
INPUT: apbs-smol.in
COMMAND: ['/<<PKGBUILDDIR>>/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 <http://www.FEtk.ORG>.
----------------------------------------------------------------------
APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically.
Aqua is a modified form of the Holst group PMG library <http://www.FEtk.ORG>
which has been modified by Patrice Koehl
<http://koehllab.genomecenter.ucdavis.edu/> for improved efficiency and
memory usage when solving the Poisson-Boltzmann equation.
----------------------------------------------------------------------
Please cite your use of APBS as:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
nanosystems: application to microtubules and the ribosome. Proc.
Natl. Acad. Sci. USA 98, 10037-10041 2001.
This executable compiled on Oct 31 2024 at 13:24:17
Parsing input file apbs-smol.in...
rank 0 size 1...
Parsed input file.
Got paths for 2 molecules
Reading PQR-format atom data from methanol.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
3 atoms
Centered at (3.086e-01, 0.000e+00, -2.417e-01)
Net charge 5.55e-17 e
Reading PQR-format atom data from methoxide.pqr.
2 atoms
Centered at (0.000e+00, 0.000e+00, -1.279e-01)
Net charge -1.00e+00 e
Preparing to run 4 PBE calculations.
----------------------------------------
CALCULATION #1 (methanol-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.253 MB total, 61.253 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.309, 0.000, -0.242)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.847860440020E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #2 (methanol-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.253 MB total, 61.328 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.309, 0.000, -0.242)
Multigrid levels: 5
Molecule ID: 1
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 1.885436377745E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #3 (methoxide-solv): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.250 MB total, 61.328 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.000, 0.000, -0.128)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 78.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.734040568569E+03 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #4 (methoxide-ref): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 61.250 MB total, 61.328 MB high water
Using linear spline charge discretization.
Grid dimensions: 65 x 65 x 65
Grid spacings: 0.250 x 0.250 x 0.250
Grid lengths: 16.000 x 16.000 x 16.000
Grid center: (0.000, 0.000, -0.128)
Multigrid levels: 5
Molecule ID: 2
Linearized traditional PBE
Multiple Debye-Huckel sphere boundary conditions
2 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
Solute dielectric: 2.000
Solvent dielectric: 1.000
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 0.000 A
Temperature: 300.000 K
Electrostatic energies will be calculated
Total electrostatic energy = 3.125279428954E+03 kJ/mol
Calculating forces...
----------------------------------------
PRINT STATEMENTS
print energy 1 (methanol-solv) - 2 (methanol-ref) end
Local net energy (PE 0) = -3.757593772492E+01 kJ/mol
Global net ELEC energy = -3.757593772492E+01 kJ/mol
print energy 3 (methoxide-solv) - 4 (methoxide-ref) end
Local net energy (PE 0) = -3.912388603848E+02 kJ/mol
Global net ELEC energy = -3.912388603848E+02 kJ/mol
print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end
Local net energy (PE 0) = -3.536629226599E+02 kJ/mol
Global net ELEC energy = -3.536629226599E+02 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying finite element structures.
Destroying 2 molecules
Final memory usage: 0.001 MB total, 61.328 MB high water
Thanks for using APBS!
Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03)
*** PASSED ***
Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03)
*** PASSED ***
Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03)
*** PASSED ***
Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03)
*** PASSED ***
Testing computed result against expected result (-3.757593772492e+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: 0.960485 seconds
--------------------------------------------------------------------------------
Total elapsed time: 1.990734 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, -37.57593772492, -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 -37.57593772492
COMPUTED RESULT -391.2388603848
COMPUTED RESULT -353.6629226599
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for example in FKBP/1d7h-dmso/UHBD/pqr2qcd \
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for example in bem-pKa/test_proteins \
pbsam-barn_bars; \
do \
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done
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dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol were not linked against libamd.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol were not linked against libmpi.so.40 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol 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/similarity debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/dxmath debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2mol were not linked against libcholmod.so.5 (they use none of the library's symbols)
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
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 apbs: substitution variable ${sphinxdoc: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: 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 'libfetk-dev' in '../libfetk-dev_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'apbs' in '../apbs_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'python3-apbslib-dbgsym' in '../python3-apbslib-dbgsym_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'libapbs3t64-dbgsym' in '../libapbs3t64-dbgsym_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'apbs-dbgsym' in '../apbs-dbgsym_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'apbs-data' in '../apbs-data_3.4.1-6_all.deb'.
dpkg-deb: building package 'libfetk1.9t64' in '../libfetk1.9t64_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'libfetk1.9t64-dbgsym' in '../libfetk1.9t64-dbgsym_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'libapbs3t64' in '../libapbs3t64_3.4.1-6_arm64.deb'.
dpkg-deb: building package 'apbs-doc' in '../apbs-doc_3.4.1-6_all.deb'.
dpkg-genbuildinfo --build=binary -O../apbs_3.4.1-6_arm64.buildinfo
dpkg-genchanges --build=binary -O../apbs_3.4.1-6_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-11-15T19:02:33Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
apbs_3.4.1-6_arm64.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 arm64
Version: 3.4.1-6
Distribution: sid
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
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
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: apbs
Binary: apbs apbs-data apbs-dbgsym apbs-doc libapbs-dev libapbs3t64 libapbs3t64-dbgsym libfetk-dev libfetk1.9t64 libfetk1.9t64-dbgsym python3-apbslib python3-apbslib-dbgsym
Architecture: all arm64
Version: 3.4.1-6
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Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Fri, 15 Nov 2024 19:02:33 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
adduser (= 3.137),
autoconf (= 2.72-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.22.5-2),
autotools-dev (= 20220109.1),
base-files (= 13.5),
base-passwd (= 3.6.5),
bash (= 5.2.32-1+b2),
binutils (= 2.43.1-5),
binutils-aarch64-linux-gnu (= 2.43.1-5),
binutils-common (= 2.43.1-5),
bsdextrautils (= 2.40.2-11),
bsdutils (= 1:2.40.2-11),
build-essential (= 12.12),
bzip2 (= 1.0.8-6),
ca-certificates (= 20240203),
cmake (= 3.31.0-1),
cmake-data (= 3.31.0-1),
coreutils (= 9.5-1+b1),
cpp (= 4:14.2.0-1),
cpp-14 (= 14.2.0-8),
cpp-14-aarch64-linux-gnu (= 14.2.0-8),
cpp-aarch64-linux-gnu (= 4:14.2.0-1),
dash (= 0.5.12-9+b1),
debconf (= 1.5.87),
debhelper (= 13.20),
debianutils (= 5.20+b1),
dh-autoreconf (= 20),
dh-python (= 6.20241024),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1+b1),
docutils-common (= 0.21.2+dfsg-2),
dpkg (= 1.22.12~1.gbp82cafd),
dpkg-dev (= 1.22.12~1.gbp82cafd),
dwz (= 0.15-1+b1),
file (= 1:5.45-3+b1),
findutils (= 4.10.0-3),
fonts-font-awesome (= 5.0.10+really4.7.0~dfsg-4.1),
fonts-lato (= 2.015-1),
fonts-mathjax (= 2.7.9+dfsg-1),
g++ (= 4:14.2.0-1),
g++-14 (= 14.2.0-8),
g++-14-aarch64-linux-gnu (= 14.2.0-8),
g++-aarch64-linux-gnu (= 4:14.2.0-1),
gcc (= 4:14.2.0-1),
gcc-14 (= 14.2.0-8),
gcc-14-aarch64-linux-gnu (= 14.2.0-8),
gcc-14-base (= 14.2.0-8),
gcc-aarch64-linux-gnu (= 4:14.2.0-1),
gettext (= 0.22.5-2),
gettext-base (= 0.22.5-2),
gfortran-14 (= 14.2.0-8),
gfortran-14-aarch64-linux-gnu (= 14.2.0-8),
grep (= 3.11-4+b1),
groff-base (= 1.23.0-5),
gzip (= 1.12-1.1+b1),
hostname (= 3.25),
ibverbs-providers (= 52.0-2+b1),
init-system-helpers (= 1.67),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.2-2+b1),
libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b2),
libamd3 (= 1:7.8.3+dfsg-2),
libamdhip64-5 (= 5.7.1-5),
libarchive-zip-perl (= 1.68-1),
libarchive13t64 (= 3.7.4-1.1),
libarpack2-dev (= 3.9.1-1.1+b2),
libarpack2t64 (= 3.9.1-1.1+b2),
libasan8 (= 14.2.0-8),
libatomic1 (= 14.2.0-8),
libattr1 (= 1:2.5.2-2),
libaudit-common (= 1:4.0.2-2),
libaudit1 (= 1:4.0.2-2),
libbinutils (= 2.43.1-5),
libblas-dev (= 3.12.0-3+b1),
libblas3 (= 3.12.0-3+b1),
libblkid1 (= 2.40.2-11),
libbrotli1 (= 1.1.0-2+b6),
libbsd0 (= 0.12.2-2),
libbtf2 (= 1:7.8.3+dfsg-2),
libbz2-1.0 (= 1.0.8-6),
libc-bin (= 2.40-3),
libc-dev-bin (= 2.40-3),
libc6 (= 2.40-3),
libc6-dev (= 2.40-3),
libcamd3 (= 1:7.8.3+dfsg-2),
libcap-ng0 (= 0.8.5-3+b1),
libcap2 (= 1:2.66-5+b1),
libcbor0.10 (= 0.10.2-2),
libcc1-0 (= 14.2.0-8),
libccolamd3 (= 1:7.8.3+dfsg-2),
libcholmod5 (= 1:7.8.3+dfsg-2),
libcolamd3 (= 1:7.8.3+dfsg-2),
libcom-err2 (= 1.47.1-1+b1),
libcrypt-dev (= 1:4.4.36-5),
libcrypt1 (= 1:4.4.36-5),
libctf-nobfd0 (= 2.43.1-5),
libctf0 (= 2.43.1-5),
libcurl4t64 (= 8.11.0-1),
libcxsparse4 (= 1:7.8.3+dfsg-2),
libdb5.3t64 (= 5.3.28+dfsg2-9),
libdebconfclient0 (= 0.273),
libdebhelper-perl (= 13.20),
libdpkg-perl (= 1.22.12~1.gbp82cafd),
libdrm-amdgpu1 (= 2.4.123-1),
libdrm-common (= 2.4.123-1),
libdrm2 (= 2.4.123-1),
libedit2 (= 3.1-20240808-1),
libelf1t64 (= 0.192-4),
libevent-2.1-7t64 (= 2.1.12-stable-10+b1),
libevent-core-2.1-7t64 (= 2.1.12-stable-10+b1),
libevent-dev (= 2.1.12-stable-10+b1),
libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b1),
libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b1),
libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b1),
libexpat1 (= 2.6.4-1),
libexpat1-dev (= 2.6.4-1),
libfabric1 (= 1.17.0-3.1),
libffi8 (= 3.4.6-1),
libfido2-1 (= 1.15.0-1+b1),
libfile-stripnondeterminism-perl (= 1.14.0-1),
libgcc-14-dev (= 14.2.0-8),
libgcc-s1 (= 14.2.0-8),
libgdbm-compat4t64 (= 1.24-2),
libgdbm6t64 (= 1.24-2),
libgfortran-14-dev (= 14.2.0-8),
libgfortran5 (= 14.2.0-8),
libgmp10 (= 2:6.3.0+dfsg-2+b2),
libgnutls30t64 (= 3.8.8-2),
libgomp1 (= 14.2.0-8),
libgprofng0 (= 2.43.1-5),
libgssapi-krb5-2 (= 1.21.3-3),
libhogweed6t64 (= 3.10-1+b1),
libhsa-runtime64-1 (= 6.1.2-2),
libhsakmt1 (= 6.1.2+ds-1),
libhwasan0 (= 14.2.0-8),
libhwloc-dev (= 2.11.2-1),
libhwloc-plugins (= 2.11.2-1),
libhwloc15 (= 2.11.2-1),
libibmad5 (= 52.0-2+b1),
libibumad3 (= 52.0-2+b1),
libibverbs-dev (= 52.0-2+b1),
libibverbs1 (= 52.0-2+b1),
libicu72 (= 72.1-5+b1),
libidn2-0 (= 2.3.7-2+b1),
libisl23 (= 0.27-1),
libitm1 (= 14.2.0-8),
libjansson4 (= 2.14-2+b3),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-jquery-ui (= 1.13.2+dfsg-1),
libjs-mathjax (= 2.7.9+dfsg-1),
libjs-sphinxdoc (= 7.4.7-4),
libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
libjson-perl (= 4.10000-1),
libjsoncpp26 (= 1.9.6-2),
libk5crypto3 (= 1.21.3-3),
libkeyutils1 (= 1.6.3-4),
libklu2 (= 1:7.8.3+dfsg-2),
libkrb5-3 (= 1.21.3-3),
libkrb5support0 (= 1.21.3-3),
liblapack-dev (= 3.12.0-3+b1),
liblapack3 (= 3.12.0-3+b1),
libldap-2.5-0 (= 2.5.18+dfsg-3+b1),
libldl3 (= 1:7.8.3+dfsg-2),
libllvm17t64 (= 1:17.0.6-18),
liblsan0 (= 14.2.0-8),
libltdl-dev (= 2.4.7-8),
libltdl7 (= 2.4.7-8),
liblz4-1 (= 1.9.4-3+b1),
liblzma5 (= 5.6.3-1+b1),
libmagic-mgc (= 1:5.45-3+b1),
libmagic1t64 (= 1:5.45-3+b1),
libmaloc-dev (= 1.5-2+b1),
libmaloc1 (= 1.5-2+b1),
libmd0 (= 1.1.0-2+b1),
libmount1 (= 2.40.2-11),
libmpc3 (= 1.3.1-1+b3),
libmpfr6 (= 4.2.1-1+b2),
libmunge2 (= 0.5.15-4+b1),
libncursesw6 (= 6.5-2+b1),
libnettle8t64 (= 3.10-1+b1),
libnghttp2-14 (= 1.64.0-1),
libnl-3-200 (= 3.7.0-0.3+b1),
libnl-3-dev (= 3.7.0-0.3+b1),
libnl-route-3-200 (= 3.7.0-0.3+b1),
libnl-route-3-dev (= 3.7.0-0.3+b1),
libnsl2 (= 1.3.0-3+b3),
libnuma-dev (= 2.0.18-1+b1),
libnuma1 (= 2.0.18-1+b1),
libopenmpi-dev (= 5.0.5-3),
libopenmpi3t64 (= 5.0.5-3),
libp11-kit0 (= 0.25.5-2+b1),
libpam-modules (= 1.5.3-7+b1),
libpam-modules-bin (= 1.5.3-7+b1),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7+b1),
libparu1 (= 1:7.8.3+dfsg-2),
libpciaccess0 (= 0.17-3+b2),
libpcre2-8-0 (= 10.44-2),
libperl5.40 (= 5.40.0-7),
libpipeline1 (= 1.5.8-1),
libpkgconf3 (= 1.8.1-4),
libpmix-dev (= 5.0.3-2+b1),
libpmix2t64 (= 5.0.3-2+b1),
libproc2-0 (= 2:4.0.4-6),
libpsl5t64 (= 0.21.2-1.1+b1),
libpython3-dev (= 3.12.7-1),
libpython3-stdlib (= 3.12.7-1),
libpython3.12-dev (= 3.12.7-3),
libpython3.12-minimal (= 3.12.7-3),
libpython3.12-stdlib (= 3.12.7-3),
libpython3.12t64 (= 3.12.7-3),
librbio4 (= 1:7.8.3+dfsg-2),
librdmacm1t64 (= 52.0-2+b1),
libreadline8t64 (= 8.2-5),
librhash1 (= 1.4.5-1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5),
libsasl2-2 (= 2.1.28+dfsg1-8),
libsasl2-modules-db (= 2.1.28+dfsg1-8),
libseccomp2 (= 2.5.5-1+b3),
libselinux1 (= 3.7-3+b1),
libsemanage-common (= 3.7-2),
libsemanage2 (= 3.7-2+b1),
libsepol2 (= 3.7-1),
libsframe1 (= 2.43.1-5),
libsmartcols1 (= 2.40.2-11),
libspex3 (= 1:7.8.3+dfsg-2),
libspqr4 (= 1:7.8.3+dfsg-2),
libsqlite3-0 (= 3.46.1-1),
libssh2-1t64 (= 1.11.1-1),
libssl3t64 (= 3.3.2-2),
libstdc++-14-dev (= 14.2.0-8),
libstdc++6 (= 14.2.0-8),
libsuitesparse-dev (= 1:7.8.3+dfsg-2),
libsuitesparse-mongoose3 (= 1:7.8.3+dfsg-2),
libsuitesparseconfig7 (= 1:7.8.3+dfsg-2),
libsuperlu-dev (= 7.0.0+dfsg1-2),
libsuperlu7 (= 7.0.0+dfsg1-2),
libsystemd0 (= 257~rc1-4),
libtasn1-6 (= 4.19.0-3+b3),
libtinfo6 (= 6.5-2+b1),
libtirpc-common (= 1.3.4+ds-1.3),
libtirpc-dev (= 1.3.4+ds-1.3+b1),
libtirpc3t64 (= 1.3.4+ds-1.3+b1),
libtool (= 2.4.7-8),
libtsan2 (= 14.2.0-8),
libubsan1 (= 14.2.0-8),
libuchardet0 (= 0.0.8-1+b2),
libucx0 (= 1.17.0+ds-3),
libudev1 (= 257~rc1-4),
libumfpack6 (= 1:7.8.3+dfsg-2),
libunistring5 (= 1.2-1+b1),
libuuid1 (= 2.40.2-11),
libuv1t64 (= 1.48.0-7),
libx11-6 (= 2:1.8.10-2),
libx11-data (= 2:1.8.10-2),
libxau6 (= 1:1.0.11-1),
libxcb1 (= 1.17.0-2+b1),
libxdmcp6 (= 1:1.1.2-3+b2),
libxext6 (= 2:1.3.4-1+b2),
libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1),
libxnvctrl0 (= 535.171.04-1+b1),
libxxhash0 (= 0.8.2-2+b2),
libyaml-0-2 (= 0.2.5-1+b2),
libz3-4 (= 4.13.3-1),
libzstd1 (= 1.5.6+dfsg-1+b1),
linux-libc-dev (= 6.11.7-1),
login.defs (= 1:4.16.0-4),
m4 (= 1.4.19-4),
make (= 4.3-4.1+b1),
man-db (= 2.13.0-1),
mawk (= 1.3.4.20240905-1),
media-types (= 10.1.0),
mpi-default-dev (= 1.17),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2+b1),
netbase (= 6.4),
ocl-icd-libopencl1 (= 2.3.2-1+b2),
openmpi-bin (= 5.0.5-3),
openmpi-common (= 5.0.5-3),
openssh-client (= 1:9.9p1-3),
openssl (= 3.3.2-2),
openssl-provider-legacy (= 3.3.2-2),
passwd (= 1:4.16.0-4),
patch (= 2.7.6-7+b1),
perl (= 5.40.0-7),
perl-base (= 5.40.0-7),
perl-modules-5.40 (= 5.40.0-7),
pkgconf (= 1.8.1-4),
pkgconf-bin (= 1.8.1-4),
po-debconf (= 1.0.21+nmu1),
procps (= 2:4.0.4-6),
pybind11-dev (= 2.13.6-1),
pybuild-plugin-pyproject (= 6.20241024),
python-babel-localedata (= 2.16.0-1),
python3 (= 3.12.7-1),
python3-alabaster (= 0.7.16-0.1),
python3-autocommand (= 2.2.2-3),
python3-babel (= 2.16.0-1),
python3-build (= 1.2.2-1),
python3-certifi (= 2024.8.30+dfsg-1),
python3-chardet (= 5.2.0+dfsg-1),
python3-charset-normalizer (= 3.4.0-1+b1),
python3-defusedxml (= 0.7.1-2),
python3-dev (= 3.12.7-1),
python3-docutils (= 0.21.2+dfsg-2),
python3-idna (= 3.8-2),
python3-imagesize (= 1.4.1-1),
python3-inflect (= 7.3.1-2),
python3-installer (= 0.7.0+dfsg1-3),
python3-jaraco.context (= 6.0.0-1),
python3-jaraco.functools (= 4.1.0-1),
python3-jaraco.text (= 4.0.0-1),
python3-jinja2 (= 3.1.3-1),
python3-markupsafe (= 2.1.5-1+b3),
python3-minimal (= 3.12.7-1),
python3-more-itertools (= 10.5.0-1),
python3-packaging (= 24.1-1),
python3-pkg-resources (= 75.2.0-1),
python3-pybind11 (= 2.13.6-1),
python3-pygments (= 2.18.0+dfsg-1),
python3-pyproject-hooks (= 1.2.0-1),
python3-requests (= 2.32.3+dfsg-1),
python3-roman (= 4.2-1),
python3-setuptools (= 75.2.0-1),
python3-snowballstemmer (= 2.2.0-4),
python3-sphinx (= 7.4.7-4),
python3-sphinx-rtd-theme (= 3.0.1+dfsg-1),
python3-sphinxcontrib.jquery (= 4.1-5),
python3-toml (= 0.10.2-1),
python3-typeguard (= 4.4.1-1),
python3-typing-extensions (= 4.12.2-2),
python3-urllib3 (= 2.0.7-2),
python3-wheel (= 0.45.0-1),
python3-yaml (= 6.0.2-1+b1),
python3-zipp (= 3.21.0-1),
python3.12 (= 3.12.7-3),
python3.12-dev (= 3.12.7-3),
python3.12-minimal (= 3.12.7-3),
readline-common (= 8.2-5),
rpcsvc-proto (= 1.4.3-1+b1),
sed (= 4.9-2+b1),
sensible-utils (= 0.0.24),
sgml-base (= 1.31),
sphinx-common (= 7.4.7-4),
sphinx-rtd-theme-common (= 3.0.1+dfsg-1),
swig (= 4.2.1-1+b1),
sysvinit-utils (= 3.11-1),
tar (= 1.35+dfsg-3+b1),
tzdata (= 2024b-3),
util-linux (= 2.40.2-11),
xml-core (= 0.19),
xz-utils (= 5.6.3-1+b1),
zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1),
zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_US.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1730381057"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
apbs-data_3.4.1-6_all.deb
-------------------------
new Debian package, version 2.0.
size 1489396 bytes: control archive=8384 bytes.
698 bytes, 19 lines control
25645 bytes, 313 lines md5sums
Package: apbs-data
Source: apbs
Version: 3.4.1-6
Architecture: all
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 15882
Breaks: apbs (<= 1.4-2)
Section: science
Priority: optional
Multi-Arch: foreign
Homepage: http://www.poissonboltzmann.org/
Description: data files for APBS (Adaptive Poisson Boltzmann Solver)
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation (PBE), one of the most popular continuum
models for describing electrostatic interactions between molecular
solutes in salty, aqueous media.
.
This package contains all data files for apbs package to reduce the
redundancy between architectures in Debian.
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/
-rw-r--r-- root/root 118791 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr
-rw-r--r-- root/root 5249 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in
-rw-r--r-- root/root 5262 2022-04-29 18:53 ./usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/1d7h-dmso/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/
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apbs-dbgsym_3.4.1-6_arm64.deb
-----------------------------
new Debian package, version 2.0.
size 110588 bytes: control archive=1412 bytes.
1037 bytes, 12 lines control
1990 bytes, 19 lines md5sums
Package: apbs-dbgsym
Source: apbs
Version: 3.4.1-6
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 272
Depends: apbs (= 3.4.1-6)
Section: debug
Priority: optional
Description: debug symbols for apbs
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apbs-doc_3.4.1-6_all.deb
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new Debian package, version 2.0.
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1432 bytes, 33 lines control
26074 bytes, 280 lines md5sums
Package: apbs-doc
Source: apbs
Version: 3.4.1-6
Architecture: all
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 7585
Depends: libjs-mathjax, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 7.4), sphinx-rtd-theme-common (>= 3.0.1+dfsg)
Recommends: apbs
Suggests: python3-apbslib
Section: science
Priority: optional
Multi-Arch: foreign
Homepage: http://www.poissonboltzmann.org/
Description: Adaptive Poisson Boltzmann Solver
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation (PBE), one of the most popular continuum
models for describing electrostatic interactions between molecular
solutes in salty, aqueous media. Continuum electrostatics plays an
important role in several areas of biomolecular simulation, including:
.
* simulation of diffusional processes to determine ligand-protein and
protein-protein binding kinetics,
* implicit solvent molecular dynamics of biomolecules ,
* solvation and binding energy calculations to determine
ligand-protein and protein-protein equilibrium binding constants
and aid in rational drug design,
* and biomolecular titration studies.
.
APBS was designed to efficiently evaluate electrostatic properties for
such simulations for a wide range of length scales to enable the
investigation of molecules with tens to millions of atoms.
.
This package contains the apbs documentation.
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apbs_3.4.1-6_arm64.deb
----------------------
new Debian package, version 2.0.
size 77040 bytes: control archive=1828 bytes.
1745 bytes, 29 lines control
1618 bytes, 25 lines md5sums
Package: apbs
Version: 3.4.1-6
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 1252
Depends: apbs-data (= 3.4.1-6), libapbs3t64 (= 3.4.1-6), libjs-mathjax, libamd3 (>= 1:7.0.1), libarpack2t64 (>= 2.1), libblas3 | libblas.so.3, libc6 (>= 2.34), libcamd3 (>= 1:7.0.1), libccolamd3 (>= 1:7.0.1), libcholmod5 (>= 1:7.3.1), libcolamd3 (>= 1:7.0.1), libfetk1.9t64 (>= 3.4.1), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi3t64 (>= 5.0.5), libspqr4 (>= 1:7.8.3+dfsg), libstdc++6 (>= 4.1.1), libsuitesparseconfig7 (>= 1:7.0.1), libsuperlu7 (>= 7.0.0+dfsg1), libumfpack6 (>= 1:7.0.1)
Section: science
Priority: optional
Homepage: http://www.poissonboltzmann.org/
Description: Adaptive Poisson Boltzmann Solver
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation (PBE), one of the most popular continuum
models for describing electrostatic interactions between molecular
solutes in salty, aqueous media. Continuum electrostatics plays an
important role in several areas of biomolecular simulation, including:
.
* simulation of diffusional processes to determine ligand-protein and
protein-protein binding kinetics,
* implicit solvent molecular dynamics of biomolecules ,
* solvation and binding energy calculations to determine
ligand-protein and protein-protein equilibrium binding constants
and aid in rational drug design,
* and biomolecular titration studies.
.
APBS was designed to efficiently evaluate electrostatic properties for
such simulations for a wide range of length scales to enable the
investigation of molecules with tens to millions of atoms.
.
This package contains the apbs program and utilities.
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/bin/
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/bin/apbs
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/apbs/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/apbs/tools/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/analysis
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/benchmark
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/born
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/coulomb
-rwxr-xr-x root/root 67760 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/del2dx
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/dx2mol
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/dx2uhbd
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/dxmath
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/mergedx
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/mergedx2
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/mgmesh
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/multivalue
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/similarity
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/smooth
-rwxr-xr-x root/root 67760 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/tensor2dx
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/uhbd_asc2bin
-rwxr-xr-x root/root 67752 2024-10-31 13:24 ./usr/lib/apbs/tools/bin/value
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/apbs/
-rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/apbs/README
-rw-r--r-- root/root 294 2024-10-31 13:24 ./usr/share/doc/apbs/README.test
-rw-r--r-- root/root 3631 2024-10-31 13:24 ./usr/share/doc/apbs/changelog.Debian.gz
-rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/apbs/changelog.gz
-rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/apbs/copyright
-rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/apbs/releases.rst.gz
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/man/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/man/man1/
-rw-r--r-- root/root 835 2024-10-31 13:24 ./usr/share/man/man1/apbs.1.gz
libapbs-dev_3.4.1-6_arm64.deb
-----------------------------
new Debian package, version 2.0.
size 103260 bytes: control archive=2236 bytes.
664 bytes, 19 lines control
4026 bytes, 60 lines md5sums
Package: libapbs-dev
Source: apbs
Version: 3.4.1-6
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 712
Depends: libapbs3t64 (= 3.4.1-6)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: http://www.poissonboltzmann.org/
Description: Adaptive Poisson Boltzmann Solver
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation (PBE), one of the most popular continuum
models for describing electrostatic interactions between molecular
solutes in salty, aqueous media.
.
This package contains the development headers to build against
libapbs_* shared libraries.
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/
-rw-r--r-- root/root 3281 2022-04-29 18:53 ./usr/include/apbs/apbs.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/fem/
-rw-r--r-- root/root 11331 2022-04-29 18:53 ./usr/include/apbs/fem/vcsm.h
-rw-r--r-- root/root 38012 2024-10-31 13:24 ./usr/include/apbs/fem/vfetk.h
-rw-r--r-- root/root 10184 2022-04-29 18:53 ./usr/include/apbs/fem/vpee.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/generic/
-rw-r--r-- root/root 8229 2022-04-29 18:53 ./usr/include/apbs/generic/apolparm.h
-rw-r--r-- root/root 6395 2022-04-29 18:53 ./usr/include/apbs/generic/bemparm.h
-rw-r--r-- root/root 8873 2022-04-29 18:53 ./usr/include/apbs/generic/femparm.h
-rw-r--r-- root/root 6121 2022-04-29 18:53 ./usr/include/apbs/generic/geoflowparm.h
-rw-r--r-- root/root 12602 2022-04-29 18:53 ./usr/include/apbs/generic/mgparm.h
-rw-r--r-- root/root 21080 2022-04-29 18:53 ./usr/include/apbs/generic/nosh.h
-rw-r--r-- root/root 10919 2022-04-29 18:53 ./usr/include/apbs/generic/pbamparm.h
-rw-r--r-- root/root 11096 2022-04-29 18:53 ./usr/include/apbs/generic/pbeparm.h
-rw-r--r-- root/root 7321 2022-04-29 18:53 ./usr/include/apbs/generic/pbsamparm.h
-rw-r--r-- root/root 23163 2022-04-29 18:53 ./usr/include/apbs/generic/vacc.h
-rw-r--r-- root/root 8494 2022-04-29 18:53 ./usr/include/apbs/generic/valist.h
-rw-r--r-- root/root 10351 2022-04-29 18:53 ./usr/include/apbs/generic/vatom.h
-rw-r--r-- root/root 5946 2022-04-29 18:53 ./usr/include/apbs/generic/vcap.h
-rw-r--r-- root/root 9280 2022-04-29 18:53 ./usr/include/apbs/generic/vclist.h
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-rw-r--r-- root/root 12145 2022-04-29 18:53 ./usr/include/apbs/generic/vparam.h
-rw-r--r-- root/root 19880 2022-04-29 18:53 ./usr/include/apbs/generic/vpbe.h
-rw-r--r-- root/root 5171 2022-04-29 18:53 ./usr/include/apbs/generic/vstring.h
-rw-r--r-- root/root 3958 2022-04-29 18:53 ./usr/include/apbs/generic/vunit.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/mg/
-rw-r--r-- root/root 14945 2022-04-29 18:53 ./usr/include/apbs/mg/vgrid.h
-rw-r--r-- root/root 6887 2022-04-29 18:53 ./usr/include/apbs/mg/vmgrid.h
-rw-r--r-- root/root 6160 2022-04-29 18:53 ./usr/include/apbs/mg/vopot.h
-rw-r--r-- root/root 52888 2022-04-29 18:53 ./usr/include/apbs/mg/vpmg.h
-rw-r--r-- root/root 11010 2022-04-29 18:53 ./usr/include/apbs/mg/vpmgp.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/apbs/pmgc/
-rw-r--r-- root/root 12319 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildAd.h
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-rw-r--r-- root/root 10038 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildPd.h
-rw-r--r-- root/root 3475 2022-04-29 18:53 ./usr/include/apbs/pmgc/cgd.h
-rw-r--r-- root/root 5776 2022-04-29 18:53 ./usr/include/apbs/pmgc/gsd.h
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-rw-r--r-- root/root 5762 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgcsd.h
-rw-r--r-- root/root 9284 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgdrvd.h
-rw-r--r-- root/root 7729 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgfasd.h
-rw-r--r-- root/root 14987 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgsubd.h
-rw-r--r-- root/root 12104 2022-04-29 18:53 ./usr/include/apbs/pmgc/mikpckd.h
-rw-r--r-- root/root 4008 2022-04-29 18:53 ./usr/include/apbs/pmgc/mlinpckd.h
-rw-r--r-- root/root 7781 2022-04-29 18:53 ./usr/include/apbs/pmgc/mypdec.h
-rw-r--r-- root/root 5950 2022-04-29 18:53 ./usr/include/apbs/pmgc/newdrvd.h
-rw-r--r-- root/root 6700 2022-04-29 18:53 ./usr/include/apbs/pmgc/newtond.h
-rw-r--r-- root/root 8220 2022-04-29 18:53 ./usr/include/apbs/pmgc/powerd.h
-rw-r--r-- root/root 4685 2022-04-29 18:53 ./usr/include/apbs/pmgc/smoothd.h
-rw-r--r-- root/root 33482 2022-04-29 18:53 ./usr/include/apbs/routines.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_fem.so -> libapbs_fem.so.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_generic.so -> libapbs_generic.so.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_mg.so -> libapbs_mg.so.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_pmgc.so -> libapbs_pmgc.so.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_routines.so -> libapbs_routines.so.3
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/cmake/
-rw-r--r-- root/root 949 2024-10-31 13:24 ./usr/share/apbs/cmake/FindAMD.cmake
-rw-r--r-- root/root 2501 2024-10-31 13:24 ./usr/share/apbs/cmake/FindARPACK.cmake
-rw-r--r-- root/root 22563 2024-10-31 13:24 ./usr/share/apbs/cmake/FindLAPACK.cmake
-rw-r--r-- root/root 23393 2024-10-31 13:24 ./usr/share/apbs/cmake/FindSuiteSparse.cmake
-rw-r--r-- root/root 2578 2024-10-31 13:24 ./usr/share/apbs/cmake/FindSuperLU.cmake
-rw-r--r-- root/root 1153 2024-10-31 13:24 ./usr/share/apbs/cmake/FindUMFPACK.cmake
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libapbs-dev/
-rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/README
-rw-r--r-- root/root 3632 2024-10-31 13:24 ./usr/share/doc/libapbs-dev/changelog.Debian.gz
-rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/changelog.gz
-rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libapbs-dev/copyright
-rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/releases.rst.gz
libapbs3t64-dbgsym_3.4.1-6_arm64.deb
------------------------------------
new Debian package, version 2.0.
size 585264 bytes: control archive=804 bytes.
542 bytes, 13 lines control
619 bytes, 6 lines md5sums
Package: libapbs3t64-dbgsym
Source: apbs
Version: 3.4.1-6
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 652
Depends: libapbs3t64 (= 3.4.1-6)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libapbs3t64
Build-Ids: 01930f76287ef83adc5c12510579c802b00505f8 0c7cdbe5ad8586dfe1214b304a712f8be721959d 32316657263abb1d87b32be1d4eea52b09a8717d 6b66227cf22d9dbb1b8a2724a42bdfcb3f32dfa1 b4df1425e79bdc8516a3215cf11c18c8b2144c44
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/01/
-rw-r--r-- root/root 69784 2024-10-31 13:24 ./usr/lib/debug/.build-id/01/930f76287ef83adc5c12510579c802b00505f8.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 187792 2024-10-31 13:24 ./usr/lib/debug/.build-id/0c/7cdbe5ad8586dfe1214b304a712f8be721959d.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/32/
-rw-r--r-- root/root 144616 2024-10-31 13:24 ./usr/lib/debug/.build-id/32/316657263abb1d87b32be1d4eea52b09a8717d.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/6b/
-rw-r--r-- root/root 75520 2024-10-31 13:24 ./usr/lib/debug/.build-id/6b/66227cf22d9dbb1b8a2724a42bdfcb3f32dfa1.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/b4/
-rw-r--r-- root/root 153448 2024-10-31 13:24 ./usr/lib/debug/.build-id/b4/df1425e79bdc8516a3215cf11c18c8b2144c44.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/aarch64-linux-gnu/
-rw-r--r-- root/root 16840 2024-10-31 13:24 ./usr/lib/debug/.dwz/aarch64-linux-gnu/libapbs3t64.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/share/doc/libapbs3t64-dbgsym -> libapbs3t64
libapbs3t64_3.4.1-6_arm64.deb
-----------------------------
new Debian package, version 2.0.
size 240184 bytes: control archive=1144 bytes.
761 bytes, 21 lines control
691 bytes, 9 lines md5sums
194 bytes, 5 lines shlibs
66 bytes, 2 lines triggers
Package: libapbs3t64
Source: apbs
Version: 3.4.1-6
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 873
Depends: libc6 (>= 2.29), libfetk1.9t64 (>= 3.4.1), libgomp1 (>= 4.9), libmaloc1 (>= 0.2-1)
Breaks: libapbs3 (<< 3.4.1-6)
Replaces: libapbs3
Provides: libapbs3 (= 3.4.1-6)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: http://www.poissonboltzmann.org/
Description: Adaptive Poisson Boltzmann Solver
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation (PBE), one of the most popular continuum
models for describing electrostatic interactions between molecular
solutes in salty, aqueous media.
.
This package contains the libapbs_* shared libraries.
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/
-rw-r--r-- root/root 69600 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_fem.so.3
-rw-r--r-- root/root 264200 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_generic.so.3
-rw-r--r-- root/root 198664 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_mg.so.3
-rw-r--r-- root/root 198512 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_pmgc.so.3
-rw-r--r-- root/root 133128 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libapbs_routines.so.3
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libapbs3t64/
-rw-r--r-- root/root 3634 2024-10-31 13:24 ./usr/share/doc/libapbs3t64/changelog.Debian.gz
-rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libapbs3t64/changelog.gz
-rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libapbs3t64/copyright
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 164 2024-10-31 13:24 ./usr/share/lintian/overrides/libapbs3t64
libfetk-dev_3.4.1-6_arm64.deb
-----------------------------
new Debian package, version 2.0.
size 148768 bytes: control archive=2044 bytes.
1256 bytes, 31 lines control
2662 bytes, 42 lines md5sums
Package: libfetk-dev
Source: apbs
Version: 3.4.1-6
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 1507
Depends: libfetk1.9t64 (= 3.4.1-6), libmaloc-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: http://www.poissonboltzmann.org/
Description: FETK libraries for APBS (development headers)
The Finite Element ToolKit (FETK) is a collection of adaptive finite
element method (AFEM) software libraries and tools for solving
coupled systems of nonlinear geometric partial differential equations
(PDE). The FETK libraries and tools are written in an object-oriented
form of ANSI-C and in C++, and include a collection of standard
numerical libraries (PUNC), a stand-alone high-quality surface and
volume simplex mesh generator (GAMer), a stand-alone networked
polygon display tool (SG), a general nonlinear finite element
modeling kernel (MC)
.
This package provides a fork of FETK intended for use by APBS
(Adaptive Poisson Boltzmann Solver).
.
The FETK component MALOC (Minimal Abstraction Layer for
Object-oriented C/C++ programs) is provided separately by
libmaloc-dev.
.
This package contains the development headers to build against
libapbs_* shared libraries.
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/gamer/
-rw-r--r-- root/root 11439 2024-10-31 13:24 ./usr/include/fetk/gamer/biom.h
-rw-r--r-- root/root 1459 2024-10-31 13:24 ./usr/include/fetk/gamer/gamer.h
-rw-r--r-- root/root 2282 2024-10-31 13:24 ./usr/include/fetk/gamer/gamer_base.h
-rw-r--r-- root/root 106910 2024-10-31 13:24 ./usr/include/fetk/gamer/tetgen.h
-rw-r--r-- root/root 22024 2024-10-31 13:24 ./usr/include/fetk/gamer/triangle.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/mc/
-rw-r--r-- root/root 27753 2024-10-31 13:24 ./usr/include/fetk/mc/am.h
-rw-r--r-- root/root 49795 2024-10-31 13:24 ./usr/include/fetk/mc/aprx.h
-rw-r--r-- root/root 1297 2024-10-31 13:24 ./usr/include/fetk/mc/bam.h
-rw-r--r-- root/root 29085 2024-10-31 13:24 ./usr/include/fetk/mc/bmat.h
-rw-r--r-- root/root 5029 2024-10-31 13:24 ./usr/include/fetk/mc/bnode.h
-rw-r--r-- root/root 32284 2024-10-31 13:24 ./usr/include/fetk/mc/bvec.h
-rw-r--r-- root/root 13191 2024-10-31 13:24 ./usr/include/fetk/mc/dyn.h
-rw-r--r-- root/root 130602 2024-10-31 13:24 ./usr/include/fetk/mc/gem.h
-rw-r--r-- root/root 47965 2024-10-31 13:24 ./usr/include/fetk/mc/mat.h
-rw-r--r-- root/root 1457 2024-10-31 13:24 ./usr/include/fetk/mc/mc.h
-rw-r--r-- root/root 5705 2024-10-31 13:24 ./usr/include/fetk/mc/mc_base.h
-rw-r--r-- root/root 4665 2024-10-31 13:24 ./usr/include/fetk/mc/mcsh.h
-rw-r--r-- root/root 14987 2024-10-31 13:24 ./usr/include/fetk/mc/mtool.h
-rw-r--r-- root/root 1189 2024-10-31 13:24 ./usr/include/fetk/mc/nam.h
-rw-r--r-- root/root 4772 2024-10-31 13:24 ./usr/include/fetk/mc/node.h
-rw-r--r-- root/root 17885 2024-10-31 13:24 ./usr/include/fetk/mc/pde.h
-rw-r--r-- root/root 17026 2024-10-31 13:24 ./usr/include/fetk/mc/re.h
-rw-r--r-- root/root 4823 2024-10-31 13:24 ./usr/include/fetk/mc/slu.h
-rw-r--r-- root/root 12682 2024-10-31 13:24 ./usr/include/fetk/mc/vec.h
-rw-r--r-- root/root 14016 2024-10-31 13:24 ./usr/include/fetk/mc/vec3.h
-rw-r--r-- root/root 26120 2024-10-31 13:24 ./usr/include/fetk/mc/vel.h
-rw-r--r-- root/root 68269 2024-10-31 13:24 ./usr/include/fetk/mc/ves.h
-rw-r--r-- root/root 50938 2024-10-31 13:24 ./usr/include/fetk/mc/whb.h
-rw-r--r-- root/root 7767 2024-10-31 13:24 ./usr/include/fetk/mc/zslu.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/include/fetk/punc/
-rw-r--r-- root/root 1569 2024-10-31 13:24 ./usr/include/fetk/punc/punc.h
-rw-r--r-- root/root 1272 2024-10-31 13:24 ./usr/include/fetk/punc/punc_base.h
-rw-r--r-- root/root 1455 2024-10-31 13:24 ./usr/include/fetk/punc/punc_base_p.h
-rw-r--r-- root/root 3987 2024-10-31 13:24 ./usr/include/fetk/punc/punccf.h
-rw-r--r-- root/root 46865 2024-10-31 13:24 ./usr/include/fetk/punc/varpack.h
-rw-r--r-- root/root 39886 2024-10-31 13:24 ./usr/include/fetk/punc/vblas.h
-rw-r--r-- root/root 17098 2024-10-31 13:24 ./usr/include/fetk/punc/vcgcode.h
-rw-r--r-- root/root 13077 2024-10-31 13:24 ./usr/include/fetk/punc/vf2c.h
-rw-r--r-- root/root 552778 2024-10-31 13:24 ./usr/include/fetk/punc/vlapack.h
-rw-r--r-- root/root 82089 2024-10-31 13:24 ./usr/include/fetk/punc/vpmg.h
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libcgcode.so -> libcgcode.so.1.9
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libgamer.so -> libgamer.so.1.9
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libmc.so -> libmc.so.1.9
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libpunc.so -> libpunc.so.1.9
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libvf2c.so -> libvf2c.so.1.9
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libfetk-dev/
-rw-r--r-- root/root 3632 2024-10-31 13:24 ./usr/share/doc/libfetk-dev/changelog.Debian.gz
-rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libfetk-dev/changelog.gz
-rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libfetk-dev/copyright
libfetk1.9t64-dbgsym_3.4.1-6_arm64.deb
--------------------------------------
new Debian package, version 2.0.
size 1601412 bytes: control archive=820 bytes.
549 bytes, 13 lines control
621 bytes, 6 lines md5sums
Package: libfetk1.9t64-dbgsym
Source: apbs
Version: 3.4.1-6
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 1709
Depends: libfetk1.9t64 (= 3.4.1-6)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libfetk1.9t64
Build-Ids: 53c2fcd43940a10075be9c19e71d062350ee6ee4 9cbc62c624addf4097f535a4cf9ac64bdc7d66b7 a129f78787e1678e9f97e9edd29b2ee27ddb510d cd1dc25ff48e1cce01bd96856eb7047bbadf9c37 f7fbf61b182b198cdb52983061045aebbd2a5b13
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drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/53/
-rw-r--r-- root/root 472672 2024-10-31 13:24 ./usr/lib/debug/.build-id/53/c2fcd43940a10075be9c19e71d062350ee6ee4.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 124072 2024-10-31 13:24 ./usr/lib/debug/.build-id/9c/bc62c624addf4097f535a4cf9ac64bdc7d66b7.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/a1/
-rw-r--r-- root/root 1030192 2024-10-31 13:24 ./usr/lib/debug/.build-id/a1/29f78787e1678e9f97e9edd29b2ee27ddb510d.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/cd/
-rw-r--r-- root/root 5600 2024-10-31 13:24 ./usr/lib/debug/.build-id/cd/1dc25ff48e1cce01bd96856eb7047bbadf9c37.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.build-id/f7/
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drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/debug/.dwz/aarch64-linux-gnu/
-rw-r--r-- root/root 2776 2024-10-31 13:24 ./usr/lib/debug/.dwz/aarch64-linux-gnu/libfetk1.9t64.debug
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64-dbgsym -> libfetk1.9t64
libfetk1.9t64_3.4.1-6_arm64.deb
-------------------------------
new Debian package, version 2.0.
size 509204 bytes: control archive=1496 bytes.
1434 bytes, 34 lines control
691 bytes, 9 lines md5sums
186 bytes, 5 lines shlibs
66 bytes, 2 lines triggers
Package: libfetk1.9t64
Source: apbs
Version: 3.4.1-6
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 1621
Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libmaloc1 (>= 0.2-1), libstdc++6 (>= 5), libsuperlu7 (>= 7.0.0+dfsg1), libumfpack6 (>= 1:7.0.1)
Breaks: libfetk1.9 (<< 3.4.1-6)
Replaces: libfetk1.9
Provides: libfetk1.9 (= 3.4.1-6)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: http://www.poissonboltzmann.org/
Description: FETK libraries for APBS (shared libraries)
The Finite Element ToolKit (FETK) is a collection of adaptive finite
element method (AFEM) software libraries and tools for solving
coupled systems of nonlinear geometric partial differential equations
(PDE). The FETK libraries and tools are written in an object-oriented
form of ANSI-C and in C++, and include a collection of standard
numerical libraries (PUNC), a stand-alone high-quality surface and
volume simplex mesh generator (GAMer), a stand-alone networked
polygon display tool (SG), a general nonlinear finite element
modeling kernel (MC)
.
This package provides a fork of FETK intended for use by APBS
(Adaptive Poisson Boltzmann Solver).
.
The FETK component MALOC (Minimal Abstraction Layer for
Object-oriented C/C++ programs) is provided separately via
libmaloc-dev.
.
This package contains the libgamer, libmc, libpunc (and libcgcode,
libvf2c) shared libraries.
drwxr-xr-x root/root 0 2024-10-31 13:24 ./
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libcgcode.so.1.9 -> libcgcode.so.1.9.3
-rw-r--r-- root/root 150344 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libcgcode.so.1.9.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libgamer.so.1.9 -> libgamer.so.1.9.3
-rw-r--r-- root/root 740952 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libgamer.so.1.9.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libmc.so.1.9 -> libmc.so.1.9.3
-rw-r--r-- root/root 534408 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libmc.so.1.9.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libpunc.so.1.9 -> libpunc.so.1.9.3
-rw-r--r-- root/root 67368 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libpunc.so.1.9.3
lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libvf2c.so.1.9 -> libvf2c.so.1.9.3
-rw-r--r-- root/root 133736 2024-10-31 13:24 ./usr/lib/aarch64-linux-gnu/libvf2c.so.1.9.3
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64/
-rw-r--r-- root/root 3635 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64/changelog.Debian.gz
-rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/libfetk1.9t64/changelog.gz
-rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/libfetk1.9t64/copyright
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 140 2024-10-31 13:24 ./usr/share/lintian/overrides/libfetk1.9t64
python3-apbslib-dbgsym_3.4.1-6_arm64.deb
----------------------------------------
new Debian package, version 2.0.
size 3537176 bytes: control archive=640 bytes.
415 bytes, 12 lines control
305 bytes, 3 lines md5sums
Package: python3-apbslib-dbgsym
Source: apbs
Version: 3.4.1-6
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 3692
Depends: python3-apbslib (= 3.4.1-6)
Section: debug
Priority: optional
Description: debug symbols for python3-apbslib
Build-Ids: 1b657d936c3e55137d6adb460b01245b7a2d6655 bea7d114197e7bfaa6342ce6e4637d00131db7ca
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lrwxrwxrwx root/root 0 2024-10-31 13:24 ./usr/share/doc/python3-apbslib-dbgsym -> python3-apbslib
python3-apbslib_3.4.1-6_arm64.deb
---------------------------------
new Debian package, version 2.0.
size 212860 bytes: control archive=2120 bytes.
833 bytes, 18 lines control
3023 bytes, 38 lines md5sums
277 bytes, 12 lines * postinst #!/bin/sh
390 bytes, 12 lines * prerm #!/bin/sh
Package: python3-apbslib
Source: apbs
Version: 3.4.1-6
Architecture: arm64
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 1184
Depends: libapbs3t64 (= 3.4.1-6), python3 (<< 3.13), python3 (>= 3.12~), python3:any, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libmaloc1 (>= 0.2-1), libpython3.12t64 (>= 3.12.7), libstdc++6 (>= 14)
Section: python
Priority: optional
Homepage: http://www.poissonboltzmann.org/
Description: Adaptive Poisson Boltzmann Solver
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation (PBE), one of the most popular continuum
models for describing electrostatic interactions between molecular
solutes in salty, aqueous media.
.
This package provides both the apbs and apbslib modules for Python3
enabling Python applications to access apbs.
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-rw-r--r-- root/root 461008 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbs.cpython-312-aarch64-linux-gnu.so
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-rw-r--r-- root/root 14524 2024-10-31 13:24 ./usr/lib/python3/dist-packages/apbslib/apbslib.py
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/python-pybind/
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-rw-r--r-- root/root 812 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_constants.hpp
-rw-r--r-- root/root 4224 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.cpp
-rw-r--r-- root/root 1906 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.hpp
-rw-r--r-- root/root 3131 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.cpp
-rw-r--r-- root/root 1018 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.hpp
-rw-r--r-- root/root 1601 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.cpp
-rw-r--r-- root/root 702 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.hpp
-rw-r--r-- root/root 988 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/module.cpp
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/python/
-rw-r--r-- root/root 1896 2024-10-31 13:24 ./usr/share/apbs/tools/python/CMakeLists.txt
-rw-r--r-- root/root 20999 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile
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-rw-r--r-- root/root 1834 2022-04-29 18:53 ./usr/share/apbs/tools/python/README
-rw-r--r-- root/root 6111 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbs.in
-rw-r--r-- root/root 260435 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.c
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-rw-r--r-- root/root 11686 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib_wrap.doc
-rw-r--r-- root/root 66 2022-04-29 18:53 ./usr/share/apbs/tools/python/ion.pqr
-rw-r--r-- root/root 15725 2022-04-29 18:53 ./usr/share/apbs/tools/python/main.py
-rw-r--r-- root/root 19499 2024-10-31 13:24 ./usr/share/apbs/tools/python/noinput.py
drwxr-xr-x root/root 0 2024-10-31 13:24 ./usr/share/apbs/tools/python/vgrid/
-rw-r--r-- root/root 15551 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile
-rw-r--r-- root/root 845 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.am
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-rw-r--r-- root/root 1638 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/README
-rw-r--r-- root/root 3134 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/average.py
-rw-r--r-- root/root 14146 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/mergedx.py
-rw-r--r-- root/root 2514 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/read.py
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-rw-r--r-- root/root 97354 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgridlib.c
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-rw-r--r-- root/root 1642 2022-04-29 18:53 ./usr/share/doc/python3-apbslib/changelog.gz
-rw-r--r-- root/root 6898 2024-10-31 13:24 ./usr/share/doc/python3-apbslib/copyright
lintian
-------
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W: apbs changes: distribution-and-changes-mismatch sid unstable
W: libapbs3t64: mismatched-override package-name-doesnt-match-sonames libapbs3 [usr/share/lintian/overrides/libapbs3t64:2]
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W: libfetk1.9t64: shared-library-lacks-prerequisites [usr/lib/aarch64-linux-gnu/libpunc.so.1.9.3]
N: 0 hints overridden; 2 unused overrides
I: Lintian run was successful.
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| Summary |
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Build Architecture: arm64
Build Type: binary
Build-Space: 386336
Build-Time: 386
Distribution: sid
Host Architecture: arm64
Install-Time: 58
Job: /tmp/debusine-fetch-exec-upload-9l_c1b39/apbs_3.4.1-6.dsc
Lintian: warn
Machine Architecture: arm64
Package: apbs
Package-Time: 481
Source-Version: 3.4.1-6
Space: 386336
Status: successful
Version: 3.4.1-6
--------------------------------------------------------------------------------
Finished at 2024-11-15T19:02:33Z
Build needed 00:08:01, 386336k disk space