0s autopkgtest [18:39:36]: starting date and time: 2025-03-15 18:39:36+0000 0s autopkgtest [18:39:36]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:39:36]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ju3j2kul/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade relion --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-22.secgroup --name adt-plucky-s390x-relion-20250315-183936-juju-7f2275-prod-proposed-migration-environment-15-4f851923-f3f5-4941-80c8-fc623b7d28ec --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/ 166s autopkgtest [18:42:22]: testbed dpkg architecture: s390x 166s autopkgtest [18:42:22]: testbed apt version: 2.9.33 167s autopkgtest [18:42:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s autopkgtest [18:42:23]: testbed release detected to be: None 168s autopkgtest [18:42:24]: updating testbed package index (apt update) 168s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 168s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 168s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 168s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 169s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 169s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 169s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 169s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 169s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 169s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 169s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 170s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 170s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 170s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 170s Fetched 1073 kB in 2s (629 kB/s) 170s Reading package lists... 171s + lsb_release --codename --short 171s + RELEASE=plucky 171s + cat 171s + [ plucky != trusty ] 171s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s Calculating upgrade... 171s Calculating upgrade... 171s The following packages were automatically installed and are no longer required: 171s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 171s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 171s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 171s linux-tools-6.11.0-8-generic 171s Use 'sudo apt autoremove' to remove them. 171s The following packages will be upgraded: 171s pinentry-curses python3-jinja2 strace 171s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 171s Need to get 652 kB of archives. 171s After this operation, 27.6 kB of additional disk space will be used. 171s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 172s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 172s Fetched 652 kB in 1s (623 kB/s) 173s (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.) 173s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 173s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 173s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 173s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 173s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 173s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 173s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 173s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 173s Setting up strace (6.13+ds-1ubuntu1) ... 173s Processing triggers for man-db (2.13.0-1) ... 173s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 173s + /usr/lib/apt/apt-helper analyze-pattern ?true 173s + uname -r 173s + sed s/\./\\./g 173s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 173s + apt list ?obsolete 173s + tail -n+2 173s + grep -v ^linux-.*6\.14\.0-10-generic.* 173s + cut -d/ -f1 174s + obsolete_pkgs=linux-headers-6.11.0-8-generic 174s linux-headers-6.11.0-8 174s linux-modules-6.11.0-8-generic 174s linux-tools-6.11.0-8-generic 174s linux-tools-6.11.0-8 174s + 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 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Solving dependencies... 174s The following packages will be REMOVED: 174s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 174s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 174s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 174s linux-tools-6.11.0-8-generic* 174s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 174s After this operation, 167 MB disk space will be freed. 174s (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.) 174s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 174s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 174s Removing libpython3.12t64:s390x (3.12.9-1) ... 174s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 174s Removing libnsl2:s390x (1.3.0-3build3) ... 174s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 174s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 174s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 175s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 175s Processing triggers for libc-bin (2.41-1ubuntu1) ... 175s (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.) 175s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 175s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 175s + grep -q trusty /etc/lsb-release 175s + [ ! -d /usr/share/doc/unattended-upgrades ] 175s + [ ! -d /usr/share/doc/lxd ] 175s + [ ! -d /usr/share/doc/lxd-client ] 175s + [ ! -d /usr/share/doc/snapd ] 175s + type iptables 175s + cat 175s + chmod 755 /etc/rc.local 175s + . /etc/rc.local 175s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 175s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 175s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 175s + uname -m 175s + [ s390x = ppc64le ] 175s + [ -d /run/systemd/system ] 175s + systemd-detect-virt --quiet --vm 175s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 175s + cat 175s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 175s + echo COMPRESS=lz4 175s autopkgtest [18:42:31]: upgrading testbed (apt dist-upgrade and autopurge) 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 176s Starting 2 pkgProblemResolver with broken count: 0 176s Done 176s Entering ResolveByKeep 176s 176s Calculating upgrade... 176s The following packages will be upgraded: 176s libc-bin libc-dev-bin libc6 libc6-dev locales 176s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 9512 kB of archives. 176s After this operation, 8192 B of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 181s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 182s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 187s Preconfiguring packages ... 187s Fetched 9512 kB in 10s (931 kB/s) 187s (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.) 187s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 187s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 187s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 187s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up libc6:s390x (2.41-1ubuntu2) ... 187s (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.) 187s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 187s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up libc-bin (2.41-1ubuntu2) ... 187s (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.) 187s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 187s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up locales (2.41-1ubuntu2) ... 188s Generating locales (this might take a while)... 188s en_US.UTF-8... done 188s Generation complete. 188s Setting up libc-dev-bin (2.41-1ubuntu2) ... 188s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 188s Processing triggers for man-db (2.13.0-1) ... 190s Processing triggers for systemd (257.3-1ubuntu3) ... 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 190s Solving dependencies... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s autopkgtest [18:42:47]: rebooting testbed after setup commands that affected boot 209s autopkgtest [18:43:05]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 211s autopkgtest [18:43:07]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 215s Get:1 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (dsc) [2136 B] 215s Get:2 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (tar) [2345 kB] 215s Get:3 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (diff) [12.1 kB] 216s gpgv: Signature made Sat Nov 30 07:03:33 2024 UTC 216s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 216s gpgv: Can't check signature: No public key 216s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-4build1.dsc: no acceptable signature found 216s autopkgtest [18:43:12]: testing package relion version 3.1.3-4build1 216s autopkgtest [18:43:12]: build not needed 217s autopkgtest [18:43:13]: test command1: preparing testbed 217s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s Starting pkgProblemResolver with broken count: 0 218s Starting 2 pkgProblemResolver with broken count: 0 218s Done 218s The following NEW packages will be installed: 218s libdeflate0 libevent-pthreads-2.1-7t64 libfabric1 libfftw3-double3 218s libfftw3-single3 libgomp1 libhwloc-plugins libhwloc15 libjbig0 218s libjpeg-turbo8 libjpeg8 libmunge2 libopenmpi40 libpciaccess0 libpmix2t64 218s librdmacm1t64 libsharpyuv0 libtiff6 libwebp7 libxnvctrl0 mpi-default-bin 218s ocl-icd-libopencl1 openmpi-bin openmpi-common relion 218s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 218s Need to get 21.1 MB of archives. 218s After this operation, 107 MB of additional disk space will be used. 218s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libevent-pthreads-2.1-7t64 s390x 2.1.12-stable-10 [7870 B] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x librdmacm1t64 s390x 55.0-1ubuntu1 [73.7 kB] 218s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libfabric1 s390x 1.17.0-3.1 [558 kB] 219s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 219s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libfftw3-double3 s390x 3.3.10-2fakesync1build1 [511 kB] 220s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libfftw3-single3 s390x 3.3.10-2fakesync1build1 [483 kB] 220s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc15 s390x 2.12.0-1 [176 kB] 220s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 220s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 220s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x libmunge2 s390x 0.5.16-1 [15.2 kB] 220s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libpciaccess0 s390x 0.17-3build1 [19.0 kB] 220s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxnvctrl0 s390x 510.47.03-0ubuntu4 [12.7 kB] 220s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x ocl-icd-libopencl1 s390x 2.3.2-1build1 [41.1 kB] 220s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x libhwloc-plugins s390x 2.12.0-1 [16.1 kB] 220s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x libpmix2t64 s390x 5.0.6-5 [715 kB] 222s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x libopenmpi40 s390x 5.0.7-1 [2196 kB] 224s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 224s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 224s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 224s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 224s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-common all 5.0.7-1 [97.9 kB] 224s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x openmpi-bin s390x 5.0.7-1 [200 kB] 224s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x mpi-default-bin s390x 1.18 [2510 B] 224s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x relion s390x 3.1.3-4build1 [15.1 MB] 240s Fetched 21.1 MB in 22s (950 kB/s) 240s Selecting previously unselected package libdeflate0:s390x. 240s (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.) 240s Preparing to unpack .../00-libdeflate0_1.23-1_s390x.deb ... 240s Unpacking libdeflate0:s390x (1.23-1) ... 240s Selecting previously unselected package libevent-pthreads-2.1-7t64:s390x. 240s Preparing to unpack .../01-libevent-pthreads-2.1-7t64_2.1.12-stable-10_s390x.deb ... 240s Unpacking libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 240s Selecting previously unselected package librdmacm1t64:s390x. 240s Preparing to unpack .../02-librdmacm1t64_55.0-1ubuntu1_s390x.deb ... 240s Unpacking librdmacm1t64:s390x (55.0-1ubuntu1) ... 240s Selecting previously unselected package libfabric1:s390x. 240s Preparing to unpack .../03-libfabric1_1.17.0-3.1_s390x.deb ... 240s Unpacking libfabric1:s390x (1.17.0-3.1) ... 240s Selecting previously unselected package libgomp1:s390x. 240s Preparing to unpack .../04-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 240s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 240s Selecting previously unselected package libfftw3-double3:s390x. 240s Preparing to unpack .../05-libfftw3-double3_3.3.10-2fakesync1build1_s390x.deb ... 240s Unpacking libfftw3-double3:s390x (3.3.10-2fakesync1build1) ... 240s Selecting previously unselected package libfftw3-single3:s390x. 240s Preparing to unpack .../06-libfftw3-single3_3.3.10-2fakesync1build1_s390x.deb ... 240s Unpacking libfftw3-single3:s390x (3.3.10-2fakesync1build1) ... 240s Selecting previously unselected package libhwloc15:s390x. 240s Preparing to unpack .../07-libhwloc15_2.12.0-1_s390x.deb ... 240s Unpacking libhwloc15:s390x (2.12.0-1) ... 240s Selecting previously unselected package libjpeg-turbo8:s390x. 240s Preparing to unpack .../08-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 240s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 240s Selecting previously unselected package libjpeg8:s390x. 240s Preparing to unpack .../09-libjpeg8_8c-2ubuntu11_s390x.deb ... 240s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 240s Selecting previously unselected package libmunge2:s390x. 240s Preparing to unpack .../10-libmunge2_0.5.16-1_s390x.deb ... 240s Unpacking libmunge2:s390x (0.5.16-1) ... 240s Selecting previously unselected package libpciaccess0:s390x. 240s Preparing to unpack .../11-libpciaccess0_0.17-3build1_s390x.deb ... 240s Unpacking libpciaccess0:s390x (0.17-3build1) ... 240s Selecting previously unselected package libxnvctrl0:s390x. 240s Preparing to unpack .../12-libxnvctrl0_510.47.03-0ubuntu4_s390x.deb ... 240s Unpacking libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 241s Selecting previously unselected package ocl-icd-libopencl1:s390x. 241s Preparing to unpack .../13-ocl-icd-libopencl1_2.3.2-1build1_s390x.deb ... 241s Unpacking ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 241s Selecting previously unselected package libhwloc-plugins:s390x. 241s Preparing to unpack .../14-libhwloc-plugins_2.12.0-1_s390x.deb ... 241s Unpacking libhwloc-plugins:s390x (2.12.0-1) ... 241s Selecting previously unselected package libpmix2t64:s390x. 241s Preparing to unpack .../15-libpmix2t64_5.0.6-5_s390x.deb ... 241s Unpacking libpmix2t64:s390x (5.0.6-5) ... 241s Selecting previously unselected package libopenmpi40:s390x. 241s Preparing to unpack .../16-libopenmpi40_5.0.7-1_s390x.deb ... 241s Unpacking libopenmpi40:s390x (5.0.7-1) ... 241s Selecting previously unselected package libsharpyuv0:s390x. 241s Preparing to unpack .../17-libsharpyuv0_1.5.0-0.1_s390x.deb ... 241s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 241s Selecting previously unselected package libjbig0:s390x. 241s Preparing to unpack .../18-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 241s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 241s Selecting previously unselected package libwebp7:s390x. 241s Preparing to unpack .../19-libwebp7_1.5.0-0.1_s390x.deb ... 241s Unpacking libwebp7:s390x (1.5.0-0.1) ... 241s Selecting previously unselected package libtiff6:s390x. 241s Preparing to unpack .../20-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 241s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 241s Selecting previously unselected package openmpi-common. 241s Preparing to unpack .../21-openmpi-common_5.0.7-1_all.deb ... 241s Unpacking openmpi-common (5.0.7-1) ... 241s Selecting previously unselected package openmpi-bin. 241s Preparing to unpack .../22-openmpi-bin_5.0.7-1_s390x.deb ... 241s Unpacking openmpi-bin (5.0.7-1) ... 241s Selecting previously unselected package mpi-default-bin. 241s Preparing to unpack .../23-mpi-default-bin_1.18_s390x.deb ... 241s Unpacking mpi-default-bin (1.18) ... 241s Selecting previously unselected package relion. 241s Preparing to unpack .../24-relion_3.1.3-4build1_s390x.deb ... 241s Unpacking relion (3.1.3-4build1) ... 241s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 241s Setting up libpciaccess0:s390x (0.17-3build1) ... 241s Setting up libevent-pthreads-2.1-7t64:s390x (2.1.12-stable-10) ... 241s Setting up libdeflate0:s390x (1.23-1) ... 241s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 241s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 241s Setting up libxnvctrl0:s390x (510.47.03-0ubuntu4) ... 241s Setting up libmunge2:s390x (0.5.16-1) ... 241s Setting up libhwloc15:s390x (2.12.0-1) ... 241s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 241s Setting up libfftw3-double3:s390x (3.3.10-2fakesync1build1) ... 241s Setting up libwebp7:s390x (1.5.0-0.1) ... 241s Setting up ocl-icd-libopencl1:s390x (2.3.2-1build1) ... 241s Setting up openmpi-common (5.0.7-1) ... 241s Setting up librdmacm1t64:s390x (55.0-1ubuntu1) ... 241s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 241s Setting up libfabric1:s390x (1.17.0-3.1) ... 241s Setting up libfftw3-single3:s390x (3.3.10-2fakesync1build1) ... 241s Setting up libhwloc-plugins:s390x (2.12.0-1) ... 241s Setting up libpmix2t64:s390x (5.0.6-5) ... 241s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 241s Setting up libopenmpi40:s390x (5.0.7-1) ... 241s Setting up openmpi-bin (5.0.7-1) ... 241s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 241s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 241s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 241s Setting up mpi-default-bin (1.18) ... 241s Setting up relion (3.1.3-4build1) ... 241s Processing triggers for libc-bin (2.41-1ubuntu2) ... 241s Processing triggers for man-db (2.13.0-1) ... 242s autopkgtest [18:43:38]: test command1: /usr/bin/relion_refine 242s autopkgtest [18:43:38]: test command1: [----------------------- 242s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 242s ====== General options ===== 242s --i () : Input images (in a star-file) 242s --o () : Output rootname 242s --iter (50) : Maximum number of iterations to perform 242s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 242s --K (1) : Number of references to be refined 242s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 242s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 242s --flatten_solvent (false) : Perform masking on the references as well? 242s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 242s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 242s --lowpass_mask (None) : User-provided mask for low-pass filtering 242s --lowpass (0) : User-provided cutoff for region specified above 242s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 242s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 242s --split_random_halves (false) : Refine two random halves of the data completely separately 242s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 242s ====== Initialisation ===== 242s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 242s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 242s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 242s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 242s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 242s ====== Orientations ===== 242s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 242s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 242s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 242s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 242s --sym (c1) : Symmetry group 242s --relax_sym () : Symmetry to be relaxed 242s --offset_range (6) : Search range for origin offsets (in pixels) 242s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 242s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 242s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 242s --auto_refine (false) : Perform 3D auto-refine procedure? 242s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 242s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 242s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 242s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 242s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 242s --skip_align (false) : Skip orientational assignment (only classify)? 242s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 242s --bimodal_psi (false) : Do bimodal searches of psi angle? 242s ====== Helical reconstruction (in development...) ===== 242s --helix (false) : Perform 3D classification or refinement for helices? 242s --ignore_helical_symmetry (false) : Ignore helical symmetry? 242s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 242s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 242s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 242s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 242s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 242s --helical_rise_initial (0.) : Helical rise (in Angstroms) 242s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 242s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 242s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 242s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 242s --helical_z_percentage (0.3) : This box length along the center of Z axis contains good information of the helix. Important in imposing and refining symmetry 242s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 242s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 242s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 242s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 242s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 242s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 242s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 242s ====== Corrections ===== 242s --ctf (false) : Perform CTF correction? 242s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 242s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 242s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 242s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 242s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 242s --norm (false) : Perform normalisation-error correction? 242s --scale (false) : Perform intensity-scale corrections on image groups? 242s --no_norm (false) : Switch off normalisation-error correction? 242s --no_scale (false) : Switch off intensity-scale corrections on image groups? 242s ====== Stochastic Gradient Descent ===== 242s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 242s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 242s --sgd_ini_iter (50) : Number of initial SGD iterations 242s --sgd_fin_iter (50) : Number of final SGD iterations 242s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 242s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 242s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 242s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 242s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 242s --mu (0.9) : Momentum parameter for SGD updates 242s --sgd_stepsize (0.5) : Step size parameter for SGD updates 242s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 242s --sgd_sigma2fudge_halflife (-1) : Initialise SGD with 8x higher noise-variance, and reduce with this half-life in # of particles (default is keep normal variance) 242s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 242s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 242s ====== Computation ===== 242s --pool (1) : Number of images to pool for each thread task 242s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 242s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 242s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 242s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 242s --preread_images (false) : Use this to let the leader process read all particles into memory. Be careful you have enough RAM for large data sets! 242s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 242s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 242s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 242s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 242s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 242s --gpu (false) : Use available gpu resources for some calculations 242s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 242s ====== Expert options ===== 242s --pad (2) : Oversampling factor for the Fourier transforms of the references 242s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 242s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 242s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 242s --verb (1) : Verbosity (1=normal, 0=silent) 242s --random_seed (-1) : Number for the random seed generator 242s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 242s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 242s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 242s --fix_sigma_noise (false) : Fix the experimental noise spectra? 242s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 242s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 242s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 242s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 242s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 242s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 242s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 242s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 242s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 242s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 242s --failsafe_threshold (40) : Maximum number of particles permitted to be handled by fail-safe mode, due to zero sum of weights, before exiting with an error (GPU only). 242s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 242s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 242s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 242s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 242s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 242s --trust_ref_size (false) : Trust the pixel and box size of the input reference; by default the program will die if these are different from the first optics group of the data 242s --maxsig (-1) : Maximum number of poses & translations to consider 242s --skip_gridding (false) : Skip gridding in the M step 242s --version : Print RELION version and exit 243s autopkgtest [18:43:39]: test command1: -----------------------] 243s command1 PASS (superficial) 243s autopkgtest [18:43:39]: test command1: - - - - - - - - - - results - - - - - - - - - - 243s autopkgtest [18:43:39]: @@@@@@@@@@@@@@@@@@@@ summary 243s command1 PASS (superficial) 248s nova [W] Using flock in prodstack6-s390x 248s Creating nova instance adt-plucky-s390x-relion-20250315-183936-juju-7f2275-prod-proposed-migration-environment-15-4f851923-f3f5-4941-80c8-fc623b7d28ec from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 248s nova [W] Timed out waiting for b8107eac-a2d2-4df9-a2e7-f643a5507dca to get deleted.