0s autopkgtest [22:45:24]: starting date and time: 2024-11-13 22:45:24+0000 0s autopkgtest [22:45:24]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [22:45:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eo9r27ao/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-18.secgroup --name adt-plucky-ppc64el-tm-align-20241113-224524-juju-7f2275-prod-proposed-migration-environment-2-c53cccf7-8318-49d7-8bf7-cb5cd250c352 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 119s autopkgtest [22:47:23]: testbed dpkg architecture: ppc64el 123s autopkgtest [22:47:27]: testbed apt version: 2.9.8 125s autopkgtest [22:47:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [974 kB] 142s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 142s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 142s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [684 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 142s Fetched 1986 kB in 1s (1376 kB/s) 143s Reading package lists... 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Calculating upgrade... 166s The following packages will be upgraded: 166s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 166s libjson-glib-1.0-common libnewt0.52 libutempter0 python3-bpfcc python3-newt 166s whiptail 166s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 4598 kB of archives. 166s After this operation, 73.7 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 167s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 167s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 167s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 167s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 168s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 168s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 169s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 169s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 169s Fetched 4598 kB in 2s (2428 kB/s) 169s (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 ... 73767 files and directories currently installed.) 169s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 169s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 169s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 169s (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 ... 73767 files and directories currently installed.) 169s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 169s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 169s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 169s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 169s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 169s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 169s Preparing to unpack .../3-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 169s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 169s Preparing to unpack .../4-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 169s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 169s Preparing to unpack .../5-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 169s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 169s Preparing to unpack .../6-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 169s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 169s Preparing to unpack .../7-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 169s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 169s Preparing to unpack .../8-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 169s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 169s Preparing to unpack .../9-libutempter0_1.2.1-4_ppc64el.deb ... 169s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 169s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 169s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 169s Setting up libutempter0:ppc64el (1.2.1-4) ... 169s Setting up whiptail (0.52.24-2ubuntu4) ... 169s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 169s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 169s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 170s Setting up bpftrace (0.21.2-2ubuntu2) ... 170s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 170s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 170s Processing triggers for man-db (2.12.1-3) ... 171s Processing triggers for libc-bin (2.40-1ubuntu3) ... 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 175s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 175s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 175s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 176s Reading package lists... 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Calculating upgrade... 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 205s autopkgtest [22:48:49]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 205s autopkgtest [22:48:49]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 213s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 213s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 213s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 213s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 213s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 213s gpgv: issuer "tille@debian.org" 213s gpgv: Can't check signature: No public key 213s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 213s autopkgtest [22:48:57]: testing package tm-align version 20190822+dfsg-3 215s autopkgtest [22:48:59]: build not needed 216s autopkgtest [22:49:00]: test run-unit-test: preparing testbed 226s Reading package lists... 226s Building dependency tree... 226s Reading state information... 226s Starting pkgProblemResolver with broken count: 0 226s Starting 2 pkgProblemResolver with broken count: 0 226s Done 226s The following additional packages will be installed: 226s libgfortran5 tm-align 226s Suggested packages: 226s pymol rasmol 226s The following NEW packages will be installed: 226s autopkgtest-satdep libgfortran5 tm-align 226s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 1464 kB/1465 kB of archives. 226s After this operation, 3633 kB of additional disk space will be used. 226s Get:1 /tmp/autopkgtest.m4kFcf/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 227s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el tm-align ppc64el 20190822+dfsg-3 [893 kB] 227s Fetched 1464 kB in 1s (1649 kB/s) 227s Selecting previously unselected package libgfortran5:ppc64el. 227s (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 ... 73768 files and directories currently installed.) 227s Preparing to unpack .../libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 227s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 227s Selecting previously unselected package tm-align. 227s Preparing to unpack .../tm-align_20190822+dfsg-3_ppc64el.deb ... 227s Unpacking tm-align (20190822+dfsg-3) ... 227s Selecting previously unselected package autopkgtest-satdep. 228s Preparing to unpack .../1-autopkgtest-satdep.deb ... 228s Unpacking autopkgtest-satdep (0) ... 228s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 228s Setting up tm-align (20190822+dfsg-3) ... 228s Setting up autopkgtest-satdep (0) ... 228s Processing triggers for man-db (2.12.1-3) ... 228s Processing triggers for libc-bin (2.40-1ubuntu3) ... 254s (Reading database ... 73784 files and directories currently installed.) 254s Removing autopkgtest-satdep (0) ... 256s autopkgtest [22:49:40]: test run-unit-test: [----------------------- 256s Run TMalign... 256s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 256s 256s ************************************************************************** 256s * TM-align (Version 20190822) * 256s * An algorithm for protein structure alignment and comparison * 256s * Based on statistics: * 256s * 0.0 < TM-score < 0.30, random structural similarity * 256s * 0.5 < TM-score < 1.00, in about the same fold * 256s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 256s * Please email your comments and suggestions to: zhng@umich.edu * 256s ************************************************************************** 256s 256s Name of Chain_1: 1ni7.pdb 256s Name of Chain_2: 5eep.pdb 256s Length of Chain_1: 149 residues 256s Length of Chain_2: 140 residues 256s 256s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 256s TM-score= 0.85044 (if normalized by length of Chain_1) 256s TM-score= 0.90009 (if normalized by length of Chain_2) 256s (You should use TM-score normalized by length of the reference protein) 256s 256s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 256s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 256s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 256s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 256s 256s Run TMscore... 256s 256s ***************************************************************************** 256s * TM-SCORE * 256s * A scoring function to assess the similarity of protein structures * 256s * Based on statistics: * 256s * 0.0 < TM-score < 0.17, random structural similarity * 256s * 0.5 < TM-score < 1.00, in about the same fold * 256s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 256s * For comments, please email to: zhng@umich.edu * 256s ***************************************************************************** 256s 256s Structure1: 1ni7.pdb Length= 149 256s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 256s Number of residues in common= 140 256s RMSD of the common residues= 1.616 256s 256s TM-score = 0.8987 (d0= 4.40) 256s MaxSub-score= 0.8459 (d0= 3.50) 256s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 256s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 256s 256s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 256s i t(i) u(i,1) u(i,2) u(i,3) 256s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 256s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 256s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 256s 256s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 256s (":" denotes the residue pairs of distance < 5.0 Angstrom) 256s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 256s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 256s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 256s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 256s 256s autopkgtest [22:49:40]: test run-unit-test: -----------------------] 267s autopkgtest [22:49:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 267s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 267s autopkgtest [22:49:51]: test run-unit-test: - - - - - - - - - - stderr - - - - - - - - - - 267s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 267s autopkgtest [22:49:51]: @@@@@@@@@@@@@@@@@@@@ summary 267s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 276s virt: nova [W] Using flock in prodstack6-ppc64el 276s virt: Creating nova instance adt-plucky-ppc64el-tm-align-20241113-224524-juju-7f2275-prod-proposed-migration-environment-2-c53cccf7-8318-49d7-8bf7-cb5cd250c352 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...