0s autopkgtest [16:11:23]: starting date and time: 2025-03-15 16:11:23+0000 1s autopkgtest [16:11:24]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [16:11:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.g2g14kl_/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-31.secgroup --name adt-plucky-arm64-relion-20250315-161123-juju-7f2275-prod-proposed-migration-environment-2-1e99fd82-0b34-4d3c-a4b1-83030543f232 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 168s autopkgtest [16:14:11]: testbed dpkg architecture: arm64 168s autopkgtest [16:14:11]: testbed apt version: 2.9.33 168s autopkgtest [16:14:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 168s autopkgtest [16:14:11]: testbed release detected to be: None 169s autopkgtest [16:14:12]: updating testbed package index (apt update) 170s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 170s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 170s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 170s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 170s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 170s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 170s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 171s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 171s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 171s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 171s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 171s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 171s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 171s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 172s Fetched 1078 kB in 2s (591 kB/s) 172s Reading package lists... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade... 174s Calculating upgrade... 174s The following packages will be upgraded: 174s pinentry-curses python3-jinja2 strace 175s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 647 kB of archives. 175s After this operation, 11.3 kB of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 175s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 175s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 176s Fetched 647 kB in 1s (658 kB/s) 176s (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 ... 117701 files and directories currently installed.) 176s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 176s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 176s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 176s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 176s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 176s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 176s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 176s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 177s Setting up strace (6.13+ds-1ubuntu1) ... 177s Processing triggers for man-db (2.13.0-1) ... 177s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Solving dependencies... 178s The following packages will be REMOVED: 178s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 178s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 178s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 178s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 179s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 179s After this operation, 267 MB disk space will be freed. 179s (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 ... 117701 files and directories currently installed.) 179s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 179s Removing libpython3.12t64:arm64 (3.12.9-1) ... 179s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 179s Removing libnsl2:arm64 (1.3.0-3build3) ... 179s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 179s Removing libunwind8:arm64 (1.6.2-3.1) ... 179s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 180s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 181s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 181s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 181s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 181s /etc/kernel/postrm.d/initramfs-tools: 181s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 182s /etc/kernel/postrm.d/zz-flash-kernel: 182s flash-kernel: Kernel 6.11.0-8-generic has been removed. 182s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 182s /etc/kernel/postrm.d/zz-update-grub: 182s Sourcing file `/etc/default/grub' 182s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 182s Generating grub configuration file ... 182s Found linux image: /boot/vmlinuz-6.14.0-10-generic 182s Found initrd image: /boot/initrd.img-6.14.0-10-generic 182s Warning: os-prober will not be executed to detect other bootable partitions. 182s Systems on them will not be added to the GRUB boot configuration. 182s Check GRUB_DISABLE_OS_PROBER documentation entry. 182s Adding boot menu entry for UEFI Firmware Settings ... 182s done 182s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 183s Processing triggers for libc-bin (2.41-1ubuntu1) ... 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 ... 81650 files and directories currently installed.) 183s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 183s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 183s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 183s autopkgtest [16:14:26]: upgrading testbed (apt dist-upgrade and autopurge) 183s Reading package lists... 184s Building dependency tree... 184s Reading state information... 184s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 184s Starting 2 pkgProblemResolver with broken count: 0 184s Done 185s Entering ResolveByKeep 185s 185s Calculating upgrade... 186s The following packages will be upgraded: 186s libc-bin libc-dev-bin libc6 libc6-dev locales 186s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 9530 kB of archives. 186s After this operation, 0 B of additional disk space will be used. 186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 188s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 188s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 192s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 193s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 199s Preconfiguring packages ... 199s Fetched 9530 kB in 13s (741 kB/s) 199s (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 ... 81647 files and directories currently installed.) 199s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 199s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 199s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 199s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 199s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Setting up libc6:arm64 (2.41-1ubuntu2) ... 200s (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 ... 81647 files and directories currently installed.) 200s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Setting up libc-bin (2.41-1ubuntu2) ... 200s (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 ... 81647 files and directories currently installed.) 200s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 200s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Setting up locales (2.41-1ubuntu2) ... 201s Generating locales (this might take a while)... 203s en_US.UTF-8... done 203s Generation complete. 203s Setting up libc-dev-bin (2.41-1ubuntu2) ... 203s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 203s Processing triggers for man-db (2.13.0-1) ... 204s Processing triggers for systemd (257.3-1ubuntu3) ... 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 206s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 206s Solving dependencies... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 207s autopkgtest [16:14:50]: rebooting testbed after setup commands that affected boot 230s autopkgtest [16:15:13]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 233s autopkgtest [16:15:16]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 238s Get:1 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (dsc) [2136 B] 238s Get:2 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (tar) [2345 kB] 238s Get:3 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (diff) [12.1 kB] 238s gpgv: Signature made Sat Nov 30 07:03:33 2024 UTC 238s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 238s gpgv: Can't check signature: No public key 238s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-4build1.dsc: no acceptable signature found 238s autopkgtest [16:15:21]: testing package relion version 3.1.3-4build1 239s autopkgtest [16:15:22]: build not needed 240s autopkgtest [16:15:23]: test command1: preparing testbed 240s Reading package lists... 240s Building dependency tree... 240s Reading state information... 241s Starting pkgProblemResolver with broken count: 0 241s Starting 2 pkgProblemResolver with broken count: 0 241s Done 242s The following NEW packages will be installed: 242s libamd-comgr2 libamdhip64-5 libdeflate0 libevent-pthreads-2.1-7t64 242s libfabric1 libfftw3-double3 libfftw3-single3 libgomp1 libhsa-runtime64-1 242s libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libjbig0 242s libjpeg-turbo8 libjpeg8 liblerc4 libllvm17t64 libmunge2 libopenmpi40 242s libpciaccess0 libpmix2t64 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 242s libwebp7 libxnvctrl0 mpi-default-bin ocl-icd-libopencl1 openmpi-bin 242s openmpi-common relion 242s 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. 242s Need to get 70.2 MB of archives. 242s After this operation, 313 MB of additional disk space will be used. 242s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-21 [24.9 MB] 271s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 286s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 286s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 286s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB] 296s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 296s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 296s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 55.0-1ubuntu1 [71.5 kB] 296s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3.1 [542 kB] 297s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 297s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1build1 [392 kB] 297s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-single3 arm64 3.3.10-2fakesync1build1 [604 kB] 298s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.12.0-1 [162 kB] 298s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 298s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 298s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 299s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.16-1 [15.2 kB] 299s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 299s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 299s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 299s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.12.0-1 [15.9 kB] 299s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.6-5 [666 kB] 299s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 55.0-1ubuntu1 [29.8 kB] 299s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 55.0-1ubuntu1 [43.3 kB] 299s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.18.1+ds-2 [1161 kB] 301s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmpi40 arm64 5.0.7-1 [2419 kB] 303s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 303s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 303s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 303s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 304s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-common all 5.0.7-1 [97.9 kB] 304s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 openmpi-bin arm64 5.0.7-1 [195 kB] 304s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 mpi-default-bin arm64 1.18 [2510 B] 304s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 relion arm64 3.1.3-4build1 [13.7 MB] 318s Fetched 70.2 MB in 1min 16s (928 kB/s) 318s Selecting previously unselected package libllvm17t64:arm64. 318s (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 ... 81647 files and directories currently installed.) 318s Preparing to unpack .../00-libllvm17t64_1%3a17.0.6-21_arm64.deb ... 318s Unpacking libllvm17t64:arm64 (1:17.0.6-21) ... 319s Selecting previously unselected package libamd-comgr2:arm64. 319s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 319s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 319s Selecting previously unselected package libhsakmt1:arm64. 319s Preparing to unpack .../02-libhsakmt1_5.7.0-1build1_arm64.deb ... 319s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 319s Selecting previously unselected package libhsa-runtime64-1. 319s Preparing to unpack .../03-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 319s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 319s Selecting previously unselected package libamdhip64-5. 319s Preparing to unpack .../04-libamdhip64-5_5.7.1-5_arm64.deb ... 319s Unpacking libamdhip64-5 (5.7.1-5) ... 319s Selecting previously unselected package libdeflate0:arm64. 319s Preparing to unpack .../05-libdeflate0_1.23-1_arm64.deb ... 319s Unpacking libdeflate0:arm64 (1.23-1) ... 319s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 319s Preparing to unpack .../06-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb ... 319s Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 319s Selecting previously unselected package librdmacm1t64:arm64. 319s Preparing to unpack .../07-librdmacm1t64_55.0-1ubuntu1_arm64.deb ... 319s Unpacking librdmacm1t64:arm64 (55.0-1ubuntu1) ... 319s Selecting previously unselected package libfabric1:arm64. 319s Preparing to unpack .../08-libfabric1_1.17.0-3.1_arm64.deb ... 319s Unpacking libfabric1:arm64 (1.17.0-3.1) ... 319s Selecting previously unselected package libgomp1:arm64. 319s Preparing to unpack .../09-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 319s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 319s Selecting previously unselected package libfftw3-double3:arm64. 319s Preparing to unpack .../10-libfftw3-double3_3.3.10-2fakesync1build1_arm64.deb ... 319s Unpacking libfftw3-double3:arm64 (3.3.10-2fakesync1build1) ... 319s Selecting previously unselected package libfftw3-single3:arm64. 319s Preparing to unpack .../11-libfftw3-single3_3.3.10-2fakesync1build1_arm64.deb ... 319s Unpacking libfftw3-single3:arm64 (3.3.10-2fakesync1build1) ... 320s Selecting previously unselected package libhwloc15:arm64. 320s Preparing to unpack .../12-libhwloc15_2.12.0-1_arm64.deb ... 320s Unpacking libhwloc15:arm64 (2.12.0-1) ... 320s Selecting previously unselected package libjpeg-turbo8:arm64. 320s Preparing to unpack .../13-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 320s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 320s Selecting previously unselected package libjpeg8:arm64. 320s Preparing to unpack .../14-libjpeg8_8c-2ubuntu11_arm64.deb ... 320s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 320s Selecting previously unselected package liblerc4:arm64. 320s Preparing to unpack .../15-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 320s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 320s Selecting previously unselected package libmunge2:arm64. 320s Preparing to unpack .../16-libmunge2_0.5.16-1_arm64.deb ... 320s Unpacking libmunge2:arm64 (0.5.16-1) ... 320s Selecting previously unselected package libpciaccess0:arm64. 320s Preparing to unpack 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... 320s Unpacking relion (3.1.3-4build1) ... 321s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 321s Setting up libpciaccess0:arm64 (0.17-3build1) ... 321s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 321s Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10) ... 321s Setting up libibumad3:arm64 (55.0-1ubuntu1) ... 321s Setting up libdeflate0:arm64 (1.23-1) ... 321s Setting up libibmad5:arm64 (55.0-1ubuntu1) ... 321s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 321s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 321s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 321s Setting up libmunge2:arm64 (0.5.16-1) ... 321s Setting up libllvm17t64:arm64 (1:17.0.6-21) ... 321s Setting up libhwloc15:arm64 (2.12.0-1) ... 321s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 321s Setting up libfftw3-double3:arm64 (3.3.10-2fakesync1build1) ... 321s Setting up libwebp7:arm64 (1.5.0-0.1) ... 321s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 321s Setting up 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file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 321s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 321s Setting up mpi-default-bin (1.18) ... 321s Setting up relion (3.1.3-4build1) ... 321s Processing triggers for libc-bin (2.41-1ubuntu2) ... 321s Processing triggers for man-db (2.13.0-1) ... 323s autopkgtest [16:16:46]: test command1: /usr/bin/relion_refine 323s autopkgtest [16:16:46]: test command1: [----------------------- 323s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 323s ====== General options ===== 323s --i () : Input images (in a star-file) 323s --o () : Output rootname 323s --iter (50) : Maximum number of iterations to perform 323s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 323s --K (1) : Number of references to be refined 323s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 323s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 323s --flatten_solvent (false) : Perform masking on the references as well? 323s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 323s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 323s --lowpass_mask (None) : User-provided mask for low-pass filtering 323s --lowpass (0) : User-provided cutoff for region specified above 323s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 323s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 323s --split_random_halves (false) : Refine two random halves of the data completely separately 323s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 323s ====== Initialisation ===== 323s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 323s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 323s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 323s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 323s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 323s ====== Orientations ===== 323s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 323s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 323s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 323s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 323s --sym (c1) : Symmetry group 323s --relax_sym () : Symmetry to be relaxed 323s --offset_range (6) : Search range for origin offsets (in pixels) 323s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 323s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 323s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 323s --auto_refine (false) : Perform 3D auto-refine procedure? 323s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 323s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 323s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 323s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 323s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 323s --skip_align (false) : Skip orientational assignment (only classify)? 323s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 323s --bimodal_psi (false) : Do bimodal searches of psi angle? 323s ====== Helical reconstruction (in development...) ===== 323s --helix (false) : Perform 3D classification or refinement for helices? 323s --ignore_helical_symmetry (false) : Ignore helical symmetry? 323s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 323s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 323s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 323s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 323s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 323s --helical_rise_initial (0.) : Helical rise (in Angstroms) 323s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 323s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 323s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 323s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 323s --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 323s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 323s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 323s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 323s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 323s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 323s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 323s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 323s ====== Corrections ===== 323s --ctf (false) : Perform CTF correction? 323s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 323s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 323s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 323s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 323s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 323s --norm (false) : Perform normalisation-error correction? 323s --scale (false) : Perform intensity-scale corrections on image groups? 323s --no_norm (false) : Switch off normalisation-error correction? 323s --no_scale (false) : Switch off intensity-scale corrections on image groups? 323s ====== Stochastic Gradient Descent ===== 323s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 323s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 323s --sgd_ini_iter (50) : Number of initial SGD iterations 323s --sgd_fin_iter (50) : Number of final SGD iterations 323s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 323s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 323s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 323s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 323s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 323s --mu (0.9) : Momentum parameter for SGD updates 323s --sgd_stepsize (0.5) : Step size parameter for SGD updates 323s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 323s --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) 323s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 323s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 323s ====== Computation ===== 323s --pool (1) : Number of images to pool for each thread task 323s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 323s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 323s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 323s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 323s --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! 323s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 323s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 323s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 323s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 323s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 323s --gpu (false) : Use available gpu resources for some calculations 323s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 323s ====== Expert options ===== 323s --pad (2) : Oversampling factor for the Fourier transforms of the references 323s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 323s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 323s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 323s --verb (1) : Verbosity (1=normal, 0=silent) 323s --random_seed (-1) : Number for the random seed generator 323s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 323s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 323s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 323s --fix_sigma_noise (false) : Fix the experimental noise spectra? 323s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 323s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 323s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 323s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 323s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 323s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 323s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 323s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 323s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 323s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 323s --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). 323s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 323s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 323s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 323s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 323s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 323s --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 323s --maxsig (-1) : Maximum number of poses & translations to consider 323s --skip_gridding (false) : Skip gridding in the M step 323s --version : Print RELION version and exit 323s autopkgtest [16:16:46]: test command1: -----------------------] 324s autopkgtest [16:16:47]: test command1: - - - - - - - - - - results - - - - - - - - - - 324s command1 PASS (superficial) 324s autopkgtest [16:16:47]: @@@@@@@@@@@@@@@@@@@@ summary 324s command1 PASS (superficial) 343s nova [W] Using flock in prodstack6-arm64 343s flock: timeout while waiting to get lock 343s Creating nova instance adt-plucky-arm64-relion-20250315-161123-juju-7f2275-prod-proposed-migration-environment-2-1e99fd82-0b34-4d3c-a4b1-83030543f232 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 343s nova [W] Timed out waiting for a95d0c25-5f89-4c25-aaf3-ad2ce1e99541 to get deleted.