0s autopkgtest [14:21:11]: starting date and time: 2025-03-15 14:21:11+0000 0s autopkgtest [14:21:11]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:21:11]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ezbkjc43/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-36.secgroup --name adt-plucky-arm64-openmm-20250315-135740-juju-7f2275-prod-proposed-migration-environment-20-99c7d5ac-c085-45a8-8ad6-384a59fbfb34 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 169s autopkgtest [14:24:00]: testbed dpkg architecture: arm64 170s autopkgtest [14:24:01]: testbed apt version: 2.9.33 170s autopkgtest [14:24:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 170s autopkgtest [14:24:01]: testbed release detected to be: None 171s autopkgtest [14:24:02]: updating testbed package index (apt update) 171s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 172s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 172s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 172s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 172s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 172s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 173s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 173s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 173s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 173s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 173s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 173s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 173s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 173s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 173s Fetched 1094 kB in 2s (563 kB/s) 174s Reading package lists... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 176s Calculating upgrade... 176s Calculating upgrade... 176s The following packages will be upgraded: 176s python3-jinja2 strace 177s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Need to get 608 kB of archives. 177s After this operation, 11.3 kB of additional disk space will be used. 177s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 177s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 178s Fetched 608 kB in 1s (621 kB/s) 178s (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 ... 117701 files and directories currently installed.) 178s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 178s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 178s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 178s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 178s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 179s Setting up strace (6.13+ds-1ubuntu1) ... 179s Processing triggers for man-db (2.13.0-1) ... 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Solving dependencies... 181s The following packages will be REMOVED: 181s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 181s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 181s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 181s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 181s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 181s After this operation, 267 MB disk space will be freed. 181s (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 ... 117701 files and directories currently installed.) 181s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 181s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 181s Removing libpython3.12t64:arm64 (3.12.9-1) ... 181s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 181s Removing libnsl2:arm64 (1.3.0-3build3) ... 181s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 181s Removing libunwind8:arm64 (1.6.2-3.1) ... 181s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 182s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 183s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 184s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 184s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 184s /etc/kernel/postrm.d/initramfs-tools: 184s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 184s /etc/kernel/postrm.d/zz-flash-kernel: 184s flash-kernel: Kernel 6.11.0-8-generic has been removed. 184s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 184s /etc/kernel/postrm.d/zz-update-grub: 184s Sourcing file `/etc/default/grub' 184s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 184s Generating grub configuration file ... 184s Found linux image: /boot/vmlinuz-6.14.0-10-generic 184s Found initrd image: /boot/initrd.img-6.14.0-10-generic 185s Warning: os-prober will not be executed to detect other bootable partitions. 185s Systems on them will not be added to the GRUB boot configuration. 185s Check GRUB_DISABLE_OS_PROBER documentation entry. 185s Adding boot menu entry for UEFI Firmware Settings ... 185s done 185s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 185s Processing triggers for libc-bin (2.41-1ubuntu1) ... 185s (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 ... 81650 files and directories currently installed.) 185s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 185s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 185s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 185s autopkgtest [14:24:16]: upgrading testbed (apt dist-upgrade and autopurge) 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 187s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 187s Starting 2 pkgProblemResolver with broken count: 0 187s Done 188s Entering ResolveByKeep 188s 188s Calculating upgrade... 189s The following packages will be upgraded: 189s libc-bin libc-dev-bin libc6 libc6-dev locales 189s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 9530 kB of archives. 189s After this operation, 0 B of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 194s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 195s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 199s Preconfiguring packages ... 200s Fetched 9530 kB in 11s (900 kB/s) 200s (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 ... 81647 files and directories currently installed.) 200s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Setting up libc6:arm64 (2.41-1ubuntu2) ... 200s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc-bin (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 201s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up locales (2.41-1ubuntu2) ... 202s Generating locales (this might take a while)... 204s en_US.UTF-8... done 204s Generation complete. 204s Setting up libc-dev-bin (2.41-1ubuntu2) ... 204s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 204s Processing triggers for man-db (2.13.0-1) ... 205s Processing triggers for systemd (257.3-1ubuntu3) ... 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 207s Solving dependencies... 208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s autopkgtest [14:24:39]: rebooting testbed after setup commands that affected boot 242s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 249s autopkgtest [14:25:20]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 252s autopkgtest [14:25:22]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 265s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-4build1 (dsc) [2527 B] 265s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-4build1 (tar) [11.5 MB] 265s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-4build1 (diff) [22.2 kB] 265s gpgv: Signature made Tue Mar 4 17:44:28 2025 UTC 265s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 265s gpgv: Can't check signature: No public key 265s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-4build1.dsc: no acceptable signature found 266s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 266s autopkgtest [14:25:37]: testing package openmm version 8.1.2+dfsg-4build1 266s autopkgtest [14:25:37]: build not needed 276s autopkgtest [14:25:47]: test command1: preparing testbed 276s Reading package lists... 277s Building dependency tree... 277s Reading state information... 278s Starting pkgProblemResolver with broken count: 0 278s Starting 2 pkgProblemResolver with broken count: 0 278s Done 279s The following NEW packages will be installed: 279s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 279s python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 279s python3-packaging python3-pluggy python3-pytest 279s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 279s Need to get 16.1 MB of archives. 279s After this operation, 119 MB of additional disk space will be used. 279s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 279s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 280s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 280s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 282s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 286s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-4build1 [985 kB] 287s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-4build1 [333 kB] 287s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 287s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openmm arm64 8.1.2+dfsg-4build1 [7414 kB] 294s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 295s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 295s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.5-1 [252 kB] 295s Fetched 16.1 MB in 16s (1010 kB/s) 295s Selecting previously unselected package python3-numpy-dev:arm64. 296s (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 ... 81647 files and directories currently installed.) 296s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 296s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 296s Selecting previously unselected package libblas3:arm64. 296s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 296s Unpacking libblas3:arm64 (3.12.1-2) ... 296s Selecting previously unselected package libgfortran5:arm64. 296s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 296s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 296s Selecting previously unselected package liblapack3:arm64. 296s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 296s Unpacking liblapack3:arm64 (3.12.1-2) ... 296s Selecting previously unselected package python3-numpy. 296s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 296s Unpacking python3-numpy (1:2.2.3+ds-5) ... 296s Selecting previously unselected package libopenmm8.1. 296s Preparing to unpack .../05-libopenmm8.1_8.1.2+dfsg-4build1_arm64.deb ... 296s Unpacking libopenmm8.1 (8.1.2+dfsg-4build1) ... 296s Selecting previously unselected package libopenmm-dev. 296s Preparing to unpack .../06-libopenmm-dev_8.1.2+dfsg-4build1_arm64.deb ... 296s Unpacking libopenmm-dev (8.1.2+dfsg-4build1) ... 296s Selecting previously unselected package python3-iniconfig. 296s Preparing to unpack .../07-python3-iniconfig_1.1.1-2_all.deb ... 296s Unpacking python3-iniconfig (1.1.1-2) ... 296s Selecting previously unselected package python3-openmm. 296s Preparing to unpack .../08-python3-openmm_8.1.2+dfsg-4build1_arm64.deb ... 296s Unpacking python3-openmm (8.1.2+dfsg-4build1) ... 297s Selecting previously unselected package python3-packaging. 297s Preparing to unpack .../09-python3-packaging_24.2-1_all.deb ... 297s Unpacking python3-packaging (24.2-1) ... 297s Selecting previously unselected package python3-pluggy. 297s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 297s Unpacking python3-pluggy (1.5.0-1) ... 297s Selecting previously unselected package python3-pytest. 297s Preparing to unpack .../11-python3-pytest_8.3.5-1_all.deb ... 297s Unpacking python3-pytest (8.3.5-1) ... 297s Setting up python3-iniconfig (1.1.1-2) ... 297s Setting up libblas3:arm64 (3.12.1-2) ... 297s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 297s Setting up python3-packaging (24.2-1) ... 297s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 297s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 297s Setting up python3-pluggy (1.5.0-1) ... 297s Setting up libopenmm8.1 (8.1.2+dfsg-4build1) ... 297s Setting up liblapack3:arm64 (3.12.1-2) ... 297s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 297s Setting up python3-pytest (8.3.5-1) ... 298s Setting up libopenmm-dev (8.1.2+dfsg-4build1) ... 298s Setting up python3-numpy (1:2.2.3+ds-5) ... 300s Setting up python3-openmm (8.1.2+dfsg-4build1) ... 300s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 300s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 300s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 300s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 300s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 300s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 300s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 300s "(?:\s*#.*$)" "|" # comments (dumped) 300s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 300s "(\S+)" # unquoted words 300s Processing triggers for man-db (2.13.0-1) ... 301s Processing triggers for libc-bin (2.41-1ubuntu2) ... 302s autopkgtest [14:26:13]: test command1: cd wrappers/python/tests && pytest-3 302s autopkgtest [14:26:13]: test command1: [----------------------- 304s ============================= test session starts ============================== 304s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 304s rootdir: /tmp/autopkgtest.Hrnd2C/build.8AL/src/wrappers/python/tests 304s configfile: pytest.ini 304s plugins: typeguard-4.4.2 304s collected 327 items 304s 304s TestAPIUnits.py .................................. [ 10%] 304s TestATMForce.py . [ 10%] 304s TestAmberInpcrdFile.py .....s [ 12%] 312s TestAmberPrmtopFile.py ....................... [ 19%] 312s TestBytes.py . [ 19%] 338s TestCharmmFiles.py ....s..........s......... [ 27%] 338s TestCheckpointReporter.py . [ 27%] 338s TestDcdFile.py ... [ 28%] 341s TestDesmondDMSFile.py ....... [ 30%] 341s TestElement.py .... [ 32%] 365s TestForceField.py s........................................ss..s.. [ 46%] 365s TestForceGroups.py ... [ 47%] 365s TestGenerators.py .. [ 48%] 365s TestGromacsGroFile.py . [ 48%] 365s TestGromacsTopFile.py sssssssssssss [ 52%] 818s TestIntegrators.py .s..... [ 54%] 819s TestMetadynamics.py . [ 55%] 859s TestModeller.py .............s............. [ 63%] 859s TestNumpyCompatibility.py ......... [ 66%] 860s TestPatches.py ..... [ 67%] 866s TestPdbFile.py ...... [ 69%] 873s TestPdbReporter.py ........ [ 71%] 875s TestPdbxFile.py ....... [ 74%] 876s TestPickle.py ... [ 74%] 879s TestSimulatedTempering.py .. [ 75%] 913s TestSimulation.py ....... [ 77%] 913s TestStateDataReporter.py . [ 77%] 913s TestSwigWrappers.py . [ 78%] 913s TestTopology.py ... [ 79%] 913s TestUnitCell.py .. [ 79%] 913s TestUnits.py ...................................................... [ 96%] 913s TestVec3.py ....... [ 98%] 913s TestXtcFile.py ..... [100%] 913s 913s =============================== warnings summary =============================== 913s :488 913s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 913s 913s :488 913s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 913s 913s :488 913s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 913s 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 913s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 913s warnings.warn( 913s 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 913s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 913s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 913s warnings.warn( 913s 913s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 913s =========== 305 passed, 22 skipped, 10 warnings in 610.39s (0:10:10) =========== 914s autopkgtest [14:36:25]: test command1: -----------------------] 914s command1 PASS 914s autopkgtest [14:36:25]: test command1: - - - - - - - - - - results - - - - - - - - - - 915s autopkgtest [14:36:26]: @@@@@@@@@@@@@@@@@@@@ summary 915s command1 PASS 932s nova [W] Using flock in prodstack6-arm64 932s Creating nova instance adt-plucky-arm64-openmm-20250315-135740-juju-7f2275-prod-proposed-migration-environment-20-99c7d5ac-c085-45a8-8ad6-384a59fbfb34 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 932s nova [W] Timed out waiting for 3ab5d820-5700-4dc6-86cd-5ea8e1014c64 to get deleted.