Start: 2018-03-07 11:51:16 UTC [wheezy] Package: cp2k Version: 2.2.426-8 Installed-Size: 55667 Maintainer: Debichem Team Architecture: amd64 Depends: libblacs-mpi1, libblas3 | libblas.so.3 | libatlas3-base, libc6 (>= 2.2.5), libfftw3-3, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libint1, liblapack3 | liblapack.so.3 | libatlas3-base, libopenmpi1.3, libquadmath0 (>= 4.6), libscalapack-mpi1 (>= 1.8.0), cp2k-data (= 2.2.426-8) Description: Ab Initio Molecular Dynamics Homepage: http://www.cp2k.org Description-md5: 1b7591df5b2f8a198994cf0a198d3fb1 Section: science Priority: optional Filename: pool/main/c/cp2k/cp2k_2.2.426-8_amd64.deb Size: 12494920 MD5sum: c373821874ba7e9c4adc102d30c43a31 SHA1: 26e9ef35d288dccbd45cd55bb36bc77e1895f757 SHA256: 921960aa2d000c9eea25a72d65b546f6d147483fbfffeb6e3f01bae2022c00c2 [wheezy-lts] Package: cp2k Version: 2.2.426-8 Installed-Size: 55667 Maintainer: Debichem Team Architecture: amd64 Depends: libblacs-mpi1, libblas3 | libblas.so.3 | libatlas3-base, libc6 (>= 2.2.5), libfftw3-3, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libint1, liblapack3 | liblapack.so.3 | libatlas3-base, libopenmpi1.3, libquadmath0 (>= 4.6), libscalapack-mpi1 (>= 1.8.0), cp2k-data (= 2.2.426-8) Description: Ab Initio Molecular Dynamics Homepage: http://www.cp2k.org Description-md5: 1b7591df5b2f8a198994cf0a198d3fb1 Section: science Priority: optional Filename: pool/main/c/cp2k/cp2k_2.2.426-8_amd64.deb Size: 12494920 MD5sum: c373821874ba7e9c4adc102d30c43a31 SHA1: 26e9ef35d288dccbd45cd55bb36bc77e1895f757 SHA256: 921960aa2d000c9eea25a72d65b546f6d147483fbfffeb6e3f01bae2022c00c2 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.bm.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 cp2k=2.2.426-8 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 0.84~201801121530~0.83-4-g6e16ed9a 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.bm.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 cp2k=2.2.426-8 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-6-amd64 #1 SMP Debian 4.9.82-1+deb9u3 (2018-03-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp7elz4i 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp7elz4i 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp7elz4i', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m4.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp7elz4i', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m4.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp7elz4i/proc'] 0m4.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp7elz4i/proc'] 0m4.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/pts'] 0m4.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/pts'] 0m4.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/ptmx'] 0m4.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/ptmx'] 0m4.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/console'] 0m4.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/console'] 0m4.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp7elz4i/run/shm'] 0m5.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp7elz4i/run/shm'] 0m5.0s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main 0m5.8s DEBUG: Created policy-rc.d and chmodded it. 0m5.8s DEBUG: Created resolv.conf. 0m5.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp7elz4i/tmp/scripts/ 0m6.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmp7elz4i/tmp/scripts/ 0m6.2s INFO: Running scripts post_chroot_unpack 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'update'] 0m9.2s DUMP: Hit http://mirror.bm.debian.org wheezy Release.gpg Hit http://mirror.bm.debian.org wheezy Release Hit http://mirror.bm.debian.org wheezy/main amd64 Packages Hit http://mirror.bm.debian.org wheezy/main Translation-en Reading package lists... 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'update'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-yf', 'dist-upgrade'] 0m9.7s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-yf', 'dist-upgrade'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.2s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.2s INFO: Running scripts post_setup 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_dummy_users'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_dummy_users'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_experimental'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_experimental'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_forbid_home'] 0m12.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_forbid_home'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_force-unsafe-io'] 0m12.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_force-unsafe-io'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_minimize'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_minimize'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_squeeze-backports'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_squeeze-backports'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m13.6s 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.bm.debian.org/debian/ wheezy/main adduser all 3.113+nmu3 [264 kB] Get:2 http://mirror.bm.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 (17.7 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) ... 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_zz_backports'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_setup_zz_backports'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.7s 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 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.7s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m14.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m15.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m15.7s INFO: Running scripts is_testable 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/is_testable_uninstallable'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/is_testable_uninstallable'] 0m15.7s INFO: Running scripts pre_test 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_test_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_test_exceptions'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_test_root_password'] 0m15.8s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_test_root_password'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'show', 'cp2k'] 0m15.8s DUMP: Package: cp2k Version: 2.2.426-8 Installed-Size: 55667 Maintainer: Debichem Team Architecture: amd64 Depends: libblacs-mpi1, libblas3 | libblas.so.3 | libatlas3-base, libc6 (>= 2.2.5), libfftw3-3, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libint1, liblapack3 | liblapack.so.3 | libatlas3-base, libopenmpi1.3, libquadmath0 (>= 4.6), libscalapack-mpi1 (>= 1.8.0), cp2k-data (= 2.2.426-8) Description-en: Ab Initio Molecular Dynamics CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-inito molecular dynamics (AIMD) simulations. Features include: . Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module: . * Density-Functional Theory (DFT) Calculations with various Exchange- Correlation (XC) functionals * Hartree-Fock (HF) Calculations * Gas phase or Periodic boundary conditions (PBC) * Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), augmented plane waves (APW) and a mixed Gaussian and (augmented) plane wave approach (GPW / GAPW) * Pseudo-Potentials (PP) including the norm-conserving, seperable Goedecker-Teter-Hutter (GTH) PP * Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE * Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS * Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3 * Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models * Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges and for HFX via Auxiliary Density Matrix Methods (ADMM) * Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation * Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer * Excited states via time-dependent DFT (TDDFT) . Ab-initio Molecular Dynamics: . * Born-Oppenheimer Molecular Dynamics (BOMD) * Ehrenfest Molecular Dynamics (EMD) * PS extrapolation of initial wavefunction * Time-reversible Always Stable Predictor-Corrector (ASPC) integrator * Approximate Car-Parinello like Langevin Born-Oppenheimer Molecular Dynamics . Mixed quantum-classical (QM/MM) simulations: . * Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part * Linear-scaling electrostatic coupling treating of periodic boundary conditions . Further Features include: . * Single-point energies, geometry optimizations and frequency calculations * Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations * Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations and density-functional tight-binding (DFTB), with or without periodic boundary conditions * Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats * Metadynamics including well-tempered Metadynamics for Free Energy calculations * Classical Force-Field (MM) simulations * Monte-Carlo (MC) KS-DFT simulations * HFX module for linear-scaling MD simulations using hybrid functionals * Static (e.g. spectra) and dynamical (e.g. diffusion) properties . CP2K does not implement Car-Parinello Molecular Dynamics (CPMD). Homepage: http://www.cp2k.org Description-md5: 1b7591df5b2f8a198994cf0a198d3fb1 Section: science Priority: optional Filename: pool/main/c/cp2k/cp2k_2.2.426-8_amd64.deb Size: 12494920 MD5sum: c373821874ba7e9c4adc102d30c43a31 SHA1: 26e9ef35d288dccbd45cd55bb36bc77e1895f757 SHA256: 921960aa2d000c9eea25a72d65b546f6d147483fbfffeb6e3f01bae2022c00c2 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'show', 'cp2k'] 0m15.8s INFO: apt-cache knows about the following packages: cp2k 0m15.8s INFO: Running scripts pre_install 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_database-server'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_database-server'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_exceptions'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_exceptions'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_extras'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_extras'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy'] 0m15.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy', 'cp2k'] 0m16.0s DUMP: cp2k: Installed: (none) Candidate: 2.2.426-8 Version table: 2.2.426-8 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy', 'cp2k'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-y', 'install', 'cp2k'] 0m21.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: cp2k-data libblacs-mpi1 libblas3 libfftw3-3 libgfortran3 libgomp1 libibverbs1 libint1 liblapack3 libnuma1 libopenmpi1.3 libquadmath0 libscalapack-mpi1 libtorque2 mpi-default-bin openmpi-bin openmpi-common Suggested packages: libfftw3-bin libfftw3-dev scalapack-doc gfortran Recommended packages: openmpi-checkpoint The following NEW packages will be installed: cp2k cp2k-data libblacs-mpi1 libblas3 libfftw3-3 libgfortran3 libgomp1 libibverbs1 libint1 liblapack3 libnuma1 libopenmpi1.3 libquadmath0 libscalapack-mpi1 libtorque2 mpi-default-bin openmpi-bin openmpi-common 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. Need to get 35.5 MB of archives. After this operation, 117 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main libgomp1 amd64 4.7.2-5 [27.5 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main libfftw3-3 amd64 3.3.2-3.1 [1665 kB] Get:3 http://mirror.bm.debian.org/debian/ wheezy/main libquadmath0 amd64 4.7.2-5 [125 kB] Get:4 http://mirror.bm.debian.org/debian/ wheezy/main libgfortran3 amd64 4.7.2-5 [351 kB] Get:5 http://mirror.bm.debian.org/debian/ wheezy/main libibverbs1 amd64 1.1.6-1 [35.3 kB] Get:6 http://mirror.bm.debian.org/debian/ wheezy/main libnuma1 amd64 2.0.8~rc4-1 [33.7 kB] Get:7 http://mirror.bm.debian.org/debian/ wheezy/main libtorque2 amd64 2.4.16+dfsg-1+deb7u4 [121 kB] Get:8 http://mirror.bm.debian.org/debian/ wheezy/main libopenmpi1.3 amd64 1.4.5-1 [1436 kB] Get:9 http://mirror.bm.debian.org/debian/ wheezy/main openmpi-common all 1.4.5-1 [101 kB] Get:10 http://mirror.bm.debian.org/debian/ wheezy/main openmpi-bin amd64 1.4.5-1 [166 kB] Get:11 http://mirror.bm.debian.org/debian/ wheezy/main mpi-default-bin amd64 1.0.1 [2990 B] Get:12 http://mirror.bm.debian.org/debian/ wheezy/main libblacs-mpi1 amd64 1.1-31 [68.4 kB] Get:13 http://mirror.bm.debian.org/debian/ wheezy/main libblas3 amd64 1.2.20110419-5 [293 kB] Get:14 http://mirror.bm.debian.org/debian/ wheezy/main libint1 amd64 1.1.4-1 [971 kB] Get:15 http://mirror.bm.debian.org/debian/ wheezy/main liblapack3 amd64 3.4.1+dfsg-1+deb70u1 [5036 kB] Get:16 http://mirror.bm.debian.org/debian/ wheezy/main libscalapack-mpi1 amd64 1.8.0-9 [3201 kB] Get:17 http://mirror.bm.debian.org/debian/ wheezy/main cp2k-data all 2.2.426-8 [9358 kB] Get:18 http://mirror.bm.debian.org/debian/ wheezy/main cp2k amd64 2.2.426-8 [12.5 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.5 MB in 1s (20.4 MB/s) Selecting previously unselected package libgomp1:amd64. (Reading database ... 6768 files and directories currently installed.) Unpacking libgomp1:amd64 (from .../libgomp1_4.7.2-5_amd64.deb) ... Selecting previously unselected package libfftw3-3:amd64. Unpacking libfftw3-3:amd64 (from .../libfftw3-3_3.3.2-3.1_amd64.deb) ... Selecting previously unselected package libquadmath0:amd64. 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 libibverbs1. Unpacking libibverbs1 (from .../libibverbs1_1.1.6-1_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 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 libblacs-mpi1. Unpacking libblacs-mpi1 (from .../libblacs-mpi1_1.1-31_amd64.deb) ... Selecting previously unselected package libblas3. Unpacking libblas3 (from .../libblas3_1.2.20110419-5_amd64.deb) ... Selecting previously unselected package libint1. Unpacking libint1 (from .../libint1_1.1.4-1_amd64.deb) ... Selecting previously unselected package liblapack3. Unpacking liblapack3 (from .../liblapack3_3.4.1+dfsg-1+deb70u1_amd64.deb) ... Selecting previously unselected package libscalapack-mpi1. Unpacking libscalapack-mpi1 (from .../libscalapack-mpi1_1.8.0-9_amd64.deb) ... Selecting previously unselected package cp2k-data. Unpacking cp2k-data (from .../cp2k-data_2.2.426-8_all.deb) ... Selecting previously unselected package cp2k. Unpacking cp2k (from .../cp2k_2.2.426-8_amd64.deb) ... Setting up libgomp1:amd64 (4.7.2-5) ... Setting up libfftw3-3:amd64 (3.3.2-3.1) ... Setting up libquadmath0:amd64 (4.7.2-5) ... Setting up libgfortran3:amd64 (4.7.2-5) ... Setting up libibverbs1 (1.1.6-1) ... Setting up libnuma1 (2.0.8~rc4-1) ... Setting up libtorque2 (2.4.16+dfsg-1+deb7u4) ... 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 libblacs-mpi1 (1.1-31) ... Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libint1 (1.1.4-1) ... Setting up liblapack3 (3.4.1+dfsg-1+deb70u1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libscalapack-mpi1 (1.8.0-9) ... Setting up cp2k-data (2.2.426-8) ... Setting up cp2k (2.2.426-8) ... 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-y', 'install', 'cp2k'] 0m21.9s INFO: Running scripts post_install 0m21.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_install_exceptions'] 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_install_exceptions'] 0m21.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m23.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m23.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp7elz4i to wheezy-lts 0m23.3s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main deb http://security.debian.org wheezy/updates main 0m23.3s INFO: Running scripts pre_distupgrade 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_exceptions'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_exceptions'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_wheezy'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_wheezy'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'update'] 0m26.6s DUMP: Hit http://mirror.bm.debian.org wheezy Release.gpg Hit http://mirror.bm.debian.org wheezy Release Get:1 http://security.debian.org wheezy/updates Release.gpg [1601 B] Hit http://mirror.bm.debian.org wheezy/main amd64 Packages Get:2 http://security.debian.org wheezy/updates Release [39.0 kB] Hit http://mirror.bm.debian.org wheezy/main Translation-en Get:3 http://security.debian.org wheezy/updates/main amd64 Packages [613 kB] Get:4 http://security.debian.org wheezy/updates/main Translation-en [335 kB] Fetched 989 kB in 1s (744 kB/s) Reading package lists... 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'update'] 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-yf', 'dist-upgrade'] 0m32.8s 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+deb7u5 [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 2018c-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 (15.1 MB/s) (Reading database ... 9301 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 ... 9301 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 ... 9301 files and directories currently installed.) Preparing to replace perl-base 5.14.2-21+deb7u3 (using .../perl-base_5.14.2-21+deb7u5_amd64.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.14.2-21+deb7u5) ... (Reading database ... 9301 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 ... 9301 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 ... 9301 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 ... 9301 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 ... 9301 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 ... 9301 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 ... 9301 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 ... 9301 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 ... 9301 files and directories currently installed.) Preparing to replace tzdata 2016d-0+deb7u1 (using .../tzdata_2018c-0+deb7u1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2018c-0+deb7u1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Mar 7 11:51:54 UTC 2018. Universal Time is now: Wed Mar 7 11:51:54 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 9313 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) ... 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-yf', 'dist-upgrade'] 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.2s DUMP: 2b0a253bdabce4c78e0bf2073791efa8 - 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'show', 'cp2k'] 0m33.2s DUMP: Package: cp2k Version: 2.2.426-8 Installed-Size: 55667 Maintainer: Debichem Team Architecture: amd64 Depends: libblacs-mpi1, libblas3 | libblas.so.3 | libatlas3-base, libc6 (>= 2.2.5), libfftw3-3, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), libint1, liblapack3 | liblapack.so.3 | libatlas3-base, libopenmpi1.3, libquadmath0 (>= 4.6), libscalapack-mpi1 (>= 1.8.0), cp2k-data (= 2.2.426-8) Description-en: Ab Initio Molecular Dynamics CP2K is a program to perform simulations of solid state, liquid, molecular and biological systems. It is especially aimed at massively parallel and linear scaling electronic structure methods and state-of-the-art ab-inito molecular dynamics (AIMD) simulations. Features include: . Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module: . * Density-Functional Theory (DFT) Calculations with various Exchange- Correlation (XC) functionals * Hartree-Fock (HF) Calculations * Gas phase or Periodic boundary conditions (PBC) * Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo- potential plane-waves (PW), augmented plane waves (APW) and a mixed Gaussian and (augmented) plane wave approach (GPW / GAPW) * Pseudo-Potentials (PP) including the norm-conserving, seperable Goedecker-Teter-Hutter (GTH) PP * Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5, PW92 and PADE * Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and HCTH120 as well as the meta-GGA XC functional TPSS * Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including B3LYP, PBE0 and MCY3 * Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models * Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges (DDAPC) charges and for HFX via Auxiliary Density Matrix Methods (ADMM) * Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS) matrix computation * Orbital Transformation (OT) or Direct Inversion of the iterative subspace (DIIS) self-consistent field (SCF) minimizer * Excited states via time-dependent DFT (TDDFT) . Ab-initio Molecular Dynamics: . * Born-Oppenheimer Molecular Dynamics (BOMD) * Ehrenfest Molecular Dynamics (EMD) * PS extrapolation of initial wavefunction * Time-reversible Always Stable Predictor-Corrector (ASPC) integrator * Approximate Car-Parinello like Langevin Born-Oppenheimer Molecular Dynamics . Mixed quantum-classical (QM/MM) simulations: . * Real-space multigrid approach for the evaluation of the Coulomb interactions between the QM and the MM part * Linear-scaling electrostatic coupling treating of periodic boundary conditions . Further Features include: . * Single-point energies, geometry optimizations and frequency calculations * Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB) for minimum energy path (MEP) calculations * Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL and PM6 parametrizations and density-functional tight-binding (DFTB), with or without periodic boundary conditions * Classical Molecular Dynamics (MD) simulations in microcanonical ensemble (NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling through velocity rescaling (CSVR) thermostats * Metadynamics including well-tempered Metadynamics for Free Energy calculations * Classical Force-Field (MM) simulations * Monte-Carlo (MC) KS-DFT simulations * HFX module for linear-scaling MD simulations using hybrid functionals * Static (e.g. spectra) and dynamical (e.g. diffusion) properties . CP2K does not implement Car-Parinello Molecular Dynamics (CPMD). Homepage: http://www.cp2k.org Description-md5: 1b7591df5b2f8a198994cf0a198d3fb1 Section: science Priority: optional Filename: pool/main/c/cp2k/cp2k_2.2.426-8_amd64.deb Size: 12494920 MD5sum: c373821874ba7e9c4adc102d30c43a31 SHA1: 26e9ef35d288dccbd45cd55bb36bc77e1895f757 SHA256: 921960aa2d000c9eea25a72d65b546f6d147483fbfffeb6e3f01bae2022c00c2 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'show', 'cp2k'] 0m33.2s INFO: apt-cache knows about the following packages: cp2k 0m33.2s INFO: Running scripts pre_install 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_database-server'] 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_database-server'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_exceptions'] 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_exceptions'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_extras'] 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_extras'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy'] 0m33.4s 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.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m33.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy'] 0m33.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy', 'cp2k'] 0m33.4s DUMP: cp2k: Installed: 2.2.426-8 Candidate: 2.2.426-8 Version table: *** 2.2.426-8 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m33.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy', 'cp2k'] 0m33.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-y', 'install', 'cp2k'] 0m34.0s DUMP: Reading package lists... Building dependency tree... Reading state information... cp2k is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-y', 'install', 'cp2k'] 0m34.0s INFO: Running scripts post_install 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_install_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_install_exceptions'] 0m34.0s INFO: Running scripts post_distupgrade 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_experimental'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_experimental'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m35.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m35.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m37.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m37.0s INFO: Running scripts pre_install 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_database-server'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_database-server'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_exceptions'] 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_exceptions'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_extras'] 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_extras'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy'] 0m37.1s 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.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy', 'cp2k'] 0m37.2s DUMP: cp2k: Installed: 2.2.426-8 Candidate: 2.2.426-8 Version table: *** 2.2.426-8 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 100 /var/lib/dpkg/status 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-cache', 'policy', 'cp2k'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-y', 'install', 'cp2k=2.2.426-8'] 0m37.8s DUMP: Reading package lists... Building dependency tree... Reading state information... cp2k is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', '-y', 'install', 'cp2k=2.2.426-8'] 0m37.8s INFO: Running scripts post_install 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_install_exceptions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_install_exceptions'] 0m37.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m39.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.4s 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 cp2k cp2k 2.2.426-8 install ok installed cp2k-data cp2k-data 2.2.426-8 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 libblacs-mpi1 libblacs-mpi1 1.1-31 install ok installed libblas3 libblas3 1.2.20110419-5 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 libfftw3-3:amd64 libfftw3-3 3.3.2-3.1 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed libgfortran3:amd64 libgfortran3 4.7.2-5 install ok installed libgomp1:amd64 libgomp1 4.7.2-5 install ok installed libibverbs1 libibverbs1 1.1.6-1 install ok installed libint1 libint1 1.1.4-1 install ok installed liblapack3 liblapack3 3.4.1+dfsg-1+deb70u1 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 libscalapack-mpi1 libscalapack-mpi1 1.8.0-9 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 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+deb7u5 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 2018c-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 0m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp7elz4i', '-ac', '--ignore-obsolete'] 0m43.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp7elz4i', '-ac', '--ignore-obsolete'] 0m43.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.5s DUMP: 0.15.1 0m43.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.5s INFO: Running adequate version 0.15.1 now. 0m43.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'cp2k'] 0m43.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'cp2k'] 0m43.8s INFO: Running scripts pre_remove 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m46.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m46.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_exceptions'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/pre_remove_exceptions'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'remove', 'liblapack3', 'libblas3', 'openmpi-bin', 'libscalapack-mpi1', 'libibverbs1', 'libblacs-mpi1', 'cp2k-data', 'libquadmath0:amd64', 'libfftw3-3:amd64', 'openmpi-common', 'libopenmpi1.3', 'libnuma1', 'libtorque2', 'libint1', 'libgomp1:amd64', 'libgfortran3:amd64', 'mpi-default-bin', 'cp2k'] 0m48.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: cp2k cp2k-data libblacs-mpi1 libblas3 libfftw3-3 libgfortran3 libgomp1 libibverbs1 libint1 liblapack3 libnuma1 libopenmpi1.3 libquadmath0 libscalapack-mpi1 libtorque2 mpi-default-bin openmpi-bin openmpi-common 0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded. After this operation, 117 MB disk space will be freed. (Reading database ... 9313 files and directories currently installed.) Removing cp2k ... Removing cp2k-data ... Removing libscalapack-mpi1 ... Removing libblacs-mpi1 ... Removing liblapack3 ... Removing libblas3 ... Removing libfftw3-3:amd64 ... Removing mpi-default-bin ... Removing openmpi-bin ... Removing libopenmpi1.3 ... Removing libgfortran3:amd64 ... Removing libgomp1:amd64 ... Removing libibverbs1 ... Removing libint1 ... Removing libnuma1 ... Removing libquadmath0:amd64 ... Removing libtorque2 ... Removing openmpi-common ... 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'remove', 'liblapack3', 'libblas3', 'openmpi-bin', 'libscalapack-mpi1', 'libibverbs1', 'libblacs-mpi1', 'cp2k-data', 'libquadmath0:amd64', 'libfftw3-3:amd64', 'openmpi-common', 'libopenmpi1.3', 'libnuma1', 'libtorque2', 'libint1', 'libgomp1:amd64', 'libgfortran3:amd64', 'mpi-default-bin', 'cp2k'] 0m48.1s INFO: Running scripts post_remove 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_remove_exceptions'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_remove_exceptions'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_remove_extras'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_remove_extras'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--purge', 'liblapack3', 'libblas3', 'openmpi-bin', 'libscalapack-mpi1', 'libibverbs1', 'libblacs-mpi1', 'cp2k-data', 'libquadmath0:amd64', 'libfftw3-3:amd64', 'openmpi-common', 'libopenmpi1.3', 'libnuma1', 'libtorque2', 'libint1', 'libgomp1:amd64', 'libgfortran3:amd64', 'mpi-default-bin'] 0m48.4s DUMP: (Reading database ... 6784 files and directories currently installed.) Removing liblapack3 ... Purging configuration files for liblapack3 ... dpkg: warning: ignoring request to remove libblas3 which isn't installed Removing openmpi-bin ... Purging configuration files for openmpi-bin ... Removing libscalapack-mpi1 ... Purging configuration files for libscalapack-mpi1 ... Removing libibverbs1 ... Purging configuration files for libibverbs1 ... Removing libblacs-mpi1 ... Purging configuration files for libblacs-mpi1 ... dpkg: warning: ignoring request to remove cp2k-data which isn't installed Removing libquadmath0:amd64 ... Purging configuration files for libquadmath0:amd64 ... Removing libfftw3-3:amd64 ... Purging configuration files for libfftw3-3:amd64 ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Removing libopenmpi1.3 ... Purging configuration files for libopenmpi1.3 ... Removing libnuma1 ... Purging configuration files for libnuma1 ... Removing libtorque2 ... Purging configuration files for libtorque2 ... Removing libint1 ... Purging configuration files for libint1 ... Removing libgomp1:amd64 ... Purging configuration files for libgomp1:amd64 ... Removing libgfortran3:amd64 ... Purging configuration files for libgfortran3:amd64 ... dpkg: warning: ignoring request to remove mpi-default-bin which isn't installed 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--purge', 'liblapack3', 'libblas3', 'openmpi-bin', 'libscalapack-mpi1', 'libibverbs1', 'libblacs-mpi1', 'cp2k-data', 'libquadmath0:amd64', 'libfftw3-3:amd64', 'openmpi-common', 'libopenmpi1.3', 'libnuma1', 'libtorque2', 'libint1', 'libgomp1:amd64', 'libgfortran3:amd64', 'mpi-default-bin'] 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--purge', 'cp2k'] 0m48.4s DUMP: dpkg: warning: ignoring request to remove cp2k which isn't installed 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--purge', 'cp2k'] 0m48.4s INFO: Running scripts post_purge 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_purge_exceptions'] 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_purge_exceptions'] 0m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--purge', '--pending'] 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--purge', '--pending'] 0m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--remove', '--pending'] 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg', '--remove', '--pending'] 0m48.5s INFO: Running scripts post_test 0m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_test_exceptions'] 0m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'tmp/scripts/post_test_exceptions'] 0m48.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m49.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg-divert', '--list'] 0m49.5s 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 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'dpkg-divert', '--list'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'clean'] 0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7elz4i', 'apt-get', 'clean'] 0m49.6s DEBUG: Recording chroot state 0m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/run/shm'] 0m52.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/run/shm'] 0m52.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/console'] 0m52.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/console'] 0m52.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/ptmx'] 0m52.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/ptmx'] 0m52.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/pts'] 0m53.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/dev/pts'] 0m53.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/proc'] 0m53.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7elz4i/proc'] 0m53.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m53.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp7elz4i'] 0m53.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp7elz4i 0m53.3s INFO: PASS: Upgrading between Debian distributions. 0m53.3s INFO: PASS: All tests. 0m53.3s INFO: piuparts run ends. ret=0 End: 2018-03-07 11:52:15 UTC