0s autopkgtest [07:54:31]: starting date and time: 2025-02-19 07:54:31+0000 0s autopkgtest [07:54:31]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [07:54:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s6p6mcdd/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:tm-align --apt-upgrade tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=tm-align/20190822+dfsg-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-4.secgroup --name adt-plucky-ppc64el-tm-align-20250219-075431-juju-7f2275-prod-proposed-migration-environment-2-947d7832-3c7e-49f7-bd99-c8cb2f8212d3 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -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/ 106s autopkgtest [07:56:17]: testbed dpkg architecture: ppc64el 106s autopkgtest [07:56:17]: testbed apt version: 2.9.29 107s autopkgtest [07:56:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 107s autopkgtest [07:56:18]: testbed release detected to be: None 108s autopkgtest [07:56:19]: updating testbed package index (apt update) 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 108s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 108s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.3 kB] 109s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [734 kB] 109s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 109s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [91.9 kB] 109s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B] 109s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [638 kB] 109s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [6324 B] 109s Fetched 1673 kB in 1s (1467 kB/s) 111s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Calculating upgrade... 112s The following NEW packages will be installed: 112s libapt-pkg7.0 112s The following packages will be upgraded: 112s apt apt-utils dhcpcd-base rsyslog 112s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 3731 kB of archives. 112s After this operation, 3926 kB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libapt-pkg7.0 ppc64el 2.9.30 [1152 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el apt ppc64el 2.9.30 [1439 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el apt-utils ppc64el 2.9.30 [228 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el dhcpcd-base ppc64el 1:10.1.0-7 [280 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el rsyslog ppc64el 8.2412.0-2ubuntu1 [632 kB] 113s Fetched 3731 kB in 1s (4517 kB/s) 113s Selecting previously unselected package libapt-pkg7.0:ppc64el. 114s (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 ... 106322 files and directories currently installed.) 114s Preparing to unpack .../libapt-pkg7.0_2.9.30_ppc64el.deb ... 114s Unpacking libapt-pkg7.0:ppc64el (2.9.30) ... 114s Setting up libapt-pkg7.0:ppc64el (2.9.30) ... 114s (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 ... 106371 files and directories currently installed.) 114s Preparing to unpack .../apt_2.9.30_ppc64el.deb ... 114s Unpacking apt (2.9.30) over (2.9.29) ... 114s Setting up apt (2.9.30) ... 115s (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 ... 106371 files and directories currently installed.) 115s Preparing to unpack .../apt-utils_2.9.30_ppc64el.deb ... 115s Unpacking apt-utils (2.9.30) over (2.9.29) ... 116s Preparing to unpack .../dhcpcd-base_1%3a10.1.0-7_ppc64el.deb ... 116s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-6) ... 116s Preparing to unpack .../rsyslog_8.2412.0-2ubuntu1_ppc64el.deb ... 116s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 116s Setting up apt-utils (2.9.30) ... 116s Setting up rsyslog (8.2412.0-2ubuntu1) ... 116s info: The user `syslog' is already a member of `adm'. 118s Setting up dhcpcd-base (1:10.1.0-7) ... 118s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for libc-bin (2.40-4ubuntu1) ... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s autopkgtest [07:56:34]: upgrading testbed (apt dist-upgrade and autopurge) 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 125s Entering ResolveByKeep 125s 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s autopkgtest [07:56:38]: rebooting testbed after setup commands that affected boot 161s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 172s autopkgtest [07:57:23]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 16:32:08 UTC 2025 175s autopkgtest [07:57:26]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 178s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 178s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 178s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 178s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 178s gpgv: issuer "tille@debian.org" 178s gpgv: Can't check signature: No public key 178s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 179s autopkgtest [07:57:30]: testing package tm-align version 20190822+dfsg-3 179s autopkgtest [07:57:30]: build not needed 180s autopkgtest [07:57:31]: test run-unit-test: preparing testbed 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 181s The following NEW packages will be installed: 181s libgfortran5 tm-align 182s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 182s Need to get 1505 kB of archives. 182s After this operation, 4036 kB of additional disk space will be used. 182s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250213-1ubuntu1 [613 kB] 182s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el tm-align ppc64el 20190822+dfsg-3 [893 kB] 183s Fetched 1505 kB in 1s (1704 kB/s) 183s Selecting previously unselected package libgfortran5:ppc64el. 183s (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 ... 106371 files and directories currently installed.) 183s Preparing to unpack .../libgfortran5_15-20250213-1ubuntu1_ppc64el.deb ... 183s Unpacking libgfortran5:ppc64el (15-20250213-1ubuntu1) ... 183s Selecting previously unselected package tm-align. 183s Preparing to unpack .../tm-align_20190822+dfsg-3_ppc64el.deb ... 183s Unpacking tm-align (20190822+dfsg-3) ... 183s Setting up libgfortran5:ppc64el (15-20250213-1ubuntu1) ... 183s Setting up tm-align (20190822+dfsg-3) ... 183s Processing triggers for libc-bin (2.40-4ubuntu1) ... 183s Processing triggers for man-db (2.13.0-1) ... 186s autopkgtest [07:57:37]: test run-unit-test: [----------------------- 186s Run TMalign... 187s 187s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 187s ************************************************************************** 187s * TM-align (Version 20190822) * 187s * An algorithm for protein structure alignment and comparison * 187s * Based on statistics: * 187s * 0.0 < TM-score < 0.30, random structural similarity * 187s * 0.5 < TM-score < 1.00, in about the same fold * 187s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 187s * Please email your comments and suggestions to: zhng@umich.edu * 187s ************************************************************************** 187s 187s Name of Chain_1: 1ni7.pdb 187s Name of Chain_2: 5eep.pdb 187s Length of Chain_1: 149 residues 187s Length of Chain_2: 140 residues 187s 187s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 187s TM-score= 0.85044 (if normalized by length of Chain_1) 187s TM-score= 0.90009 (if normalized by length of Chain_2) 187s (You should use TM-score normalized by length of the reference protein) 187s 187s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 187s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 187s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 187s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 187s 187s Run TMscore... 187s 187s ***************************************************************************** 187s * TM-SCORE * 187s * A scoring function to assess the similarity of protein structures * 187s * Based on statistics: * 187s * 0.0 < TM-score < 0.17, random structural similarity * 187s * 0.5 < TM-score < 1.00, in about the same fold * 187s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 187s * For comments, please email to: zhng@umich.edu * 187s ***************************************************************************** 187s 187s Structure1: 1ni7.pdb Length= 149 187s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 187s Number of residues in common= 140 187s RMSD of the common residues= 1.616 187s 187s TM-score = 0.8987 (d0= 4.40) 187s MaxSub-score= 0.8459 (d0= 3.50) 187s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 187s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 187s 187s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 187s i t(i) u(i,1) u(i,2) u(i,3) 187s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 187s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 187s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 187s 187s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 187s (":" denotes the residue pairs of distance < 5.0 Angstrom) 187s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 187s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 187s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 187s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 187s 187s autopkgtest [07:57:38]: test run-unit-test: -----------------------] 187s autopkgtest [07:57:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 187s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 188s autopkgtest [07:57:39]: test run-unit-test: - - - - - - - - - - stderr - - - - - - - - - - 188s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 188s autopkgtest [07:57:39]: @@@@@@@@@@@@@@@@@@@@ summary 188s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 193s nova [W] Using flock in prodstack6-ppc64el 193s Creating nova instance adt-plucky-ppc64el-tm-align-20250219-075431-juju-7f2275-prod-proposed-migration-environment-2-947d7832-3c7e-49f7-bd99-c8cb2f8212d3 from image adt/ubuntu-plucky-ppc64el-server-20250218.img (UUID 9318aa34-3d3c-43c5-86d2-aaf9390f2f5d)... 193s nova [W] Timed out waiting for 1fb6fb9d-b618-4995-b9a2-15d15e4ec92f to get deleted.