1s autopkgtest [00:38:21]: starting date and time: 2025-02-21 00:38:21+0000 1s autopkgtest [00:38:21]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [00:38:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sxyet9pi/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-15@lcy02-1.secgroup --name adt-plucky-amd64-openmm-20250221-003820-juju-7f2275-prod-proposed-migration-environment-15-51804e44-b161-4ded-8fdb-4e56853e2d4d --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 44s autopkgtest [00:39:04]: testbed dpkg architecture: amd64 44s autopkgtest [00:39:04]: testbed apt version: 2.9.30 44s autopkgtest [00:39:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 44s autopkgtest [00:39:04]: testbed release detected to be: None 45s autopkgtest [00:39:05]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 45s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 45s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 45s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 45s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [729 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [89.5 kB] 45s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.8 kB] 45s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 45s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [110 kB] 45s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [136 kB] 45s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 45s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 45s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [261 kB] 45s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [691 kB] 45s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [22.5 kB] 45s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9128 B] 45s Fetched 2187 kB in 0s (6276 kB/s) 46s Reading package lists... 47s + lsb_release --codename --short 47s + RELEASE=plucky 47s + cat 47s + [ plucky != trusty ] 47s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 47s Reading package lists... 47s Building dependency tree... 47s Reading state information... 47s Calculating upgrade... 47s The following package was automatically installed and is no longer required: 47s libapt-pkg6.0t64 47s Use 'sudo apt autoremove' to remove it. 48s The following packages will be upgraded: 48s apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 48s cryptsetup-bin fwupd inetutils-telnet kbd libapt-pkg7.0 libbinutils 48s libcbor0.10 libcryptsetup12 libctf-nobfd0 libctf0 libfwupd3 libgprofng0 48s libplymouth5 libsframe1 libssl3t64 lto-disabled-list openssl 48s openssl-provider-legacy plymouth plymouth-theme-ubuntu-text python3-requests 48s telnet ubuntu-pro-client ubuntu-pro-client-l10n 48s 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 48s Need to get 16.7 MB of archives. 48s After this operation, 230 kB of additional disk space will be used. 48s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 openssl-provider-legacy amd64 3.4.1-1ubuntu1 [38.8 kB] 48s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl3t64 amd64 3.4.1-1ubuntu1 [2334 kB] 48s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30ubuntu1 [1132 kB] 48s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30ubuntu1 [1436 kB] 48s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30ubuntu1 [222 kB] 48s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 kbd amd64 2.7.1-2ubuntu1 [242 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 openssl amd64 3.4.1-1ubuntu1 [1189 kB] 48s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-pro-client-l10n amd64 34.1.3 [18.3 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-pro-client amd64 34.1.3 [241 kB] 48s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 inetutils-telnet amd64 2:2.5-6ubuntu1 [116 kB] 48s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcbor0.10 amd64 0.10.2-2ubuntu1 [26.0 kB] 48s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libplymouth5 amd64 24.004.60-2ubuntu5 [146 kB] 48s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth-theme-ubuntu-text amd64 24.004.60-2ubuntu5 [10.3 kB] 48s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth amd64 24.004.60-2ubuntu5 [140 kB] 48s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 telnet all 0.17+2.5-6ubuntu1 [3694 B] 48s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-2ubuntu1 [885 kB] 48s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-2ubuntu1 [96.5 kB] 48s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-2ubuntu1 [98.9 kB] 48s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-2ubuntu1 [1108 kB] 48s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-2ubuntu1 [585 kB] 48s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-2ubuntu1 [208 kB] 48s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-2ubuntu1 [215 kB] 48s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-2ubuntu1 [14.9 kB] 48s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libcryptsetup12 amd64 2:2.7.5-1ubuntu2 [321 kB] 48s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 cryptsetup-bin amd64 2:2.7.5-1ubuntu2 [222 kB] 48s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-3 [5408 kB] 48s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-3 [136 kB] 48s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 lto-disabled-list all 56 [12.4 kB] 48s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-requests all 2.32.3+dfsg-4ubuntu1 [52.9 kB] 48s Fetched 16.7 MB in 0s (69.1 MB/s) 48s (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 ... 109023 files and directories currently installed.) 48s Preparing to unpack .../openssl-provider-legacy_3.4.1-1ubuntu1_amd64.deb ... 48s Unpacking openssl-provider-legacy (3.4.1-1ubuntu1) over (3.4.0-1ubuntu2) ... 48s Setting up openssl-provider-legacy (3.4.1-1ubuntu1) ... 49s (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 ... 109023 files and directories currently installed.) 49s Preparing to unpack .../libssl3t64_3.4.1-1ubuntu1_amd64.deb ... 49s Unpacking libssl3t64:amd64 (3.4.1-1ubuntu1) over (3.4.0-1ubuntu2) ... 49s Setting up libssl3t64:amd64 (3.4.1-1ubuntu1) ... 49s (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 ... 109023 files and directories currently installed.) 49s Preparing to unpack .../libapt-pkg7.0_2.9.30ubuntu1_amd64.deb ... 49s Unpacking libapt-pkg7.0:amd64 (2.9.30ubuntu1) over (2.9.30) ... 49s Setting up libapt-pkg7.0:amd64 (2.9.30ubuntu1) ... 49s (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 ... 109023 files and directories currently installed.) 49s Preparing to unpack .../apt_2.9.30ubuntu1_amd64.deb ... 49s Unpacking apt (2.9.30ubuntu1) over (2.9.30) ... 49s Setting up apt (2.9.30ubuntu1) ... 50s (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 ... 109023 files and directories currently installed.) 50s Preparing to unpack .../00-apt-utils_2.9.30ubuntu1_amd64.deb ... 50s Unpacking apt-utils (2.9.30ubuntu1) over (2.9.30) ... 50s Preparing to unpack .../01-kbd_2.7.1-2ubuntu1_amd64.deb ... 50s Unpacking kbd (2.7.1-2ubuntu1) over (2.6.4-2ubuntu3) ... 50s Preparing to unpack .../02-openssl_3.4.1-1ubuntu1_amd64.deb ... 50s Unpacking openssl (3.4.1-1ubuntu1) over (3.4.0-1ubuntu2) ... 50s Preparing to unpack .../03-ubuntu-pro-client-l10n_34.1.3_amd64.deb ... 50s Unpacking ubuntu-pro-client-l10n (34.1.3) over (34.1.2) ... 50s Preparing to unpack .../04-ubuntu-pro-client_34.1.3_amd64.deb ... 50s /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. 50s for fn in glob1(directory, "%s.*" % fname): 50s Unpacking ubuntu-pro-client (34.1.3) over (34.1.2) ... 50s Preparing to unpack .../05-inetutils-telnet_2%3a2.5-6ubuntu1_amd64.deb ... 50s Unpacking inetutils-telnet (2:2.5-6ubuntu1) over (2:2.5-5ubuntu1) ... 50s Preparing to unpack .../06-libcbor0.10_0.10.2-2ubuntu1_amd64.deb ... 50s Unpacking libcbor0.10:amd64 (0.10.2-2ubuntu1) over (0.10.2-1.2ubuntu2) ... 50s Preparing to unpack .../07-libplymouth5_24.004.60-2ubuntu5_amd64.deb ... 50s Unpacking libplymouth5:amd64 (24.004.60-2ubuntu5) over (24.004.60-2ubuntu4) ... 50s Preparing to unpack .../08-plymouth-theme-ubuntu-text_24.004.60-2ubuntu5_amd64.deb ... 50s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) over (24.004.60-2ubuntu4) ... 50s Preparing to unpack .../09-plymouth_24.004.60-2ubuntu5_amd64.deb ... 50s Unpacking plymouth (24.004.60-2ubuntu5) over (24.004.60-2ubuntu4) ... 51s Preparing to unpack .../10-telnet_0.17+2.5-6ubuntu1_all.deb ... 51s Unpacking telnet (0.17+2.5-6ubuntu1) over (0.17+2.5-5ubuntu1) ... 51s Preparing to unpack .../11-libgprofng0_2.44-2ubuntu1_amd64.deb ... 51s Unpacking libgprofng0:amd64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../12-libctf0_2.44-2ubuntu1_amd64.deb ... 51s Unpacking libctf0:amd64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../13-libctf-nobfd0_2.44-2ubuntu1_amd64.deb ... 51s Unpacking libctf-nobfd0:amd64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../14-binutils-x86-64-linux-gnu_2.44-2ubuntu1_amd64.deb ... 51s Unpacking binutils-x86-64-linux-gnu (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../15-libbinutils_2.44-2ubuntu1_amd64.deb ... 51s Unpacking libbinutils:amd64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../16-binutils_2.44-2ubuntu1_amd64.deb ... 51s Unpacking binutils (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../17-binutils-common_2.44-2ubuntu1_amd64.deb ... 51s Unpacking binutils-common:amd64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../18-libsframe1_2.44-2ubuntu1_amd64.deb ... 51s Unpacking libsframe1:amd64 (2.44-2ubuntu1) over (2.44-1ubuntu1) ... 51s Preparing to unpack .../19-libcryptsetup12_2%3a2.7.5-1ubuntu2_amd64.deb ... 51s Unpacking libcryptsetup12:amd64 (2:2.7.5-1ubuntu2) over (2:2.7.2-2ubuntu1) ... 51s Preparing to unpack .../20-cryptsetup-bin_2%3a2.7.5-1ubuntu2_amd64.deb ... 51s Unpacking cryptsetup-bin (2:2.7.5-1ubuntu2) over (2:2.7.2-2ubuntu1) ... 51s Preparing to unpack .../21-fwupd_2.0.6-3_amd64.deb ... 51s Unpacking fwupd (2.0.6-3) over (2.0.5-1) ... 51s Preparing to unpack .../22-libfwupd3_2.0.6-3_amd64.deb ... 51s Unpacking libfwupd3:amd64 (2.0.6-3) over (2.0.5-1) ... 51s Preparing to unpack .../23-lto-disabled-list_56_all.deb ... 51s Unpacking lto-disabled-list (56) over (55) ... 51s Preparing to unpack .../24-python3-requests_2.32.3+dfsg-4ubuntu1_all.deb ... 52s /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. 52s for fn in glob1(directory, "%s.*" % fname): 52s Unpacking python3-requests (2.32.3+dfsg-4ubuntu1) over (2.32.3+dfsg-1ubuntu1) ... 52s Setting up lto-disabled-list (56) ... 52s Setting up apt-utils (2.9.30ubuntu1) ... 52s Setting up libcbor0.10:amd64 (0.10.2-2ubuntu1) ... 52s Setting up binutils-common:amd64 (2.44-2ubuntu1) ... 52s Setting up inetutils-telnet (2:2.5-6ubuntu1) ... 52s Setting up libctf-nobfd0:amd64 (2.44-2ubuntu1) ... 52s Setting up libfwupd3:amd64 (2.0.6-3) ... 52s Setting up libsframe1:amd64 (2.44-2ubuntu1) ... 52s Setting up python3-requests (2.32.3+dfsg-4ubuntu1) ... 52s Setting up libplymouth5:amd64 (24.004.60-2ubuntu5) ... 52s Setting up libcryptsetup12:amd64 (2:2.7.5-1ubuntu2) ... 52s Setting up kbd (2.7.1-2ubuntu1) ... 52s Setting up libbinutils:amd64 (2.44-2ubuntu1) ... 52s Setting up openssl (3.4.1-1ubuntu1) ... 52s Setting up ubuntu-pro-client (34.1.3) ... 54s Setting up fwupd (2.0.6-3) ... 54s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 54s fwupd.service is a disabled or a static unit not running, not starting it. 54s Setting up libctf0:amd64 (2.44-2ubuntu1) ... 54s Setting up cryptsetup-bin (2:2.7.5-1ubuntu2) ... 54s Setting up ubuntu-pro-client-l10n (34.1.3) ... 54s Setting up telnet (0.17+2.5-6ubuntu1) ... 54s Setting up plymouth (24.004.60-2ubuntu5) ... 54s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 55s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 55s Setting up libgprofng0:amd64 (2.44-2ubuntu1) ... 55s Setting up binutils-x86-64-linux-gnu (2.44-2ubuntu1) ... 55s Setting up binutils (2.44-2ubuntu1) ... 55s Processing triggers for dbus (1.16.0-1ubuntu1) ... 55s Processing triggers for initramfs-tools (0.145ubuntu2) ... 55s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 55s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 66s Processing triggers for libc-bin (2.40-4ubuntu1) ... 66s Processing triggers for man-db (2.13.0-1) ... 68s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) ... 68s Processing triggers for initramfs-tools (0.145ubuntu2) ... 68s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 68s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 78s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 78s + /usr/lib/apt/apt-helper analyze-pattern ?true 78s + uname -r 78s + sed s/\./\\./g 78s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 78s + apt list ?obsolete 78s + tail -n+2 78s + cut -d/ -f1 78s + grep -v ^linux-.*6\.12\.0-15-generic.* 80s + true 80s + obsolete_pkgs= 80s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 81s The following packages will be REMOVED: 81s libapt-pkg6.0t64* 81s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 81s After this operation, 3725 kB disk space will be freed. 81s (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 ... 109020 files and directories currently installed.) 81s Removing libapt-pkg6.0t64:amd64 (2.9.29) ... 81s Processing triggers for libc-bin (2.40-4ubuntu1) ... 81s + grep -q trusty /etc/lsb-release 81s + [ ! -d /usr/share/doc/unattended-upgrades ] 81s + [ ! -d /usr/share/doc/lxd ] 81s + [ ! -d /usr/share/doc/lxd-client ] 81s + [ ! -d /usr/share/doc/snapd ] 81s + type iptables 81s + cat 81s + chmod 755 /etc/rc.local 81s + . /etc/rc.local 81s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 81s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 81s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 81s + uname -m 81s + [ x86_64 = ppc64le ] 81s + [ -d /run/systemd/system ] 81s + systemd-detect-virt --quiet --vm 81s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 81s + cat 81s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 81s + echo COMPRESS=lz4 81s autopkgtest [00:39:41]: upgrading testbed (apt dist-upgrade and autopurge) 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 82s Starting 2 pkgProblemResolver with broken count: 0 82s Done 83s Entering ResolveByKeep 83s 83s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Starting pkgProblemResolver with broken count: 0 84s Starting 2 pkgProblemResolver with broken count: 0 84s Done 84s Solving dependencies... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s autopkgtest [00:39:45]: rebooting testbed after setup commands that affected boot 89s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 100s autopkgtest [00:40:00]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 101s autopkgtest [00:40:01]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 104s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (dsc) [2508 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (tar) [11.5 MB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-3 (diff) [20.6 kB] 104s gpgv: Signature made Tue Feb 4 09:57:44 2025 UTC 104s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 104s gpgv: issuer "merkys@debian.org" 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-3.dsc: no acceptable signature found 105s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 105s autopkgtest [00:40:05]: testing package openmm version 8.1.2+dfsg-3 105s autopkgtest [00:40:05]: build not needed 107s autopkgtest [00:40:07]: test command1: preparing testbed 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Starting pkgProblemResolver with broken count: 0 107s Starting 2 pkgProblemResolver with broken count: 0 107s Done 108s The following NEW packages will be installed: 108s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 108s python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 108s python3-packaging python3-pluggy python3-pytest 108s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 22.9 MB of archives. 108s After this operation, 154 MB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [147 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [8537 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-3 [1120 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm-dev amd64 8.1.2+dfsg-3 [349 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 108s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openmm amd64 8.1.2+dfsg-3 [7948 kB] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 108s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 108s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 108s Fetched 22.9 MB in 0s (68.3 MB/s) 108s Selecting previously unselected package python3-numpy-dev:amd64. 109s (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 ... 108970 files and directories currently installed.) 109s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-2_amd64.deb ... 109s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... 109s Selecting previously unselected package libblas3:amd64. 109s Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... 109s Unpacking libblas3:amd64 (3.12.1-2) ... 109s Selecting previously unselected package libgfortran5:amd64. 109s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 109s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 109s Selecting previously unselected package liblapack3:amd64. 109s Preparing to unpack .../03-liblapack3_3.12.1-2_amd64.deb ... 109s Unpacking liblapack3:amd64 (3.12.1-2) ... 109s Selecting previously unselected package python3-numpy. 109s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-2_amd64.deb ... 109s Unpacking python3-numpy (1:2.2.3+ds-2) ... 109s Selecting previously unselected package libopenmm8.1. 109s Preparing to unpack .../05-libopenmm8.1_8.1.2+dfsg-3_amd64.deb ... 109s Unpacking libopenmm8.1 (8.1.2+dfsg-3) ... 109s Selecting previously unselected package libopenmm-dev. 109s Preparing to unpack .../06-libopenmm-dev_8.1.2+dfsg-3_amd64.deb ... 109s Unpacking libopenmm-dev (8.1.2+dfsg-3) ... 109s Selecting previously unselected package python3-iniconfig. 109s Preparing to unpack .../07-python3-iniconfig_1.1.1-2_all.deb ... 109s Unpacking python3-iniconfig (1.1.1-2) ... 109s Selecting previously unselected package python3-openmm. 109s Preparing to unpack .../08-python3-openmm_8.1.2+dfsg-3_amd64.deb ... 109s Unpacking python3-openmm (8.1.2+dfsg-3) ... 110s Selecting previously unselected package python3-packaging. 110s Preparing to unpack .../09-python3-packaging_24.2-1_all.deb ... 110s Unpacking python3-packaging (24.2-1) ... 110s Selecting previously unselected package python3-pluggy. 110s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 110s Unpacking python3-pluggy (1.5.0-1) ... 110s Selecting previously unselected package python3-pytest. 110s Preparing to unpack .../11-python3-pytest_8.3.4-1_all.deb ... 110s Unpacking python3-pytest (8.3.4-1) ... 110s Setting up python3-iniconfig (1.1.1-2) ... 110s Setting up libblas3:amd64 (3.12.1-2) ... 110s 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 110s Setting up python3-packaging (24.2-1) ... 110s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2) ... 110s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 110s Setting up python3-pluggy (1.5.0-1) ... 110s Setting up libopenmm8.1 (8.1.2+dfsg-3) ... 110s Setting up liblapack3:amd64 (3.12.1-2) ... 110s 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 110s Setting up python3-pytest (8.3.4-1) ... 111s Setting up libopenmm-dev (8.1.2+dfsg-3) ... 111s Setting up python3-numpy (1:2.2.3+ds-2) ... 112s Setting up python3-openmm (8.1.2+dfsg-3) ... 112s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 112s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 113s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 113s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 113s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 113s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 113s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 113s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 113s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 113s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 113s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 113s "(?:\s*#.*$)" "|" # comments (dumped) 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 113s "(\S+)" # unquoted words 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 113s """ Tokenizer method for the mmCIF syntax file - 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 113s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 113s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 113s "(?:\s*#.*$)" "|" # comments (dumped) 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 113s "(\S+)" # unquoted words 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 113s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 113s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 113s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 113s "(?:\s*#.*$)" "|" # comments (dumped) 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 113s "(\S+)" # unquoted words 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 113s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 113s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 113s "(?:\s*#.*$)" "|" # comments (dumped) 113s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 113s "(\S+)" # unquoted words 113s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 113s pattern = re.compile('bias_(.*)_(.*)\.npy') 113s /usr/lib/python3/dist-packages/openmm/openmm.py:6170: SyntaxWarning: invalid escape sequence '\S' 113s match = re.search("<([^?]\S*)", inputString) 113s Processing triggers for man-db (2.13.0-1) ... 113s Processing triggers for libc-bin (2.40-4ubuntu1) ... 114s autopkgtest [00:40:14]: test command1: cd wrappers/python/tests && pytest-3 114s autopkgtest [00:40:14]: test command1: [----------------------- 116s ============================= test session starts ============================== 116s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 116s rootdir: /tmp/autopkgtest.M6xTF7/build.4OM/src/wrappers/python/tests 116s configfile: pytest.ini 116s plugins: typeguard-4.4.1 116s collected 327 items 116s 116s TestAPIUnits.py .................................. [ 10%] 116s TestATMForce.py . [ 10%] 116s TestAmberInpcrdFile.py .....s [ 12%] 125s TestAmberPrmtopFile.py ....................... [ 19%] 125s TestBytes.py . [ 19%] 156s TestCharmmFiles.py ....s..........s......... [ 27%] 156s TestCheckpointReporter.py . [ 27%] 156s TestDcdFile.py ... [ 28%] 158s TestDesmondDMSFile.py ....... [ 30%] 158s TestElement.py .... [ 32%] 181s TestForceField.py s........................................ss..s.. [ 46%] 181s TestForceGroups.py ... [ 47%] 181s TestGenerators.py .. [ 48%] 181s TestGromacsGroFile.py . [ 48%] 181s TestGromacsTopFile.py sssssssssssss [ 52%] 797s TestIntegrators.py .s..... [ 54%] 798s TestMetadynamics.py . [ 55%] 834s TestModeller.py .............s............. [ 63%] 834s TestNumpyCompatibility.py ......... [ 66%] 834s TestPatches.py ..... [ 67%] 840s TestPdbFile.py ...... [ 69%] 846s TestPdbReporter.py ........ [ 71%] 848s TestPdbxFile.py ....... [ 74%] 849s TestPickle.py ... [ 74%] 852s TestSimulatedTempering.py .. [ 75%] 893s TestSimulation.py ....... [ 77%] 893s TestStateDataReporter.py . [ 77%] 893s TestSwigWrappers.py . [ 78%] 893s TestTopology.py ... [ 79%] 893s TestUnitCell.py .. [ 79%] 893s TestUnits.py ...................................................... [ 96%] 893s TestVec3.py ....... [ 98%] 894s TestXtcFile.py ..... [100%] 894s 894s =============================== warnings summary =============================== 894s :488 894s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 894s 894s :488 894s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 894s 894s :488 894s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 894s 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 894s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 894s warnings.warn( 894s 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 894s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 894s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 894s warnings.warn( 894s 894s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 894s =========== 305 passed, 22 skipped, 10 warnings in 778.59s (0:12:58) =========== 894s autopkgtest [00:53:14]: test command1: -----------------------] 894s autopkgtest [00:53:14]: test command1: - - - - - - - - - - results - - - - - - - - - - 894s command1 PASS 894s autopkgtest [00:53:14]: @@@@@@@@@@@@@@@@@@@@ summary 894s command1 PASS 916s nova [W] Skipping flock for amd64 916s Creating nova instance adt-plucky-amd64-openmm-20250221-003820-juju-7f2275-prod-proposed-migration-environment-15-51804e44-b161-4ded-8fdb-4e56853e2d4d from image adt/ubuntu-plucky-amd64-server-20250220.img (UUID 0ec9a92a-064a-4cac-a94d-46a889669cdf)... 916s nova [W] Timed out waiting for 5d60d560-2f83-412c-813b-3eeba1131f92 to get deleted.