0s autopkgtest [11:28:09]: starting date and time: 2024-11-15 11:28:09+0000 0s autopkgtest [11:28:09]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:28:09]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ujdzphgw/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-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-24.secgroup --name adt-plucky-amd64-openmm-20241115-112808-juju-7f2275-prod-proposed-migration-environment-15-dae185b5-35b4-4497-bb4a-a925314fd3d0 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/ 38s autopkgtest [11:28:47]: testbed dpkg architecture: amd64 38s autopkgtest [11:28:47]: testbed apt version: 2.9.8 38s autopkgtest [11:28:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1056 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [833 kB] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [297 kB] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 39s Fetched 2704 kB in 1s (3333 kB/s) 39s Reading package lists... 42s Reading package lists... 42s Building dependency tree... 42s Reading state information... 42s Calculating upgrade... 42s The following packages will be upgraded: 42s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 42s libexpat1 lxd-installer man-db pastebinit python3-systemd xfsprogs 42s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 42s Need to get 13.6 MB of archives. 42s After this operation, 477 kB of additional disk space will be used. 42s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 43s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 43s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 43s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 43s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 43s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 43s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 43s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 43s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 43s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 43s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 43s Preconfiguring packages ... 44s Fetched 13.6 MB in 1s (13.4 MB/s) 44s (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 ... 75542 files and directories currently installed.) 44s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 44s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 44s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 44s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 44s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 44s (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 ... 75568 files and directories currently installed.) 44s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 44s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 44s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 44s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 44s Preparing to unpack .../2-grub2-common_2.12-5ubuntu7_amd64.deb ... 44s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 44s Preparing to unpack .../3-grub-pc_2.12-5ubuntu7_amd64.deb ... 44s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 44s Preparing to unpack .../4-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 44s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 44s Preparing to unpack .../5-grub-common_2.12-5ubuntu7_amd64.deb ... 44s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 45s Preparing to unpack .../6-lxd-installer_9_all.deb ... 45s Unpacking lxd-installer (9) over (8) ... 45s Preparing to unpack .../7-pastebinit_1.7.1-1_all.deb ... 45s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 45s Preparing to unpack .../8-python3-systemd_235-1build5_amd64.deb ... 45s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 45s Preparing to unpack .../9-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 45s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 45s Setting up libexpat1:amd64 (2.6.4-1) ... 45s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 45s Setting up pastebinit (1.7.1-1) ... 45s Setting up man-db (2.13.0-1) ... 45s Updating database of manual pages ... 47s man-db.service is a disabled or a static unit not running, not starting it. 47s Setting up grub-common (2.12-5ubuntu7) ... 47s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 48s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 48s update-initramfs: deferring update (trigger activated) 48s Setting up lxd-installer (9) ... 48s Setting up python3-systemd (235-1build5) ... 48s Setting up grub2-common (2.12-5ubuntu7) ... 48s Setting up grub-pc-bin (2.12-5ubuntu7) ... 48s Setting up grub-pc (2.12-5ubuntu7) ... 49s Installing for i386-pc platform. 49s Installation finished. No error reported. 49s Sourcing file `/etc/default/grub' 49s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 49s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 49s Generating grub configuration file ... 49s Found linux image: /boot/vmlinuz-6.11.0-8-generic 49s Found initrd image: /boot/initrd.img-6.11.0-8-generic 50s Warning: os-prober will not be executed to detect other bootable partitions. 50s Systems on them will not be added to the GRUB boot configuration. 50s Check GRUB_DISABLE_OS_PROBER documentation entry. 50s Adding boot menu entry for UEFI Firmware Settings ... 50s done 50s Processing triggers for libc-bin (2.40-1ubuntu3) ... 50s Processing triggers for install-info (7.1.1-1) ... 50s Processing triggers for initramfs-tools (0.142ubuntu34) ... 50s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 50s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 58s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 59s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 59s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 59s Reading package lists... 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [11:29:10]: rebooting testbed after setup commands that affected boot 77s autopkgtest [11:29:26]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 80s autopkgtest [11:29:29]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 84s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (dsc) [2508 B] 84s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (tar) [11.5 MB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (diff) [18.6 kB] 84s gpgv: Signature made Tue Sep 10 14:07:52 2024 UTC 84s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 84s gpgv: issuer "merkys@debian.org" 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-1.dsc: no acceptable signature found 85s autopkgtest [11:29:34]: testing package openmm version 8.1.2+dfsg-1 85s autopkgtest [11:29:34]: build not needed 90s autopkgtest [11:29:39]: test command1: preparing testbed 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Starting pkgProblemResolver with broken count: 0 91s Starting 2 pkgProblemResolver with broken count: 0 91s Done 92s The following additional packages will be installed: 92s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 92s python3-iniconfig python3-numpy python3-openmm python3-packaging 92s python3-pluggy python3-pytest 92s Suggested packages: 92s gcc gfortran python-numpy-doc python3-dev 92s The following NEW packages will be installed: 92s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 92s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 92s python3-packaging python3-pluggy python3-pytest 92s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 18.5 MB/18.5 MB of archives. 92s After this operation, 141 MB of additional disk space will be used. 92s Get:1 /tmp/autopkgtest.iBLiHd/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 92s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-1 [1120 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm-dev amd64 8.1.2+dfsg-1 [349 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 92s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 93s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openmm amd64 8.1.2+dfsg-1 [7536 kB] 93s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 93s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 93s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 93s Fetched 18.5 MB in 1s (16.5 MB/s) 93s Selecting previously unselected package libblas3:amd64. 93s (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 ... 75575 files and directories currently installed.) 93s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 93s Unpacking libblas3:amd64 (3.12.0-3build2) ... 94s Selecting previously unselected package libgfortran5:amd64. 94s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 94s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 94s Selecting previously unselected package liblapack3:amd64. 94s Preparing to unpack .../02-liblapack3_3.12.0-3build2_amd64.deb ... 94s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 94s Selecting previously unselected package libopenmm8.1. 94s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_amd64.deb ... 94s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 94s Selecting previously unselected package libopenmm-dev. 94s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_amd64.deb ... 94s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 94s Selecting previously unselected package python3-iniconfig. 94s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 94s Unpacking python3-iniconfig (1.1.1-2) ... 94s Selecting previously unselected package python3-numpy. 94s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 94s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 94s Selecting previously unselected package python3-openmm. 94s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_amd64.deb ... 94s Unpacking python3-openmm (8.1.2+dfsg-1) ... 94s Selecting previously unselected package python3-packaging. 94s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 94s Unpacking python3-packaging (24.1-1) ... 94s Selecting previously unselected package python3-pluggy. 94s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 94s Unpacking python3-pluggy (1.5.0-1) ... 94s Selecting previously unselected package python3-pytest. 94s Preparing to unpack .../10-python3-pytest_8.3.3-1_all.deb ... 94s Unpacking python3-pytest (8.3.3-1) ... 94s Selecting previously unselected package autopkgtest-satdep. 94s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 94s Unpacking autopkgtest-satdep (0) ... 94s Setting up python3-iniconfig (1.1.1-2) ... 94s Setting up libblas3:amd64 (3.12.0-3build2) ... 94s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 94s Setting up python3-packaging (24.1-1) ... 95s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 95s Setting up python3-pluggy (1.5.0-1) ... 95s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 95s Setting up liblapack3:amd64 (3.12.0-3build2) ... 95s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 95s Setting up python3-pytest (8.3.3-1) ... 95s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 95s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 96s Setting up python3-openmm (8.1.2+dfsg-1) ... 96s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 96s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 96s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 96s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 96s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 96s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 96s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 96s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 96s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 96s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 96s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 96s "(?:\s*#.*$)" "|" # comments (dumped) 96s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 96s "(\S+)" # unquoted words 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 97s """ Tokenizer method for the mmCIF syntax file - 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 97s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 97s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 97s "(?:\s*#.*$)" "|" # comments (dumped) 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 97s "(\S+)" # unquoted words 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 97s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 97s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 97s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 97s "(?:\s*#.*$)" "|" # comments (dumped) 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 97s "(\S+)" # unquoted words 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 97s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 97s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 97s "(?:\s*#.*$)" "|" # comments (dumped) 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 97s "(\S+)" # unquoted words 97s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 97s pattern = re.compile('bias_(.*)_(.*)\.npy') 97s /usr/lib/python3/dist-packages/openmm/openmm.py:7208: SyntaxWarning: invalid escape sequence '\S' 97s match = re.search("<([^?]\S*)", inputString) 97s Setting up autopkgtest-satdep (0) ... 97s Processing triggers for man-db (2.13.0-1) ... 97s Processing triggers for libc-bin (2.40-1ubuntu3) ... 99s (Reading database ... 77225 files and directories currently installed.) 99s Removing autopkgtest-satdep (0) ... 100s autopkgtest [11:29:49]: test command1: cd wrappers/python/tests && pytest-3 100s autopkgtest [11:29:49]: test command1: [----------------------- 101s ============================= test session starts ============================== 101s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 101s rootdir: /tmp/autopkgtest.iBLiHd/build.Alv/src/wrappers/python/tests 101s configfile: pytest.ini 101s plugins: typeguard-4.4.1 101s collected 327 items 101s 102s TestAPIUnits.py .................................. [ 10%] 102s TestATMForce.py . [ 10%] 102s TestAmberInpcrdFile.py .....s [ 12%] 108s TestAmberPrmtopFile.py ....................... [ 19%] 108s TestBytes.py . [ 19%] 133s TestCharmmFiles.py ....s..........s......... [ 27%] 133s TestCheckpointReporter.py . [ 27%] 133s TestDcdFile.py ... [ 28%] 135s TestDesmondDMSFile.py ....... [ 30%] 135s TestElement.py .... [ 32%] 154s TestForceField.py s........................................ss..s.. [ 46%] 154s TestForceGroups.py ... [ 47%] 155s TestGenerators.py .. [ 48%] 155s TestGromacsGroFile.py . [ 48%] 155s TestGromacsTopFile.py sssssssssssss [ 52%] 652s TestIntegrators.py .s..... [ 54%] 653s TestMetadynamics.py . [ 55%] 682s TestModeller.py .............s............. [ 63%] 683s TestNumpyCompatibility.py ......... [ 66%] 683s TestPatches.py ..... [ 67%] 689s TestPdbFile.py ...... [ 69%] 694s TestPdbReporter.py ........ [ 71%] 695s TestPdbxFile.py ....... [ 74%] 696s TestPickle.py ... [ 74%] 699s TestSimulatedTempering.py .. [ 75%] 732s TestSimulation.py ....... [ 77%] 732s TestStateDataReporter.py . [ 77%] 732s TestSwigWrappers.py . [ 78%] 732s TestTopology.py ... [ 79%] 732s TestUnitCell.py .. [ 79%] 732s TestUnits.py ...................................................... [ 96%] 732s TestVec3.py ....... [ 98%] 732s TestXtcFile.py ..... [100%] 732s 732s =============================== warnings summary =============================== 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 732s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 732s warnings.warn( 732s 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 732s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 732s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 732s warnings.warn( 732s 732s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 732s =========== 305 passed, 22 skipped, 7 warnings in 631.89s (0:10:31) ============ 733s autopkgtest [11:40:22]: test command1: -----------------------] 733s command1 PASS 733s autopkgtest [11:40:22]: test command1: - - - - - - - - - - results - - - - - - - - - - 733s autopkgtest [11:40:22]: @@@@@@@@@@@@@@@@@@@@ summary 733s command1 PASS 747s nova [W] Skipping flock for amd64 747s Creating nova instance adt-plucky-amd64-openmm-20241115-112808-juju-7f2275-prod-proposed-migration-environment-15-dae185b5-35b4-4497-bb4a-a925314fd3d0 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...