0s autopkgtest [19:20:27]: starting date and time: 2024-11-14 19:20:27+0000 0s autopkgtest [19:20:27]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [19:20:27]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eunus0bz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-23.secgroup --name adt-plucky-ppc64el-openmm-20241114-192027-juju-7f2275-prod-proposed-migration-environment-20-43f6e25f-eb04-4a84-919d-a0dff272b376 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 138s autopkgtest [19:22:45]: testbed dpkg architecture: ppc64el 139s autopkgtest [19:22:46]: testbed apt version: 2.9.8 139s autopkgtest [19:22:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 140s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 140s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 140s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 140s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [114 kB] 140s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [697 kB] 140s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 141s Fetched 1957 kB in 1s (1720 kB/s) 141s Reading package lists... 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Calculating upgrade... 146s The following packages will be upgraded: 146s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 146s libjson-glib-1.0-common libnewt0.52 libutempter0 pastebinit python3-bpfcc 146s python3-newt python3-systemd whiptail 146s 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 4678 kB of archives. 146s After this operation, 423 kB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 146s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 146s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 146s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 146s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 146s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 147s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 147s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 147s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 147s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 147s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 147s Fetched 4678 kB in 1s (5634 kB/s) 148s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 148s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 148s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 148s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 148s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 148s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 148s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 148s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 148s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 148s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 148s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 148s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 148s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 148s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 148s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 148s Preparing to unpack .../03-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 148s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 148s Preparing to unpack .../04-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 148s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 148s Preparing to unpack .../05-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 148s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 149s Preparing to unpack .../06-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 149s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 149s Preparing to unpack .../07-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 149s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 149s Preparing to unpack .../08-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 149s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 149s Preparing to unpack .../09-libutempter0_1.2.1-4_ppc64el.deb ... 149s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 149s Preparing to unpack .../10-pastebinit_1.7.1-1_all.deb ... 149s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 149s Preparing to unpack .../11-python3-systemd_235-1build5_ppc64el.deb ... 149s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 149s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 149s Setting up pastebinit (1.7.1-1) ... 149s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 149s Setting up libutempter0:ppc64el (1.2.1-4) ... 149s Setting up whiptail (0.52.24-2ubuntu4) ... 149s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 149s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 149s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 150s Setting up python3-systemd (235-1build5) ... 150s Setting up bpftrace (0.21.2-2ubuntu2) ... 150s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 150s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 150s Processing triggers for man-db (2.12.1-3) ... 152s Processing triggers for libc-bin (2.40-1ubuntu3) ... 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 153s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 153s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 153s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 155s Reading package lists... 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Calculating upgrade... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [19:23:07]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 161s autopkgtest [19:23:08]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 166s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (dsc) [2508 B] 166s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (tar) [11.5 MB] 166s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (diff) [18.6 kB] 166s gpgv: Signature made Tue Sep 10 14:07:52 2024 UTC 166s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 166s gpgv: issuer "merkys@debian.org" 166s gpgv: Can't check signature: No public key 166s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-1.dsc: no acceptable signature found 167s autopkgtest [19:23:14]: testing package openmm version 8.1.2+dfsg-1 168s autopkgtest [19:23:15]: build not needed 172s autopkgtest [19:23:19]: test command1: preparing testbed 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 175s Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 175s The following additional packages will be installed: 175s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 175s python3-iniconfig python3-numpy python3-openmm python3-packaging 175s python3-pluggy python3-pytest 175s Suggested packages: 175s gcc gfortran python-numpy-doc python3-dev 175s The following NEW packages will be installed: 175s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 175s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 175s python3-packaging python3-pluggy python3-pytest 176s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 17.9 MB/17.9 MB of archives. 176s After this operation, 138 MB of additional disk space will be used. 176s Get:1 /tmp/autopkgtest.EU9xnV/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 176s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 176s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 176s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 176s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm8.1 ppc64el 8.1.2+dfsg-1 [922 kB] 176s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm-dev ppc64el 8.1.2+dfsg-1 [352 kB] 176s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 176s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 176s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-openmm ppc64el 8.1.2+dfsg-1 [7509 kB] 177s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 177s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 177s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 177s Fetched 17.9 MB in 1s (16.4 MB/s) 177s Selecting previously unselected package libblas3:ppc64el. 177s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73773 files and directories currently installed.) 177s Preparing to unpack .../00-libblas3_3.12.0-3build2_ppc64el.deb ... 177s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 177s Selecting previously unselected package libgfortran5:ppc64el. 177s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 177s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 177s Selecting previously unselected package liblapack3:ppc64el. 177s Preparing to unpack .../02-liblapack3_3.12.0-3build2_ppc64el.deb ... 177s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 177s Selecting previously unselected package libopenmm8.1. 177s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_ppc64el.deb ... 177s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 178s Selecting previously unselected package libopenmm-dev. 178s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_ppc64el.deb ... 178s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 178s Selecting previously unselected package python3-iniconfig. 178s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 178s Unpacking python3-iniconfig (1.1.1-2) ... 178s Selecting previously unselected package python3-numpy. 178s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 178s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 178s Selecting previously unselected package python3-openmm. 178s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_ppc64el.deb ... 178s Unpacking python3-openmm (8.1.2+dfsg-1) ... 179s Selecting previously unselected package python3-packaging. 179s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 179s Unpacking python3-packaging (24.1-1) ... 179s Selecting previously unselected package python3-pluggy. 179s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 179s Unpacking python3-pluggy (1.5.0-1) ... 179s Selecting previously unselected package python3-pytest. 179s Preparing to unpack .../10-python3-pytest_8.3.3-1_all.deb ... 179s Unpacking python3-pytest (8.3.3-1) ... 179s Selecting previously unselected package autopkgtest-satdep. 179s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 179s Unpacking autopkgtest-satdep (0) ... 179s Setting up python3-iniconfig (1.1.1-2) ... 179s Setting up libblas3:ppc64el (3.12.0-3build2) ... 179s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 179s Setting up python3-packaging (24.1-1) ... 179s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 179s Setting up python3-pluggy (1.5.0-1) ... 180s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 180s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 180s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 180s Setting up python3-pytest (8.3.3-1) ... 180s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 180s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 184s Setting up python3-openmm (8.1.2+dfsg-1) ... 184s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 184s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 184s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 184s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 184s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 184s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 184s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 184s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 184s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 184s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 184s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 184s "(?:\s*#.*$)" "|" # comments (dumped) 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 184s "(\S+)" # unquoted words 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 184s """ Tokenizer method for the mmCIF syntax file - 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 184s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 184s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 184s "(?:\s*#.*$)" "|" # comments (dumped) 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 184s "(\S+)" # unquoted words 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 184s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 184s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 184s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 184s "(?:\s*#.*$)" "|" # comments (dumped) 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 184s "(\S+)" # unquoted words 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 184s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 184s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 184s "(?:\s*#.*$)" "|" # comments (dumped) 184s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 184s "(\S+)" # unquoted words 184s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 184s pattern = re.compile('bias_(.*)_(.*)\.npy') 184s /usr/lib/python3/dist-packages/openmm/openmm.py:8376: SyntaxWarning: invalid escape sequence '\S' 184s match = re.search("<([^?]\S*)", inputString) 184s Setting up autopkgtest-satdep (0) ... 184s Processing triggers for man-db (2.12.1-3) ... 185s Processing triggers for libc-bin (2.40-1ubuntu3) ... 188s (Reading database ... 75423 files and directories currently installed.) 188s Removing autopkgtest-satdep (0) ... 189s autopkgtest [19:23:36]: test command1: cd wrappers/python/tests && pytest-3 189s autopkgtest [19:23:36]: test command1: [----------------------- 191s ============================= test session starts ============================== 191s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 191s rootdir: /tmp/autopkgtest.EU9xnV/build.5xk/src/wrappers/python/tests 191s configfile: pytest.ini 191s plugins: typeguard-4.4.1 191s collected 327 items 191s 191s TestAPIUnits.py .................................. [ 10%] 191s TestATMForce.py . [ 10%] 191s TestAmberInpcrdFile.py .....s [ 12%] 207s TestAmberPrmtopFile.py ....................... [ 19%] 207s TestBytes.py . [ 19%] 256s TestCharmmFiles.py ....s..........s......... [ 27%] 256s TestCheckpointReporter.py . [ 27%] 256s TestDcdFile.py ... [ 28%] 261s TestDesmondDMSFile.py ....... [ 30%] 262s TestElement.py .... [ 32%] 306s TestForceField.py s........................................ss..s.. [ 46%] 306s TestForceGroups.py ... [ 47%] 307s TestGenerators.py .. [ 48%] 307s TestGromacsGroFile.py . [ 48%] 307s TestGromacsTopFile.py sssssssssssss [ 52%] 1081s TestIntegrators.py .s..... [ 54%] 1084s TestMetadynamics.py . [ 55%] 1144s TestModeller.py .............s............. [ 63%] 1144s TestNumpyCompatibility.py ......... [ 66%] 1145s TestPatches.py ..... [ 67%] 1155s TestPdbFile.py ...... [ 69%] 1163s TestPdbReporter.py ........ [ 71%] 1166s TestPdbxFile.py ....... [ 74%] 1167s TestPickle.py ... [ 74%] 1173s TestSimulatedTempering.py .. [ 75%] 1219s TestSimulation.py ....... [ 77%] 1219s TestStateDataReporter.py . [ 77%] 1219s TestSwigWrappers.py . [ 78%] 1219s TestTopology.py ... [ 79%] 1219s TestUnitCell.py .. [ 79%] 1219s TestUnits.py ...................................................... [ 96%] 1219s TestVec3.py ....... [ 98%] 1220s TestXtcFile.py ..... [100%] 1220s 1220s =============================== warnings summary =============================== 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1220s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 1220s warnings.warn( 1220s 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1220s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1220s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 1220s warnings.warn( 1220s 1220s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1220s =========== 305 passed, 22 skipped, 7 warnings in 1030.10s (0:17:10) =========== 1220s autopkgtest [19:40:47]: test command1: -----------------------] 1221s command1 PASS 1221s autopkgtest [19:40:48]: test command1: - - - - - - - - - - results - - - - - - - - - - 1221s autopkgtest [19:40:48]: @@@@@@@@@@@@@@@@@@@@ summary 1221s command1 PASS 1225s nova [W] Using flock in prodstack6-ppc64el 1225s Creating nova instance adt-plucky-ppc64el-openmm-20241114-192027-juju-7f2275-prod-proposed-migration-environment-20-43f6e25f-eb04-4a84-919d-a0dff272b376 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...