Start: 2018-06-18 08:42:18 UTC [wheezy] Package: nwchem Version: 6.1-6 Installed-Size: 58285 Maintainer: Debichem Team Architecture: amd64 Depends: mpi-default-bin, nwchem-data (= 6.1-6), libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libopenmpi1.3, libquadmath0 (>= 4.6) Description: High-performance computational chemistry software Homepage: http://www.nwchem-sw.org Description-md5: dfcc0e06a4c1541597d48a663d8e6511 Tag: field::chemistry, role::program Section: science Priority: optional Filename: pool/main/n/nwchem/nwchem_6.1-6_amd64.deb Size: 14094474 MD5sum: 8de191225cc084fc1a02410b3e222c25 SHA1: d345679a9cf9e6189a7c6b21c2d2eee181b6f50e SHA256: 4322205b787656964434b14554d3727b9fc0e3aa6af8078985463a89134e44fb [wheezy-lts] Package: nwchem Version: 6.1-6 Installed-Size: 58285 Maintainer: Debichem Team Architecture: amd64 Depends: mpi-default-bin, nwchem-data (= 6.1-6), libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libopenmpi1.3, libquadmath0 (>= 4.6) Description: High-performance computational chemistry software Homepage: http://www.nwchem-sw.org Description-md5: dfcc0e06a4c1541597d48a663d8e6511 Tag: field::chemistry, role::program Section: science Priority: optional Filename: pool/main/n/nwchem/nwchem_6.1-6_amd64.deb Size: 14094474 MD5sum: 8de191225cc084fc1a02410b3e222c25 SHA1: d345679a9cf9e6189a7c6b21c2d2eee181b6f50e SHA256: 4322205b787656964434b14554d3727b9fc0e3aa6af8078985463a89134e44fb Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy -d wheezy-lts -B reference-chroot-metadata.dat --apt nwchem=6.1-6 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 0.90~201806121501~0.89-1-g6355f063 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror-ubc.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy -d wheezy-lts -B reference-chroot-metadata.dat --apt nwchem=6.1-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.9.0-6-amd64 #1 SMP Debian 4.9.88-1+deb9u1 (2018-05-07) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpeHzAZ1 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpeHzAZ1 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/run/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/run/shm'] 0m1.7s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ wheezy main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Created resolv.conf. 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpeHzAZ1/tmp/scripts/ 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmpeHzAZ1/tmp/scripts/ 0m1.7s INFO: Running scripts post_chroot_unpack 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'update'] 0m3.4s DUMP: Hit http://mirror-ubc.debian.org wheezy Release.gpg Hit http://mirror-ubc.debian.org wheezy Release Hit http://mirror-ubc.debian.org wheezy/main amd64 Packages Hit http://mirror-ubc.debian.org wheezy/main Translation-en Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s INFO: Running scripts post_setup 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_dummy_users'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_dummy_users'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m5.1s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 335 kB of archives. After this operation, 1327 kB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian/ wheezy/main adduser all 3.113+nmu3 [264 kB] Get:2 http://mirror-ubc.debian.org/debian/ wheezy/main ucf all 3.0025+nmu3 [70.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 335 kB in 0s (24.5 MB/s) Selecting previously unselected package adduser. (Reading database ... 6639 files and directories currently installed.) Unpacking adduser (from .../adduser_3.113+nmu3_all.deb) ... Selecting previously unselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu3_all.deb) ... Moving old data out of the way Setting up adduser (3.113+nmu3) ... Setting up ucf (3.0025+nmu3) ... 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u3 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u7 install ok installed gpgv gpgv 1.4.12-7+deb7u7 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u10 install ok installed libc6:amd64 libc6 2.13-38+deb7u10 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u10 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1 install ok installed perl-base perl-base 5.14.2-21+deb7u3 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1 install ok installed tzdata tzdata 2016d-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m5.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m6.1s INFO: Running scripts is_testable 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s INFO: Running scripts pre_test 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_test_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_test_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_test_root_password'] 0m6.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_test_root_password'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'show', '--no-all-versions', 'nwchem'] 0m6.2s DUMP: Package: nwchem Version: 6.1-6 Installed-Size: 58285 Maintainer: Debichem Team Architecture: amd64 Depends: mpi-default-bin, nwchem-data (= 6.1-6), libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libopenmpi1.3, libquadmath0 (>= 4.6) Description-en: High-performance computational chemistry software NWCHem is a computational chemistry program package. It provides methods which are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. . NWChem can handle: . * Molecular electronic structure methods using gaussian basis functions for high-accuracy calculations of molecules * Pseudopotentials plane-wave electronic structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals * Ab-initio and classical molecular dynamics simulations * Mixed quantum-classical simulations * Parallel scaling to thousands of processors . Features include: * Molecular electronic structure methods, analytic second derivatives: - Restricted/unrestricted Hartree-Fock (RHF, UHF) - Restricted Density Functional Theory (DFT) using many local, non-local (gradient-corrected) or hybrid (local, non-local, and HF) exchange-correlation potentials * Molecular electronic structure methods, analytic gradients: - Restricted open-shell Hartree-Fock (ROHF) - Unrestricted Density Functional Theory (DFT) - Second-order Moeller-Plesset perturbation theory (MP2), using RHF and UHF reference - Complete active space SCF (CASSCF) * Molecular electronic structure methods, single-point energies: - MP2 with resolution of the identity integral approximation (RI-MP2), using RHF and UHF reference - Coupled cluster singles and doubles, triples or pertubative triples (CCSD, CCSDT, CCSD(T)), with RHF and UHF reference - Configuration interaction (CISD, CISDT, and CISDTQ) - Second-order approximate coupled-cluster singles doubles (CC2) * Further molecular electronic structure features: - Geometry optimization including transition state searches, constraints and minimum energy paths - Vibrational frequencies - Equation-of-motion (EOM)-CCSD, EOM-CCSDT, EOM-CCSD(T), CC2, Configuration-Interaction singles (CIS), time-dependent HF (TDHF) and TDDFT, for excited states with RHF, UHF, RDFT, or UDFT reference - Solvatisation using the Conductor-like screening model (COSMO) for RHF, ROHF and DFT - Hybrid calculations using the two- and three-layer ONIOM method - Relativistic effects via spin-free and spin-orbit one-electron Douglas-Kroll and zeroth-order regular approximations (ZORA) and one-electron spin-orbit effects for DFT via spin-orbit potentials * Pseudopotential plane-wave electronic structure: - Pseudopotential Plane-Wave (PSPW), Projector Augmented Wave (PAW) or band structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals - Geometry/unit cell optimization including transition state searches - Vibrational frequencies - LDA, PBE96, and PBE0 exchange-correlation potentials (restricted and unrestricted) - SIC, pert-OEP, Hartree-Fock, and hybrid functionals (restricted and unrestricted) - Hamann, Troullier-Martins and Hartwigsen-Goedecker-Hutter norm-conserving pseudopotentials with semicore corrections - Wavefunction, density, electrostatic and Wannier plotting - Band structure and density of states generation * Car-Parrinello ab-initio molecular dynamics: - Constant energy and constant temperature dynamics - Verlet algorithm for integration - Geometry constraints in cartesian coordinates * Classical molecular dynamics: - Single configuration energy evaluation - Energy minimization - Molecular dynamics simulation - Free energy simulation (multistep thermodynamic perturbation (MSTP) or multiconfiguration thermodynamic integration (MCTI) methods with options of single and/or dual topologies, double wide sampling, and separation- shifted scaling) - Force fields providing effective pair potentials, first order polarization, self consistent polarization, smooth particle mesh Ewald (SPME), periodic boundary conditions and SHAKE constraints * Mixed quantum-classical: - Mixed quantum-mechanics and molecular-mechanics (QM/MM) minimizations and molecular dynamics simulations - Quantum molecular dynamics simulation by using any of the quantum mechanical methods capable of returning gradients. Homepage: http://www.nwchem-sw.org Description-md5: dfcc0e06a4c1541597d48a663d8e6511 Tag: field::chemistry, role::program Section: science Priority: optional Filename: pool/main/n/nwchem/nwchem_6.1-6_amd64.deb Size: 14094474 MD5sum: 8de191225cc084fc1a02410b3e222c25 SHA1: d345679a9cf9e6189a7c6b21c2d2eee181b6f50e SHA256: 4322205b787656964434b14554d3727b9fc0e3aa6af8078985463a89134e44fb 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'show', '--no-all-versions', 'nwchem'] 0m6.2s INFO: apt-cache knows about the following packages: nwchem 0m6.2s INFO: Running scripts pre_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy'] 0m6.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian/ wheezy/main Translation-en 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror-ubc.debian.org Pinned packages: 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy', 'nwchem'] 0m6.3s DUMP: nwchem: Installed: (none) Candidate: 6.1-6 Version table: 6.1-6 0 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy', 'nwchem'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-y', 'install', 'nwchem'] 0m9.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libgfortran3 libibverbs1 libnuma1 libopenmpi1.3 libquadmath0 libtorque2 mpi-default-bin nwchem-data openmpi-bin openmpi-common Suggested packages: gfortran Recommended packages: openmpi-checkpoint The following NEW packages will be installed: libgfortran3 libibverbs1 libnuma1 libopenmpi1.3 libquadmath0 libtorque2 mpi-default-bin nwchem nwchem-data openmpi-bin openmpi-common 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 25.8 MB of archives. After this operation, 103 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian/ wheezy/main libquadmath0 amd64 4.7.2-5 [125 kB] Get:2 http://mirror-ubc.debian.org/debian/ wheezy/main libgfortran3 amd64 4.7.2-5 [351 kB] Get:3 http://mirror-ubc.debian.org/debian/ wheezy/main libnuma1 amd64 2.0.8~rc4-1 [33.7 kB] Get:4 http://mirror-ubc.debian.org/debian/ wheezy/main libtorque2 amd64 2.4.16+dfsg-1+deb7u4 [121 kB] Get:5 http://mirror-ubc.debian.org/debian/ wheezy/main libibverbs1 amd64 1.1.6-1 [35.3 kB] Get:6 http://mirror-ubc.debian.org/debian/ wheezy/main libopenmpi1.3 amd64 1.4.5-1 [1436 kB] Get:7 http://mirror-ubc.debian.org/debian/ wheezy/main openmpi-common all 1.4.5-1 [101 kB] Get:8 http://mirror-ubc.debian.org/debian/ wheezy/main openmpi-bin amd64 1.4.5-1 [166 kB] Get:9 http://mirror-ubc.debian.org/debian/ wheezy/main mpi-default-bin amd64 1.0.1 [2990 B] Get:10 http://mirror-ubc.debian.org/debian/ wheezy/main nwchem-data all 6.1-6 [9326 kB] Get:11 http://mirror-ubc.debian.org/debian/ wheezy/main nwchem amd64 6.1-6 [14.1 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.8 MB in 0s (26.1 MB/s) Selecting previously unselected package libquadmath0:amd64. (Reading database ... 6768 files and directories currently installed.) Unpacking libquadmath0:amd64 (from .../libquadmath0_4.7.2-5_amd64.deb) ... Selecting previously unselected package libgfortran3:amd64. Unpacking libgfortran3:amd64 (from .../libgfortran3_4.7.2-5_amd64.deb) ... Selecting previously unselected package libnuma1. Unpacking libnuma1 (from .../libnuma1_2.0.8~rc4-1_amd64.deb) ... Selecting previously unselected package libtorque2. Unpacking libtorque2 (from .../libtorque2_2.4.16+dfsg-1+deb7u4_amd64.deb) ... Selecting previously unselected package libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.6-1_amd64.deb) ... Selecting previously unselected package libopenmpi1.3. Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.5-1_amd64.deb) ... Selecting previously unselected package openmpi-common. Unpacking openmpi-common (from .../openmpi-common_1.4.5-1_all.deb) ... Selecting previously unselected package openmpi-bin. Unpacking openmpi-bin (from .../openmpi-bin_1.4.5-1_amd64.deb) ... Selecting previously unselected package mpi-default-bin. Unpacking mpi-default-bin (from .../mpi-default-bin_1.0.1_amd64.deb) ... Selecting previously unselected package nwchem-data. Unpacking nwchem-data (from .../nwchem-data_6.1-6_all.deb) ... Selecting previously unselected package nwchem. Unpacking nwchem (from .../nwchem_6.1-6_amd64.deb) ... Setting up libquadmath0:amd64 (4.7.2-5) ... Setting up libgfortran3:amd64 (4.7.2-5) ... Setting up libnuma1 (2.0.8~rc4-1) ... Setting up libtorque2 (2.4.16+dfsg-1+deb7u4) ... Setting up libibverbs1 (1.1.6-1) ... Setting up libopenmpi1.3 (1.4.5-1) ... Setting up openmpi-common (1.4.5-1) ... Setting up openmpi-bin (1.4.5-1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode Setting up mpi-default-bin (1.0.1) ... Setting up nwchem-data (6.1-6) ... Setting up nwchem (6.1-6) ... 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-y', 'install', 'nwchem'] 0m9.3s INFO: Running scripts post_install 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_install_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_install_exceptions'] 0m9.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m9.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m9.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpeHzAZ1 to wheezy-lts 0m9.9s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ wheezy main deb http://security.debian.org wheezy/updates main 0m9.9s INFO: Running scripts pre_distupgrade 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_wheezy'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_wheezy'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'update'] 0m12.3s DUMP: Get:1 http://security.debian.org wheezy/updates Release.gpg [1601 B] Hit http://mirror-ubc.debian.org wheezy Release.gpg Hit http://mirror-ubc.debian.org wheezy Release Get:2 http://security.debian.org wheezy/updates Release [52.3 kB] Hit http://mirror-ubc.debian.org wheezy/main amd64 Packages Hit http://mirror-ubc.debian.org wheezy/main Translation-en Get:3 http://security.debian.org wheezy/updates/main amd64 Packages [589 kB] Get:4 http://security.debian.org wheezy/updates/main Translation-en [338 kB] Fetched 981 kB in 1s (839 kB/s) Reading package lists... 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'update'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-yf', 'dist-upgrade'] 0m16.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: bash gnupg gpgv libc-bin libc6 libdb5.1 login multiarch-support passwd perl-base sensible-utils tar tzdata 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 15.3 MB of archives. After this operation, 664 kB of additional disk space will be used. Get:1 http://security.debian.org/ wheezy/updates/main bash amd64 4.2+dfsg-0.1+deb7u4 [1499 kB] Get:2 http://security.debian.org/ wheezy/updates/main login amd64 1:4.1.5.1-1+deb7u1 [984 kB] Get:3 http://security.debian.org/ wheezy/updates/main perl-base amd64 5.14.2-21+deb7u6 [1534 kB] Get:4 http://security.debian.org/ wheezy/updates/main tar amd64 1.26+dfsg-0.1+deb7u1 [984 kB] Get:5 http://security.debian.org/ wheezy/updates/main libc-bin amd64 2.13-38+deb7u12 [1275 kB] Get:6 http://security.debian.org/ wheezy/updates/main libc6 amd64 2.13-38+deb7u12 [4226 kB] Get:7 http://security.debian.org/ wheezy/updates/main libdb5.1 amd64 5.1.29-5+deb7u1 [723 kB] Get:8 http://security.debian.org/ wheezy/updates/main gpgv amd64 1.4.12-7+deb7u9 [229 kB] Get:9 http://security.debian.org/ wheezy/updates/main gnupg amd64 1.4.12-7+deb7u9 [1954 kB] Get:10 http://security.debian.org/ wheezy/updates/main passwd amd64 1:4.1.5.1-1+deb7u1 [1262 kB] Get:11 http://security.debian.org/ wheezy/updates/main sensible-utils all 0.0.7+deb7u1 [9000 B] Get:12 http://security.debian.org/ wheezy/updates/main tzdata all 2018e-0+deb7u1 [496 kB] Get:13 http://security.debian.org/ wheezy/updates/main multiarch-support amd64 2.13-38+deb7u12 [152 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.3 MB in 1s (10.8 MB/s) (Reading database ... 8330 files and directories currently installed.) Preparing to replace bash 4.2+dfsg-0.1+deb7u3 (using .../bash_4.2+dfsg-0.1+deb7u4_amd64.deb) ... Unpacking replacement bash ... Setting up bash (4.2+dfsg-0.1+deb7u4) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 8330 files and directories currently installed.) Preparing to replace login 1:4.1.5.1-1 (using .../login_1%3a4.1.5.1-1+deb7u1_amd64.deb) ... Unpacking replacement login ... Setting up login (1:4.1.5.1-1+deb7u1) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace perl-base 5.14.2-21+deb7u3 (using .../perl-base_5.14.2-21+deb7u6_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-21+deb7u6) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace tar 1.26+dfsg-0.1 (using .../tar_1.26+dfsg-0.1+deb7u1_amd64.deb) ... Unpacking replacement tar ... Setting up tar (1.26+dfsg-0.1+deb7u1) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace libc-bin 2.13-38+deb7u10 (using .../libc-bin_2.13-38+deb7u12_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-38+deb7u12) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace libc6:amd64 2.13-38+deb7u10 (using .../libc6_2.13-38+deb7u12_amd64.deb) ... Unpacking replacement libc6:amd64 ... Setting up libc6:amd64 (2.13-38+deb7u12) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace libdb5.1:amd64 5.1.29-5 (using .../libdb5.1_5.1.29-5+deb7u1_amd64.deb) ... Unpacking replacement libdb5.1:amd64 ... Setting up libdb5.1:amd64 (5.1.29-5+deb7u1) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace gpgv 1.4.12-7+deb7u7 (using .../gpgv_1.4.12-7+deb7u9_amd64.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.12-7+deb7u9) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace gnupg 1.4.12-7+deb7u7 (using .../gnupg_1.4.12-7+deb7u9_amd64.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.12-7+deb7u9) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace passwd 1:4.1.5.1-1 (using .../passwd_1%3a4.1.5.1-1+deb7u1_amd64.deb) ... Unpacking replacement passwd ... Setting up passwd (1:4.1.5.1-1+deb7u1) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace sensible-utils 0.0.7 (using .../sensible-utils_0.0.7+deb7u1_all.deb) ... Unpacking replacement sensible-utils ... Setting up sensible-utils (0.0.7+deb7u1) ... (Reading database ... 8330 files and directories currently installed.) Preparing to replace tzdata 2016d-0+deb7u1 (using .../tzdata_2018e-0+deb7u1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2018e-0+deb7u1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 18 08:42:35 UTC 2018. Universal Time is now: Mon Jun 18 08:42:35 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 8342 files and directories currently installed.) Preparing to replace multiarch-support 2.13-38+deb7u10 (using .../multiarch-support_2.13-38+deb7u12_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-38+deb7u12) ... 0m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-yf', 'dist-upgrade'] 0m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m17.0s DUMP: c16ce146adddf40566e495d132dec083 - 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'show', '--no-all-versions', 'nwchem'] 0m17.0s DUMP: Package: nwchem Version: 6.1-6 Installed-Size: 58285 Maintainer: Debichem Team Architecture: amd64 Depends: mpi-default-bin, nwchem-data (= 6.1-6), libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libopenmpi1.3, libquadmath0 (>= 4.6) Description-en: High-performance computational chemistry software NWCHem is a computational chemistry program package. It provides methods which are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. . NWChem can handle: . * Molecular electronic structure methods using gaussian basis functions for high-accuracy calculations of molecules * Pseudopotentials plane-wave electronic structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals * Ab-initio and classical molecular dynamics simulations * Mixed quantum-classical simulations * Parallel scaling to thousands of processors . Features include: * Molecular electronic structure methods, analytic second derivatives: - Restricted/unrestricted Hartree-Fock (RHF, UHF) - Restricted Density Functional Theory (DFT) using many local, non-local (gradient-corrected) or hybrid (local, non-local, and HF) exchange-correlation potentials * Molecular electronic structure methods, analytic gradients: - Restricted open-shell Hartree-Fock (ROHF) - Unrestricted Density Functional Theory (DFT) - Second-order Moeller-Plesset perturbation theory (MP2), using RHF and UHF reference - Complete active space SCF (CASSCF) * Molecular electronic structure methods, single-point energies: - MP2 with resolution of the identity integral approximation (RI-MP2), using RHF and UHF reference - Coupled cluster singles and doubles, triples or pertubative triples (CCSD, CCSDT, CCSD(T)), with RHF and UHF reference - Configuration interaction (CISD, CISDT, and CISDTQ) - Second-order approximate coupled-cluster singles doubles (CC2) * Further molecular electronic structure features: - Geometry optimization including transition state searches, constraints and minimum energy paths - Vibrational frequencies - Equation-of-motion (EOM)-CCSD, EOM-CCSDT, EOM-CCSD(T), CC2, Configuration-Interaction singles (CIS), time-dependent HF (TDHF) and TDDFT, for excited states with RHF, UHF, RDFT, or UDFT reference - Solvatisation using the Conductor-like screening model (COSMO) for RHF, ROHF and DFT - Hybrid calculations using the two- and three-layer ONIOM method - Relativistic effects via spin-free and spin-orbit one-electron Douglas-Kroll and zeroth-order regular approximations (ZORA) and one-electron spin-orbit effects for DFT via spin-orbit potentials * Pseudopotential plane-wave electronic structure: - Pseudopotential Plane-Wave (PSPW), Projector Augmented Wave (PAW) or band structure methods for calculating molecules, liquids, crystals, surfaces, semi-conductors or metals - Geometry/unit cell optimization including transition state searches - Vibrational frequencies - LDA, PBE96, and PBE0 exchange-correlation potentials (restricted and unrestricted) - SIC, pert-OEP, Hartree-Fock, and hybrid functionals (restricted and unrestricted) - Hamann, Troullier-Martins and Hartwigsen-Goedecker-Hutter norm-conserving pseudopotentials with semicore corrections - Wavefunction, density, electrostatic and Wannier plotting - Band structure and density of states generation * Car-Parrinello ab-initio molecular dynamics: - Constant energy and constant temperature dynamics - Verlet algorithm for integration - Geometry constraints in cartesian coordinates * Classical molecular dynamics: - Single configuration energy evaluation - Energy minimization - Molecular dynamics simulation - Free energy simulation (multistep thermodynamic perturbation (MSTP) or multiconfiguration thermodynamic integration (MCTI) methods with options of single and/or dual topologies, double wide sampling, and separation- shifted scaling) - Force fields providing effective pair potentials, first order polarization, self consistent polarization, smooth particle mesh Ewald (SPME), periodic boundary conditions and SHAKE constraints * Mixed quantum-classical: - Mixed quantum-mechanics and molecular-mechanics (QM/MM) minimizations and molecular dynamics simulations - Quantum molecular dynamics simulation by using any of the quantum mechanical methods capable of returning gradients. Homepage: http://www.nwchem-sw.org Description-md5: dfcc0e06a4c1541597d48a663d8e6511 Tag: field::chemistry, role::program Section: science Priority: optional Filename: pool/main/n/nwchem/nwchem_6.1-6_amd64.deb Size: 14094474 MD5sum: 8de191225cc084fc1a02410b3e222c25 SHA1: d345679a9cf9e6189a7c6b21c2d2eee181b6f50e SHA256: 4322205b787656964434b14554d3727b9fc0e3aa6af8078985463a89134e44fb 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'show', '--no-all-versions', 'nwchem'] 0m17.0s INFO: apt-cache knows about the following packages: nwchem 0m17.0s INFO: Running scripts pre_install 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_database-server'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_database-server'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_exceptions'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_exceptions'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_extras'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_extras'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy'] 0m17.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ wheezy/updates/main Translation-en 500 http://security.debian.org/ wheezy/updates/main amd64 Packages release v=7.0,o=Debian,a=oldoldstable,n=wheezy,l=Debian-Security,c=main origin security.debian.org 500 http://mirror-ubc.debian.org/debian/ wheezy/main Translation-en 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror-ubc.debian.org Pinned packages: 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy', 'nwchem'] 0m17.1s DUMP: nwchem: Installed: 6.1-6 Candidate: 6.1-6 Version table: *** 6.1-6 0 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy', 'nwchem'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-y', 'install', 'nwchem'] 0m17.4s DUMP: Reading package lists... Building dependency tree... Reading state information... nwchem is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-y', 'install', 'nwchem'] 0m17.4s INFO: Running scripts post_install 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_install_exceptions'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_install_exceptions'] 0m17.4s INFO: Running scripts post_distupgrade 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_exceptions'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_exceptions'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_zz_backports'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_distupgrade_zz_backports'] 0m17.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m18.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m18.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m18.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m18.7s INFO: Running scripts pre_install 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_database-server'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_database-server'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_exceptions'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_exceptions'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_extras'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_extras'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy'] 0m18.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ wheezy/updates/main Translation-en 500 http://security.debian.org/ wheezy/updates/main amd64 Packages release v=7.0,o=Debian,a=oldoldstable,n=wheezy,l=Debian-Security,c=main origin security.debian.org 500 http://mirror-ubc.debian.org/debian/ wheezy/main Translation-en 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror-ubc.debian.org Pinned packages: 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy', 'nwchem'] 0m18.8s DUMP: nwchem: Installed: 6.1-6 Candidate: 6.1-6 Version table: *** 6.1-6 0 500 http://mirror-ubc.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-cache', 'policy', 'nwchem'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-y', 'install', 'nwchem=6.1-6'] 0m19.0s DUMP: Reading package lists... Building dependency tree... Reading state information... nwchem is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', '-y', 'install', 'nwchem=6.1-6'] 0m19.0s INFO: Running scripts post_install 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_install_exceptions'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_install_exceptions'] 0m19.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m19.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.6s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u4 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u9 install ok installed gpgv gpgv 1.4.12-7+deb7u9 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u12 install ok installed libc6:amd64 libc6 2.13-38+deb7u12 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5+deb7u1 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed libgfortran3:amd64 libgfortran3 4.7.2-5 install ok installed libibverbs1 libibverbs1 1.1.6-1 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libnuma1 libnuma1 2.0.8~rc4-1 install ok installed libopenmpi1.3 libopenmpi1.3 1.4.5-1 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libquadmath0:amd64 libquadmath0 4.7.2-5 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libtorque2 libtorque2 2.4.16+dfsg-1+deb7u4 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1+deb7u1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed mpi-default-bin mpi-default-bin 1.0.1 install ok installed multiarch-support multiarch-support 2.13-38+deb7u12 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed nwchem nwchem 6.1-6 install ok installed nwchem-data nwchem-data 6.1-6 install ok installed openmpi-bin openmpi-bin 1.4.5-1 install ok installed openmpi-common openmpi-common 1.4.5-1 install ok installed passwd passwd 1:4.1.5.1-1+deb7u1 install ok installed perl-base perl-base 5.14.2-21+deb7u6 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7+deb7u1 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1+deb7u1 install ok installed tzdata tzdata 2018e-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', '-ac', '--ignore-obsolete'] 0m21.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', '-ac', '--ignore-obsolete'] 0m21.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.4s DUMP: 0.15.1 0m21.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.4s INFO: Running adequate version 0.15.1 now. 0m21.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'nwchem'] 0m21.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'nwchem'] 0m21.5s INFO: Running scripts pre_remove 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_exceptions'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/pre_remove_exceptions'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'remove', 'libibverbs1', 'openmpi-common', 'openmpi-bin', 'libnuma1', 'libopenmpi1.3', 'libquadmath0:amd64', 'nwchem-data', 'libtorque2', 'libgfortran3:amd64', 'mpi-default-bin', 'nwchem'] 0m22.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libgfortran3 libibverbs1 libnuma1 libopenmpi1.3 libquadmath0 libtorque2 mpi-default-bin nwchem nwchem-data openmpi-bin openmpi-common 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. After this operation, 103 MB disk space will be freed. (Reading database ... 8342 files and directories currently installed.) Removing nwchem ... Removing mpi-default-bin ... Removing openmpi-bin ... Removing libopenmpi1.3 ... Removing libgfortran3:amd64 ... Removing libibverbs1 ... Removing libnuma1 ... Removing libquadmath0:amd64 ... Removing libtorque2 ... Removing nwchem-data ... Removing openmpi-common ... 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'remove', 'libibverbs1', 'openmpi-common', 'openmpi-bin', 'libnuma1', 'libopenmpi1.3', 'libquadmath0:amd64', 'nwchem-data', 'libtorque2', 'libgfortran3:amd64', 'mpi-default-bin', 'nwchem'] 0m22.5s INFO: Running scripts post_remove 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_remove_exceptions'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_remove_exceptions'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--purge', 'libibverbs1', 'openmpi-common', 'openmpi-bin', 'libnuma1', 'libopenmpi1.3', 'libquadmath0:amd64', 'nwchem-data', 'libtorque2', 'libgfortran3:amd64', 'mpi-default-bin'] 0m22.5s DUMP: (Reading database ... 6784 files and directories currently installed.) Removing libibverbs1 ... Purging configuration files for libibverbs1 ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Removing openmpi-bin ... Purging configuration files for openmpi-bin ... Removing libnuma1 ... Purging configuration files for libnuma1 ... Removing libopenmpi1.3 ... Purging configuration files for libopenmpi1.3 ... Removing libquadmath0:amd64 ... Purging configuration files for libquadmath0:amd64 ... dpkg: warning: ignoring request to remove nwchem-data which isn't installed Removing libtorque2 ... Purging configuration files for libtorque2 ... Removing libgfortran3:amd64 ... Purging configuration files for libgfortran3:amd64 ... dpkg: warning: ignoring request to remove mpi-default-bin which isn't installed 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--purge', 'libibverbs1', 'openmpi-common', 'openmpi-bin', 'libnuma1', 'libopenmpi1.3', 'libquadmath0:amd64', 'nwchem-data', 'libtorque2', 'libgfortran3:amd64', 'mpi-default-bin'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--purge', 'nwchem'] 0m22.6s DUMP: dpkg: warning: ignoring request to remove nwchem which isn't installed 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--purge', 'nwchem'] 0m22.6s INFO: Running scripts post_purge 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_purge_exceptions'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_purge_exceptions'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--purge', '--pending'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--purge', '--pending'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--remove', '--pending'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg', '--remove', '--pending'] 0m22.6s INFO: Running scripts post_test 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_test_exceptions'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'tmp/scripts/post_test_exceptions'] 0m22.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m23.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg-divert', '--list'] 0m23.1s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'dpkg-divert', '--list'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'clean'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1', 'apt-get', 'clean'] 0m23.1s DEBUG: Recording chroot state 0m24.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/run/shm'] 0m24.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/run/shm'] 0m24.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/console'] 0m24.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/console'] 0m24.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/ptmx'] 0m24.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/ptmx'] 0m24.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/pts'] 0m24.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/dev/pts'] 0m24.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/proc'] 0m24.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1/proc'] 0m24.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m24.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpeHzAZ1'] 0m24.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpeHzAZ1 0m24.3s INFO: PASS: Upgrading between Debian distributions. 0m24.3s INFO: PASS: All tests. 0m24.3s INFO: piuparts run ends. ret=0 End: 2018-06-18 08:42:43 UTC