0s autopkgtest [11:37:50]: starting date and time: 2025-03-15 11:37:50+0000 1s autopkgtest [11:37:51]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [11:37:51]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4ay7v3f2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade sibelia --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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-17.secgroup --name adt-plucky-s390x-sibelia-20250315-113750-juju-7f2275-prod-proposed-migration-environment-15-42024692-6239-4324-ae66-c7ce93449150 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/ 142s autopkgtest [11:40:12]: testbed dpkg architecture: s390x 143s autopkgtest [11:40:13]: testbed apt version: 2.9.33 143s autopkgtest [11:40:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 143s autopkgtest [11:40:13]: testbed release detected to be: None 144s autopkgtest [11:40:14]: updating testbed package index (apt update) 145s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 146s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 146s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 146s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 146s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB] 146s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 146s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.7 kB] 146s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1852 B] 146s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 146s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [335 kB] 146s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB] 146s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 146s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B] 146s Fetched 1034 kB in 1s (746 kB/s) 147s Reading package lists... 147s + lsb_release --codename --short 147s + RELEASE=plucky 147s + cat 147s + [ plucky != trusty ] 147s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 147s Calculating upgrade... 148s The following packages were automatically installed and are no longer required: 148s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 148s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 148s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 148s linux-tools-6.11.0-8-generic 148s Use 'sudo apt autoremove' to remove them. 148s The following packages will be upgraded: 148s python3-jinja2 strace 148s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 609 kB of archives. 148s After this operation, 27.6 kB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 148s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 149s Fetched 609 kB in 1s (706 kB/s) 149s (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 ... 81428 files and directories currently installed.) 149s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 149s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 149s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 149s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 149s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 149s Setting up strace (6.13+ds-1ubuntu1) ... 149s Processing triggers for man-db (2.13.0-1) ... 150s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 150s + /usr/lib/apt/apt-helper analyze-pattern ?true 150s + uname -r 150s + sed s/\./\\./g 150s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 150s + apt list ?obsolete 150s + + cut -d/ -f1 150s tail -n+2 150s + grep -v ^linux-.*6\.14\.0-10-generic.* 150s + obsolete_pkgs=linux-headers-6.11.0-8-generic 150s linux-headers-6.11.0-8 150s linux-modules-6.11.0-8-generic 150s linux-tools-6.11.0-8-generic 150s linux-tools-6.11.0-8 150s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Solving dependencies... 150s The following packages will be REMOVED: 150s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 150s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 150s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 150s linux-tools-6.11.0-8-generic* 150s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 150s After this operation, 167 MB disk space will be freed. 150s (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 ... 81428 files and directories currently installed.) 150s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 150s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 150s Removing libpython3.12t64:s390x (3.12.9-1) ... 150s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 150s Removing libnsl2:s390x (1.3.0-3build3) ... 150s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 150s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 150s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 151s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 151s Processing triggers for libc-bin (2.41-1ubuntu1) ... 151s (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 ... 56328 files and directories currently installed.) 151s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 151s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 151s + grep -q trusty /etc/lsb-release 151s + [ ! -d /usr/share/doc/unattended-upgrades ] 151s + [ ! -d /usr/share/doc/lxd ] 151s + [ ! -d /usr/share/doc/lxd-client ] 151s + [ ! -d /usr/share/doc/snapd ] 151s + type iptables 151s + cat 151s + chmod 755 /etc/rc.local 151s + . /etc/rc.local 151s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 151s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 151s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 151s + uname -m 151s + [ s390x = ppc64le ] 151s + [ -d /run/systemd/system ] 151s + systemd-detect-virt --quiet --vm 151s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 151s + cat 151s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 151s + echo COMPRESS=lz4 151s autopkgtest [11:40:21]: upgrading testbed (apt dist-upgrade and autopurge) 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 152s Entering ResolveByKeep 152s 152s Calculating upgrade... 152s The following packages will be upgraded: 152s libc-bin libc-dev-bin libc6 libc6-dev locales 153s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 9512 kB of archives. 153s After this operation, 8192 B of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 154s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 154s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 156s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 157s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 160s Preconfiguring packages ... 160s Fetched 9512 kB in 7s (1323 kB/s) 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up libc6:s390x (2.41-1ubuntu2) ... 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 160s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up libc-bin (2.41-1ubuntu2) ... 160s (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 ... 56326 files and directories currently installed.) 160s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 160s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 160s Setting up locales (2.41-1ubuntu2) ... 161s Generating locales (this might take a while)... 162s en_US.UTF-8... done 162s Generation complete. 162s Setting up libc-dev-bin (2.41-1ubuntu2) ... 162s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 162s Processing triggers for man-db (2.13.0-1) ... 162s Processing triggers for systemd (257.3-1ubuntu3) ... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 164s Solving dependencies... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s autopkgtest [11:40:34]: rebooting testbed after setup commands that affected boot 183s autopkgtest [11:40:53]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 186s autopkgtest [11:40:56]: @@@@@@@@@@@@@@@@@@@@ apt-source sibelia 193s Get:1 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (dsc) [2132 B] 193s Get:2 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (tar) [4833 kB] 193s Get:3 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (diff) [10.2 kB] 193s gpgv: Signature made Tue Apr 14 08:37:29 2020 UTC 193s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 193s gpgv: issuer "tillea@rki.de" 193s gpgv: Can't check signature: No public key 193s dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-3.dsc: no acceptable signature found 193s autopkgtest [11:41:03]: testing package sibelia version 3.0.7+dfsg-3 194s autopkgtest [11:41:04]: build not needed 195s autopkgtest [11:41:05]: test run-unit-test: preparing testbed 196s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s Starting pkgProblemResolver with broken count: 0 196s Starting 2 pkgProblemResolver with broken count: 0 196s Done 196s The following NEW packages will be installed: 196s lagan libdivsufsort3 sibelia sibelia-examples 196s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 7637 kB of archives. 196s After this operation, 11.6 MB of additional disk space will be used. 196s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x lagan s390x 2.0-10 [221 kB] 197s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libdivsufsort3 s390x 2.0.1-6 [62.7 kB] 197s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x sibelia s390x 3.0.7+dfsg-3 [299 kB] 197s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x sibelia-examples all 3.0.7+dfsg-3 [7055 kB] 205s Fetched 7637 kB in 9s (823 kB/s) 206s Selecting previously unselected package lagan. 206s (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 ... 56326 files and directories currently installed.) 206s Preparing to unpack .../lagan_2.0-10_s390x.deb ... 206s Unpacking lagan (2.0-10) ... 206s Selecting previously unselected package libdivsufsort3:s390x. 206s Preparing to unpack .../libdivsufsort3_2.0.1-6_s390x.deb ... 206s Unpacking libdivsufsort3:s390x (2.0.1-6) ... 206s Selecting previously unselected package sibelia. 206s Preparing to unpack .../sibelia_3.0.7+dfsg-3_s390x.deb ... 206s Unpacking sibelia (3.0.7+dfsg-3) ... 206s Selecting previously unselected package sibelia-examples. 206s Preparing to unpack .../sibelia-examples_3.0.7+dfsg-3_all.deb ... 206s Unpacking sibelia-examples (3.0.7+dfsg-3) ... 206s Setting up lagan (2.0-10) ... 206s Setting up sibelia-examples (3.0.7+dfsg-3) ... 206s Setting up libdivsufsort3:s390x (2.0.1-6) ... 206s Setting up sibelia (3.0.7+dfsg-3) ... 206s Processing triggers for man-db (2.13.0-1) ... 206s Processing triggers for libc-bin (2.41-1ubuntu2) ... 207s autopkgtest [11:41:17]: test run-unit-test: [----------------------- 207s + cd C-Sibelia/Staphylococcus_aureus 207s + C-Sibelia.py NCTC8325.fasta RN4220.fasta 207s Calculating synteny blocks... 212s Simplification stage 1 of 3 212s Enumerating vertices of the graph, then performing bulge removal... 214s [..................................................] 219s Simplification stage 2 of 3 219s Enumerating vertices of the graph, then performing bulge removal... 221s [..................................................] 226s Simplification stage 3 of 3 226s Enumerating vertices of the graph, then performing bulge removal... 227s [..................................................] 228s Finding synteny blocks and generating the output... 233s Calling variants... 234s An error occured: b"mlagan: multial.c:459: readSubstMatrix: Assertion `file' failed.\n" 234s + cd /tmp/autopkgtest.kfLD45/autopkgtest_tmp/Sibelia/Helicobacter_pylori 234s + Sibelia -s loose Helicobacter_pylori.fasta 234s Simplification stage 1 of 4 234s Enumerating vertices of the graph, then performing bulge removal... 238s [..................................................] 238s Simplification stage 2 of 4 238s Enumerating vertices of the graph, then performing bulge removal... 240s [..................................................] 240s Simplification stage 3 of 4 240s Enumerating vertices of the graph, then performing bulge removal... 242s [..................................................] 242s Simplification stage 4 of 4 242s Enumerating vertices of the graph, then performing bulge removal... 244s [..................................................] 244s Finding synteny blocks and generating the output... 248s autopkgtest [11:41:58]: test run-unit-test: -----------------------] 248s run-unit-test PASS 248s autopkgtest [11:41:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 249s autopkgtest [11:41:59]: @@@@@@@@@@@@@@@@@@@@ summary 249s run-unit-test PASS 254s nova [W] Using flock in prodstack6-s390x 254s flock: timeout while waiting to get lock 254s Creating nova instance adt-plucky-s390x-sibelia-20250315-113750-juju-7f2275-prod-proposed-migration-environment-15-42024692-6239-4324-ae66-c7ce93449150 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 254s nova [W] Timed out waiting for e2529bf6-c5f3-4c6c-b862-6e3e989db2bf to get deleted.