0s autopkgtest [21:06:13]: starting date and time: 2024-03-13 21:06:13+0000 0s autopkgtest [21:06:13]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:06:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5washlc2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:fftw3,src:openmpi,src:pmix --apt-upgrade relion --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=fftw3/3.3.10-1ubuntu2 openmpi/4.1.6-5.1ubuntu3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-16.secgroup --name adt-noble-arm64-relion-20240313-210613-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 154s autopkgtest [21:08:47]: testbed dpkg architecture: arm64 155s autopkgtest [21:08:48]: testbed apt version: 2.7.12 155s autopkgtest [21:08:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 157s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 157s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 157s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2820 kB] 157s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 157s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 157s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 157s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 157s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3215 kB] 158s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 158s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [41.7 kB] 158s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 167s Fetched 7326 kB in 4s (1642 kB/s) 168s Reading package lists... 169s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 171s Reading package lists... 186s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Calculating upgrade... 189s The following packages will be upgraded: 189s console-setup console-setup-linux keyboard-configuration 189s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 2202 kB of archives. 189s After this operation, 2048 B of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 190s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 190s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 191s Preconfiguring packages ... 192s Fetched 2202 kB in 1s (2916 kB/s) 192s (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 ... 75867 files and directories currently installed.) 192s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 192s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 193s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 193s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 193s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 193s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 193s Setting up keyboard-configuration (1.226ubuntu1) ... 196s Your console font configuration will be updated the next time your system 196s boots. If you want to update it now, run 'setupcon' from a virtual console. 196s update-initramfs: deferring update (trigger activated) 196s Setting up console-setup-linux (1.226ubuntu1) ... 202s Setting up console-setup (1.226ubuntu1) ... 205s update-initramfs: deferring update (trigger activated) 205s Processing triggers for man-db (2.12.0-3) ... 206s Processing triggers for initramfs-tools (0.142ubuntu20) ... 206s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 206s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 270s System running in EFI mode, skipping. 271s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 271s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 271s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 271s Reading package lists... 271s Building dependency tree... 271s Reading state information... 273s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 274s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 274s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 274s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 274s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 274s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 287s Reading package lists... 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 287s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 287s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 289s Calculating upgrade... 291s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 293s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 293s autopkgtest [21:11:06]: rebooting testbed after setup commands that affected boot 452s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 460s autopkgtest [21:13:53]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 464s autopkgtest [21:13:57]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 470s Get:1 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (dsc) [2135 B] 470s Get:2 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (tar) [2345 kB] 470s Get:3 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (diff) [12.0 kB] 470s gpgv: Signature made Sat Feb 4 12:33:57 2023 UTC 470s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 470s gpgv: Can't check signature: No public key 470s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found 471s autopkgtest [21:14:04]: testing package relion version 3.1.3-3build1 471s autopkgtest [21:14:04]: build not needed 479s autopkgtest [21:14:12]: test command1: preparing testbed 482s Reading package lists... 483s Building dependency tree... 483s Reading state information... 483s Starting pkgProblemResolver with broken count: 0 484s Starting 2 pkgProblemResolver with broken count: 0 484s Done 485s The following additional packages will be installed: 485s libamd-comgr2 libamdhip64-5 libatomic1 libdeflate0 libdrm-amdgpu1 485s libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 libfftw3-single3 485s libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libjbig0 485s libjpeg-turbo8 libjpeg8 liblerc4 libllvm17 libmunge2 libopenmpi3t64 485s libpciaccess0 libpmix2t64 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 485s libwebp7 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common relion 485s Suggested packages: 485s libfftw3-bin libfftw3-dev opencl-icd gfortran | fortran-compiler 485s The following NEW packages will be installed: 485s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libatomic1 libdeflate0 485s libdrm-amdgpu1 libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 485s libfftw3-single3 libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins 485s libhwloc15 libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 libllvm17 libmunge2 485s libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 libsharpyuv0 libtiff6 485s libucx0 libwebp7 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common 485s relion 486s 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. 486s Need to get 64.2 MB/64.2 MB of archives. 486s After this operation, 299 MB of additional disk space will be used. 486s Get:1 /tmp/autopkgtest.gBLu1x/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 486s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 490s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3 [14.1 MB] 490s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 490s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] 490s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1 [286 kB] 490s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] 491s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 491s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 491s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9 [7738 B] 491s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 librdmacm1t64 arm64 50.0-2 [70.6 kB] 491s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libfabric1 arm64 1.17.0-3 [537 kB] 491s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 491s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu2 [384 kB] 491s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-single3 arm64 3.3.10-1ubuntu2 [584 kB] 491s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] 491s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 491s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 491s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 491s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] 491s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] 491s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] 491s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] 491s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] 491s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix2t64 arm64 5.0.1-4.1 [655 kB] 491s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] 491s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi3t64 arm64 4.1.6-5.1ubuntu3 [2233 kB] 491s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 491s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 491s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 491s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 491s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-common all 4.1.6-5.1ubuntu3 [169 kB] 491s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-bin arm64 4.1.6-5.1ubuntu3 [113 kB] 491s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 relion arm64 3.1.3-3build1 [12.5 MB] 493s Fetched 64.2 MB in 6s (10.7 MB/s) 493s Selecting previously unselected package libllvm17:arm64. 493s (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 ... 75867 files and directories currently installed.) 493s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 493s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 496s Selecting previously unselected package libamd-comgr2:arm64. 496s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_arm64.deb ... 496s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3) ... 497s Selecting previously unselected package libdrm-amdgpu1:arm64. 497s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 497s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 497s Selecting previously unselected package libhsakmt1:arm64. 497s Preparing to unpack .../03-libhsakmt1_5.7.0-1_arm64.deb ... 497s Unpacking libhsakmt1:arm64 (5.7.0-1) ... 497s Selecting previously unselected package libhsa-runtime64-1. 497s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_arm64.deb ... 497s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 497s Selecting previously unselected package libamdhip64-5. 497s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_arm64.deb ... 497s Unpacking libamdhip64-5 (5.2.3-12) ... 498s Selecting previously unselected package libatomic1:arm64. 498s Preparing to unpack .../06-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 498s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 498s Selecting previously unselected package libdeflate0:arm64. 498s Preparing to unpack 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autopkgtest-satdep. 502s Preparing to unpack .../33-1-autopkgtest-satdep.deb ... 502s Unpacking autopkgtest-satdep (0) ... 502s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 502s Setting up libpciaccess0:arm64 (0.17-3) ... 502s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 502s Setting up libdeflate0:arm64 (1.19-1) ... 502s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 502s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 502s Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... 502s Setting up libmunge2:arm64 (0.5.15-3ubuntu1) ... 502s Setting up libhwloc15:arm64 (2.10.0-1) ... 502s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 502s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 502s Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu2) ... 502s Setting up libwebp7:arm64 (1.3.2-0.4) ... 502s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1) ... 502s Setting up openmpi-common (4.1.6-5.1ubuntu3) ... 502s Setting up librdmacm1t64:arm64 (50.0-2) ... 502s Setting up 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/usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 502s Setting up relion (3.1.3-3build1) ... 502s Setting up autopkgtest-satdep (0) ... 502s Processing triggers for man-db (2.12.0-3) ... 504s Processing triggers for libc-bin (2.39-0ubuntu2) ... 513s (Reading database ... 76523 files and directories currently installed.) 513s Removing autopkgtest-satdep (0) ... 513s autopkgtest [21:14:46]: test command1: /usr/bin/relion_refine 513s autopkgtest [21:14:46]: test command1: [----------------------- 514s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 514s ====== General options ===== 514s --i () : Input images (in a star-file) 514s --o () : Output rootname 514s --iter (50) : Maximum number of iterations to perform 514s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 514s --K (1) : Number of references to be refined 514s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 514s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 514s --flatten_solvent (false) : Perform masking on the references as well? 514s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 514s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 514s --lowpass_mask (None) : User-provided mask for low-pass filtering 514s --lowpass (0) : User-provided cutoff for region specified above 514s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 514s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 514s --split_random_halves (false) : Refine two random halves of the data completely separately 514s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 514s ====== Initialisation ===== 514s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 514s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 514s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 514s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 514s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 514s ====== Orientations ===== 514s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 514s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 514s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 514s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 514s --sym (c1) : Symmetry group 514s --relax_sym () : Symmetry to be relaxed 514s --offset_range (6) : Search range for origin offsets (in pixels) 514s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 514s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 514s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 514s --auto_refine (false) : Perform 3D auto-refine procedure? 514s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 514s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 514s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 514s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 514s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 514s --skip_align (false) : Skip orientational assignment (only classify)? 514s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 514s --bimodal_psi (false) : Do bimodal searches of psi angle? 514s ====== Helical reconstruction (in development...) ===== 514s --helix (false) : Perform 3D classification or refinement for helices? 514s --ignore_helical_symmetry (false) : Ignore helical symmetry? 514s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 514s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 514s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 514s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 514s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 514s --helical_rise_initial (0.) : Helical rise (in Angstroms) 514s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 514s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 514s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 514s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 514s --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 514s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 514s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 514s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 514s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 514s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 514s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 514s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 514s ====== Corrections ===== 514s --ctf (false) : Perform CTF correction? 514s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 514s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 514s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 514s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 514s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 514s --norm (false) : Perform normalisation-error correction? 514s --scale (false) : Perform intensity-scale corrections on image groups? 514s --no_norm (false) : Switch off normalisation-error correction? 514s --no_scale (false) : Switch off intensity-scale corrections on image groups? 514s ====== Stochastic Gradient Descent ===== 514s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 514s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 514s --sgd_ini_iter (50) : Number of initial SGD iterations 514s --sgd_fin_iter (50) : Number of final SGD iterations 514s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 514s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 514s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 514s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 514s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 514s --mu (0.9) : Momentum parameter for SGD updates 514s --sgd_stepsize (0.5) : Step size parameter for SGD updates 514s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 514s --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) 514s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 514s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 514s ====== Computation ===== 514s --pool (1) : Number of images to pool for each thread task 514s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 514s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 514s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 514s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 514s --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! 514s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 514s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 514s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 514s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 514s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 514s --gpu (false) : Use available gpu resources for some calculations 514s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 514s ====== Expert options ===== 514s --pad (2) : Oversampling factor for the Fourier transforms of the references 514s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 514s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 514s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 514s --verb (1) : Verbosity (1=normal, 0=silent) 514s --random_seed (-1) : Number for the random seed generator 514s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 514s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 514s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 514s --fix_sigma_noise (false) : Fix the experimental noise spectra? 514s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 514s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 514s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 514s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 514s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 514s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 514s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 514s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 514s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 514s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 514s --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). 514s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 514s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 514s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 514s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 514s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 514s --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 514s --maxsig (-1) : Maximum number of poses & translations to consider 514s --skip_gridding (false) : Skip gridding in the M step 514s --version : Print RELION version and exit 514s autopkgtest [21:14:47]: test command1: -----------------------] 515s autopkgtest [21:14:48]: test command1: - - - - - - - - - - results - - - - - - - - - - 515s command1 PASS (superficial) 516s autopkgtest [21:14:49]: @@@@@@@@@@@@@@@@@@@@ summary 516s command1 PASS (superficial) 528s Creating nova instance adt-noble-arm64-relion-20240313-210613-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 20618c62-409e-4a2f-a5b9-d20441a97bde)...