0s autopkgtest [23:47:44]: starting date and time: 2025-02-20 23:47:44+0000 0s autopkgtest [23:47:44]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:47:44]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w2ympkbf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy,src:geophar,src:mpi4py,src:onnxruntime,src:petsc4py,src:pyinstaller,src:sympy,src:umap-learn --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=numpy/1:2.2.3+ds-2 geophar/18.10+dfsg1-6 mpi4py/4.0.3-1ubuntu1 onnxruntime/1.20.1+dfsg-2 petsc4py/3.22.3-1 pyinstaller/6.12.0+ds-2 sympy/1.13.3-3 umap-learn/0.5.4+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-40.secgroup --name adt-plucky-arm64-openmm-20250220-234744-juju-7f2275-prod-proposed-migration-environment-20-fbc52f26-eb0f-4aec-9b06-6bf36e7415a4 --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/ 89s autopkgtest [23:49:13]: testbed dpkg architecture: arm64 89s autopkgtest [23:49:13]: testbed apt version: 2.9.30 89s autopkgtest [23:49:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 89s autopkgtest [23:49:13]: testbed release detected to be: None 90s autopkgtest [23:49:14]: updating testbed package index (apt update) 91s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 91s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 91s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 91s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 91s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.8 kB] 91s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [89.5 kB] 91s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [729 kB] 91s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 91s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [127 kB] 91s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 91s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [676 kB] 91s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.7 kB] 92s Fetched 1768 kB in 1s (1689 kB/s) 93s Reading package lists... 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 95s The following package was automatically installed and is no longer required: 95s libapt-pkg6.0t64 95s Use 'sudo apt autoremove' to remove it. 95s The following packages will be upgraded: 95s apt apt-utils binutils binutils-aarch64-linux-gnu binutils-common 95s cryptsetup-bin fwupd inetutils-telnet kbd libapt-pkg7.0 libbinutils 95s libcryptsetup12 libctf-nobfd0 libctf0 libfwupd3 libgprofng0 libplymouth5 95s libsframe1 libssl3t64 openssl openssl-provider-legacy plymouth 95s plymouth-theme-ubuntu-text python3-requests telnet ubuntu-pro-client 95s ubuntu-pro-client-l10n 95s 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 16.4 MB of archives. 95s After this operation, 60.4 kB disk space will be freed. 95s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 openssl-provider-legacy arm64 3.4.1-1ubuntu1 [38.6 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libssl3t64 arm64 3.4.1-1ubuntu1 [2641 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30ubuntu1 [1024 kB] 96s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30ubuntu1 [1367 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30ubuntu1 [207 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 kbd arm64 2.7.1-2ubuntu1 [230 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 openssl arm64 3.4.1-1ubuntu1 [1162 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 ubuntu-pro-client-l10n arm64 34.1.3 [18.3 kB] 96s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 ubuntu-pro-client arm64 34.1.3 [240 kB] 96s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 inetutils-telnet arm64 2:2.5-6ubuntu1 [104 kB] 96s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libplymouth5 arm64 24.004.60-2ubuntu5 [141 kB] 96s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60-2ubuntu5 [9948 B] 96s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 plymouth arm64 24.004.60-2ubuntu5 [135 kB] 96s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 telnet all 0.17+2.5-6ubuntu1 [3694 B] 96s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgprofng0 arm64 2.44-2ubuntu1 [778 kB] 96s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libctf0 arm64 2.44-2ubuntu1 [99.2 kB] 96s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libctf-nobfd0 arm64 2.44-2ubuntu1 [103 kB] 96s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 binutils-aarch64-linux-gnu arm64 2.44-2ubuntu1 [965 kB] 96s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libbinutils arm64 2.44-2ubuntu1 [784 kB] 96s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 binutils arm64 2.44-2ubuntu1 [209 kB] 96s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 binutils-common arm64 2.44-2ubuntu1 [215 kB] 96s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libsframe1 arm64 2.44-2ubuntu1 [14.6 kB] 96s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libcryptsetup12 arm64 2:2.7.5-1ubuntu2 [271 kB] 96s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 cryptsetup-bin arm64 2:2.7.5-1ubuntu2 [217 kB] 96s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 fwupd arm64 2.0.6-3 [5288 kB] 96s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libfwupd3 arm64 2.0.6-3 [129 kB] 96s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-requests all 2.32.3+dfsg-4ubuntu1 [52.9 kB] 97s Fetched 16.4 MB in 1s (15.4 MB/s) 97s (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 ... 116718 files and directories currently installed.) 97s Preparing to unpack .../openssl-provider-legacy_3.4.1-1ubuntu1_arm64.deb ... 97s Unpacking openssl-provider-legacy (3.4.1-1ubuntu1) over (3.4.0-1ubuntu2) ... 97s Setting up openssl-provider-legacy (3.4.1-1ubuntu1) ... 97s (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 ... 116718 files and directories currently installed.) 97s Preparing to unpack .../libssl3t64_3.4.1-1ubuntu1_arm64.deb ... 97s Unpacking libssl3t64:arm64 (3.4.1-1ubuntu1) over (3.4.0-1ubuntu2) ... 97s Setting up libssl3t64:arm64 (3.4.1-1ubuntu1) ... 97s (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 ... 116717 files and directories currently installed.) 97s Preparing to unpack .../libapt-pkg7.0_2.9.30ubuntu1_arm64.deb ... 97s Unpacking libapt-pkg7.0:arm64 (2.9.30ubuntu1) over (2.9.30) ... 98s Setting up libapt-pkg7.0:arm64 (2.9.30ubuntu1) ... 98s (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 ... 116717 files and directories currently installed.) 98s Preparing to unpack .../apt_2.9.30ubuntu1_arm64.deb ... 98s Unpacking apt (2.9.30ubuntu1) over (2.9.30) ... 98s Setting up apt (2.9.30ubuntu1) ... 99s (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 ... 116717 files and directories currently installed.) 99s Preparing to unpack .../00-apt-utils_2.9.30ubuntu1_arm64.deb ... 99s Unpacking apt-utils (2.9.30ubuntu1) over (2.9.30) ... 99s Preparing to unpack .../01-kbd_2.7.1-2ubuntu1_arm64.deb ... 99s Unpacking kbd (2.7.1-2ubuntu1) over (2.6.4-2ubuntu3) ... 99s Preparing to unpack .../02-openssl_3.4.1-1ubuntu1_arm64.deb ... 99s Unpacking openssl (3.4.1-1ubuntu1) over (3.4.0-1ubuntu2) ... 99s Preparing to unpack .../03-ubuntu-pro-client-l10n_34.1.3_arm64.deb ... 99s Unpacking ubuntu-pro-client-l10n (34.1.3) over (34.1.2) ... 99s Preparing to unpack .../04-ubuntu-pro-client_34.1.3_arm64.deb ... 100s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 100s for fn in glob1(directory, "%s.*" % fname): 100s Unpacking ubuntu-pro-client (34.1.3) over (34.1.2) ... 100s Preparing to unpack .../05-inetutils-telnet_2%3a2.5-6ubuntu1_arm64.deb ... 100s Unpacking inetutils-telnet (2:2.5-6ubuntu1) over (2:2.5-5ubuntu1) ... 100s Preparing to unpack .../06-libplymouth5_24.004.60-2ubuntu5_arm64.deb ... 100s Unpacking libplymouth5:arm64 (24.004.60-2ubuntu5) over (24.004.60-2ubuntu4) ... 100s Preparing to unpack .../07-plymouth-theme-ubuntu-text_24.004.60-2ubuntu5_arm64.deb ... 100s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) over (24.004.60-2ubuntu4) ... 100s Preparing to unpack .../08-plymouth_24.004.60-2ubuntu5_arm64.deb ... 100s Unpacking plymouth (24.004.60-2ubuntu5) over (24.004.60-2ubuntu4) ... 100s Preparing to unpack .../09-telnet_0.17+2.5-6ubuntu1_all.deb ... 100s Unpacking telnet (0.17+2.5-6ubuntu1) over (0.17+2.5-5ubuntu1) ... 100s Preparing to unpack .../10-libgprofng0_2.44-2ubuntu1_arm64.deb ... 100s Unpacking libgprofng0:arm64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 101s Preparing to unpack .../11-libctf0_2.44-2ubuntu1_arm64.deb ... 101s Unpacking libctf0:arm64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 101s Preparing to unpack .../12-libctf-nobfd0_2.44-2ubuntu1_arm64.deb ... 101s Unpacking libctf-nobfd0:arm64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 101s Preparing to unpack .../13-binutils-aarch64-linux-gnu_2.44-2ubuntu1_arm64.deb ... 101s Unpacking binutils-aarch64-linux-gnu (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 102s Preparing to unpack .../14-libbinutils_2.44-2ubuntu1_arm64.deb ... 102s Unpacking libbinutils:arm64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 102s Preparing to unpack .../15-binutils_2.44-2ubuntu1_arm64.deb ... 102s Unpacking binutils (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 102s Preparing to unpack .../16-binutils-common_2.44-2ubuntu1_arm64.deb ... 102s Unpacking binutils-common:arm64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 103s Preparing to unpack .../17-libsframe1_2.44-2ubuntu1_arm64.deb ... 103s Unpacking libsframe1:arm64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 103s Preparing to unpack .../18-libcryptsetup12_2%3a2.7.5-1ubuntu2_arm64.deb ... 103s Unpacking libcryptsetup12:arm64 (2:2.7.5-1ubuntu2) over (2:2.7.2-2ubuntu1) ... 103s Preparing to unpack .../19-cryptsetup-bin_2%3a2.7.5-1ubuntu2_arm64.deb ... 103s Unpacking cryptsetup-bin (2:2.7.5-1ubuntu2) over (2:2.7.2-2ubuntu1) ... 103s Preparing to unpack .../20-fwupd_2.0.6-3_arm64.deb ... 104s Unpacking fwupd (2.0.6-3) over (2.0.5-1) ... 104s Preparing to unpack .../21-libfwupd3_2.0.6-3_arm64.deb ... 104s Unpacking libfwupd3:arm64 (2.0.6-3) over (2.0.5-1) ... 104s Preparing to unpack .../22-python3-requests_2.32.3+dfsg-4ubuntu1_all.deb ... 104s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 104s for fn in glob1(directory, "%s.*" % fname): 104s Unpacking python3-requests (2.32.3+dfsg-4ubuntu1) over (2.32.3+dfsg-1ubuntu1) ... 104s Setting up apt-utils (2.9.30ubuntu1) ... 104s Setting up binutils-common:arm64 (2.44-2ubuntu1) ... 104s Setting up inetutils-telnet (2:2.5-6ubuntu1) ... 104s Setting up libctf-nobfd0:arm64 (2.44-2ubuntu1) ... 104s Setting up libfwupd3:arm64 (2.0.6-3) ... 104s Setting up libsframe1:arm64 (2.44-2ubuntu1) ... 104s Setting up python3-requests (2.32.3+dfsg-4ubuntu1) ... 104s Setting up libplymouth5:arm64 (24.004.60-2ubuntu5) ... 104s Setting up libcryptsetup12:arm64 (2:2.7.5-1ubuntu2) ... 104s Setting up kbd (2.7.1-2ubuntu1) ... 104s Setting up libbinutils:arm64 (2.44-2ubuntu1) ... 104s Setting up openssl (3.4.1-1ubuntu1) ... 104s Setting up ubuntu-pro-client (34.1.3) ... 106s Setting up fwupd (2.0.6-3) ... 107s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 107s fwupd.service is a disabled or a static unit not running, not starting it. 107s Setting up libctf0:arm64 (2.44-2ubuntu1) ... 107s Setting up cryptsetup-bin (2:2.7.5-1ubuntu2) ... 107s Setting up ubuntu-pro-client-l10n (34.1.3) ... 107s Setting up telnet (0.17+2.5-6ubuntu1) ... 107s Setting up plymouth (24.004.60-2ubuntu5) ... 107s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 107s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 108s Setting up binutils-aarch64-linux-gnu (2.44-2ubuntu1) ... 108s Setting up libgprofng0:arm64 (2.44-2ubuntu1) ... 108s Setting up binutils (2.44-2ubuntu1) ... 108s Processing triggers for dbus (1.16.0-1ubuntu1) ... 108s Processing triggers for initramfs-tools (0.145ubuntu2) ... 108s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 108s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 130s System running in EFI mode, skipping. 130s Processing triggers for libc-bin (2.40-4ubuntu1) ... 130s Processing triggers for man-db (2.13.0-1) ... 132s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) ... 132s Processing triggers for initramfs-tools (0.145ubuntu2) ... 132s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 132s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 152s System running in EFI mode, skipping. 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Solving dependencies... 154s The following packages will be REMOVED: 154s libapt-pkg6.0t64* 155s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 155s After this operation, 3410 kB disk space will be freed. 155s (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 ... 116714 files and directories currently installed.) 155s Removing libapt-pkg6.0t64:arm64 (2.9.29) ... 155s Processing triggers for libc-bin (2.40-4ubuntu1) ... 155s autopkgtest [23:50:19]: upgrading testbed (apt dist-upgrade and autopurge) 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 157s Entering ResolveByKeep 158s 158s Calculating upgrade... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s Starting pkgProblemResolver with broken count: 0 159s Starting 2 pkgProblemResolver with broken count: 0 159s Done 160s Solving dependencies... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s autopkgtest [23:50:24]: rebooting testbed after setup commands that affected boot 185s autopkgtest [23:50:49]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 189s autopkgtest [23:50:53]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 193s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (dsc) [2508 B] 193s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (tar) [11.5 MB] 193s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (diff) [20.6 kB] 194s gpgv: Signature made Tue Feb 4 09:57:44 2025 UTC 194s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 194s gpgv: issuer "merkys@debian.org" 194s gpgv: Can't check signature: No public key 194s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-3.dsc: no acceptable signature found 194s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 195s autopkgtest [23:50:59]: testing package openmm version 8.1.2+dfsg-3 195s autopkgtest [23:50:59]: build not needed 203s autopkgtest [23:51:07]: test command1: preparing testbed 203s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Starting pkgProblemResolver with broken count: 0 204s Starting 2 pkgProblemResolver with broken count: 0 204s Done 205s The following NEW packages will be installed: 205s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 205s python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 205s python3-packaging python3-pluggy python3-pytest 205s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 205s Need to get 17.0 MB of archives. 205s After this operation, 132 MB of additional disk space will be used. 205s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-2 [145 kB] 205s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 206s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 206s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 206s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:2.2.3+ds-2 [4583 kB] 207s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-3 [987 kB] 207s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-3 [333 kB] 207s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 207s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openmm arm64 8.1.2+dfsg-3 [7726 kB] 207s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 207s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 207s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 208s Fetched 17.0 MB in 2s (7261 kB/s) 208s Selecting previously unselected package python3-numpy-dev:arm64. 208s (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 ... 116664 files and directories currently installed.) 208s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-2_arm64.deb ... 208s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-2) ... 208s Selecting previously unselected package libblas3:arm64. 208s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 208s Unpacking libblas3:arm64 (3.12.1-2) ... 208s Selecting previously unselected package libgfortran5:arm64. 208s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 208s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 208s Selecting previously unselected package liblapack3:arm64. 208s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 208s Unpacking liblapack3:arm64 (3.12.1-2) ... 208s Selecting previously unselected package python3-numpy. 209s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-2_arm64.deb ... 209s Unpacking python3-numpy (1:2.2.3+ds-2) ... 209s Selecting previously unselected package libopenmm8.1. 209s Preparing to unpack .../05-libopenmm8.1_8.1.2+dfsg-3_arm64.deb ... 209s Unpacking libopenmm8.1 (8.1.2+dfsg-3) ... 209s Selecting previously unselected package libopenmm-dev. 209s Preparing to unpack .../06-libopenmm-dev_8.1.2+dfsg-3_arm64.deb ... 209s Unpacking libopenmm-dev (8.1.2+dfsg-3) ... 209s Selecting previously unselected package python3-iniconfig. 209s Preparing to unpack .../07-python3-iniconfig_1.1.1-2_all.deb ... 209s Unpacking python3-iniconfig (1.1.1-2) ... 209s Selecting previously unselected package python3-openmm. 209s Preparing to unpack .../08-python3-openmm_8.1.2+dfsg-3_arm64.deb ... 209s Unpacking python3-openmm (8.1.2+dfsg-3) ... 209s Selecting previously unselected package python3-packaging. 209s Preparing to unpack .../09-python3-packaging_24.2-1_all.deb ... 209s Unpacking python3-packaging (24.2-1) ... 209s Selecting previously unselected package python3-pluggy. 209s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 209s Unpacking python3-pluggy (1.5.0-1) ... 209s Selecting previously unselected package python3-pytest. 209s Preparing to unpack .../11-python3-pytest_8.3.4-1_all.deb ... 209s Unpacking python3-pytest (8.3.4-1) ... 210s Setting up python3-iniconfig (1.1.1-2) ... 210s Setting up libblas3:arm64 (3.12.1-2) ... 210s 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 210s Setting up python3-packaging (24.2-1) ... 210s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-2) ... 210s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 210s Setting up python3-pluggy (1.5.0-1) ... 210s Setting up libopenmm8.1 (8.1.2+dfsg-3) ... 210s Setting up liblapack3:arm64 (3.12.1-2) ... 210s 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 210s Setting up python3-pytest (8.3.4-1) ... 210s Setting up libopenmm-dev (8.1.2+dfsg-3) ... 210s Setting up python3-numpy (1:2.2.3+ds-2) ... 213s Setting up python3-openmm (8.1.2+dfsg-3) ... 213s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 213s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 213s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 213s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 213s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 213s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 213s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 213s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 213s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 213s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 213s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 213s "(?:\s*#.*$)" "|" # comments (dumped) 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 213s "(\S+)" # unquoted words 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 213s """ Tokenizer method for the mmCIF syntax file - 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 213s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 213s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 213s "(?:\s*#.*$)" "|" # comments (dumped) 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 213s "(\S+)" # unquoted words 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 213s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 213s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 213s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 213s "(?:\s*#.*$)" "|" # comments (dumped) 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 213s "(\S+)" # unquoted words 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 213s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 213s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 213s "(?:\s*#.*$)" "|" # comments (dumped) 213s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 213s "(\S+)" # unquoted words 213s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 213s pattern = re.compile('bias_(.*)_(.*)\.npy') 213s /usr/lib/python3/dist-packages/openmm/openmm.py:11753: SyntaxWarning: invalid escape sequence '\S' 213s match = re.search("<([^?]\S*)", inputString) 213s Processing triggers for man-db (2.13.0-1) ... 214s Processing triggers for libc-bin (2.40-4ubuntu1) ... 215s autopkgtest [23:51:19]: test command1: cd wrappers/python/tests && pytest-3 215s autopkgtest [23:51:19]: test command1: [----------------------- 217s ============================= test session starts ============================== 217s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 217s rootdir: /tmp/autopkgtest.wJv4RS/build.Pu8/src/wrappers/python/tests 217s configfile: pytest.ini 217s plugins: typeguard-4.4.1 217s collected 327 items 217s 217s TestAPIUnits.py .................................. [ 10%] 217s TestATMForce.py . [ 10%] 217s TestAmberInpcrdFile.py .....s [ 12%] 224s TestAmberPrmtopFile.py ....................... [ 19%] 224s TestBytes.py . [ 19%] 254s TestCharmmFiles.py ....s..........s......... [ 27%] 254s TestCheckpointReporter.py . [ 27%] 254s TestDcdFile.py ... [ 28%] 256s TestDesmondDMSFile.py ....... [ 30%] 257s TestElement.py .... [ 32%] 283s TestForceField.py s........................................ss..s.. [ 46%] 283s TestForceGroups.py ... [ 47%] 283s TestGenerators.py .. [ 48%] 283s TestGromacsGroFile.py . [ 48%] 283s TestGromacsTopFile.py sssssssssssss [ 52%] 744s TestIntegrators.py .s..... [ 54%] 746s TestMetadynamics.py . [ 55%] 788s TestModeller.py .............s............. [ 63%] 788s TestNumpyCompatibility.py ......... [ 66%] 788s TestPatches.py ..... [ 67%] 795s TestPdbFile.py ...... [ 69%] 801s TestPdbReporter.py ........ [ 71%] 803s TestPdbxFile.py ....... [ 74%] 804s TestPickle.py ... [ 74%] 807s TestSimulatedTempering.py .. [ 75%] 840s TestSimulation.py ....... [ 77%] 840s TestStateDataReporter.py . [ 77%] 840s TestSwigWrappers.py . [ 78%] 840s TestTopology.py ... [ 79%] 840s TestUnitCell.py .. [ 79%] 840s TestUnits.py ...................................................... [ 96%] 840s TestVec3.py ....... [ 98%] 841s TestXtcFile.py ..... [100%] 841s 841s =============================== warnings summary =============================== 841s :488 841s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 841s 841s :488 841s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 841s 841s :488 841s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 841s 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 841s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 841s warnings.warn( 841s 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 841s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 841s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 841s warnings.warn( 841s 841s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 841s =========== 305 passed, 22 skipped, 10 warnings in 624.62s (0:10:24) =========== 841s autopkgtest [00:01:45]: test command1: -----------------------] 842s command1 PASS 842s autopkgtest [00:01:46]: test command1: - - - - - - - - - - results - - - - - - - - - - 842s autopkgtest [00:01:46]: @@@@@@@@@@@@@@@@@@@@ summary 842s command1 PASS 860s nova [W] Using flock in prodstack6-arm64 860s Creating nova instance adt-plucky-arm64-openmm-20250220-234744-juju-7f2275-prod-proposed-migration-environment-20-fbc52f26-eb0f-4aec-9b06-6bf36e7415a4 from image adt/ubuntu-plucky-arm64-server-20250220.img (UUID 397b70ef-022d-4aca-a546-c65dd921737c)... 860s nova [W] Timed out waiting for 6d55bc94-b9d2-4f46-836b-3da0d2f35777 to get deleted.