0s autopkgtest [16:53:02]: starting date and time: 2025-03-15 16:53:02+0000 0s autopkgtest [16:53:02]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:53:02]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gtri2asx/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.149 lxd-armhf-10.145.243.149:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [16:53:23]: testbed dpkg architecture: armhf 22s autopkgtest [16:53:24]: testbed apt version: 2.9.33 26s autopkgtest [16:53:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [16:53:30]: testbed release detected to be: None 35s autopkgtest [16:53:37]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 40s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 41s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 67s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 67s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 67s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 90s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 92s Fetched 41.0 MB in 54s (756 kB/s) 93s Reading package lists... 98s autopkgtest [16:54:40]: upgrading testbed (apt dist-upgrade and autopurge) 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 101s Starting 2 pkgProblemResolver with broken count: 0 101s Done 102s Entering ResolveByKeep 102s 102s Calculating upgrade... 103s The following packages will be upgraded: 103s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 103s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 8683 kB of archives. 103s After this operation, 23.6 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 113s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 114s Preconfiguring packages ... 114s Fetched 8683 kB in 11s (824 kB/s) 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 114s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 114s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 114s Setting up libc6:armhf (2.41-1ubuntu2) ... 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 115s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 115s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Setting up libc-bin (2.41-1ubuntu2) ... 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 115s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 115s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 115s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 115s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 115s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 115s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 116s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 116s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 116s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 116s Setting up sos (4.9.0-5) ... 117s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 117s Setting up locales (2.41-1ubuntu2) ... 117s Generating locales (this might take a while)... 119s en_US.UTF-8... done 119s Generation complete. 119s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 119s Setting up strace (6.13+ds-1ubuntu1) ... 120s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for systemd (257.3-1ubuntu3) ... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 124s Solving dependencies... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s autopkgtest [16:55:09]: rebooting testbed after setup commands that affected boot 170s autopkgtest [16:55:52]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 198s autopkgtest [16:56:20]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 214s Get:1 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (dsc) [2136 B] 214s Get:2 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (tar) [2345 kB] 214s Get:3 http://ftpmaster.internal/ubuntu plucky/universe relion 3.1.3-4build1 (diff) [12.1 kB] 214s gpgv: Signature made Sat Nov 30 07:03:33 2024 UTC 214s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 214s gpgv: Can't check signature: No public key 214s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-4build1.dsc: no acceptable signature found 214s autopkgtest [16:56:36]: testing package relion version 3.1.3-4build1 216s autopkgtest [16:56:38]: build not needed 219s autopkgtest [16:56:41]: test command1: preparing testbed 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 221s Starting pkgProblemResolver with broken count: 0 221s Starting 2 pkgProblemResolver with broken count: 0 221s Done 222s The following NEW packages will be installed: 222s hwloc-nox libdeflate0 libfftw3-double3 libfftw3-single3 libgfortran5 222s libgomp1 libhwloc15 libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 libmpich12 222s libsharpyuv0 libslurm42t64 libtiff6 libwebp7 mpi-default-bin mpich relion 222s 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. 222s Need to get 17.3 MB of archives. 222s After this operation, 77.8 MB of additional disk space will be used. 222s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libfftw3-double3 armhf 3.3.10-2fakesync1build1 [369 kB] 223s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libfftw3-single3 armhf 3.3.10-2fakesync1build1 [581 kB] 224s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 224s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhwloc15 armhf 2.12.0-1 [147 kB] 224s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 225s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 225s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 225s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 225s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf libslurm42t64 armhf 24.11.1-1 [769 kB] 226s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 226s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 226s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 226s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf hwloc-nox armhf 2.12.0-1 [213 kB] 226s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpich12 armhf 4.2.1-5 [1574 kB] 228s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf mpich armhf 4.2.1-5 [214 kB] 228s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf mpi-default-bin armhf 1.18 [2504 B] 228s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf relion armhf 3.1.3-4build1 [12.2 MB] 243s Fetched 17.3 MB in 21s (838 kB/s) 243s Selecting previously unselected package libdeflate0:armhf. 243s (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 ... 64655 files and directories currently installed.) 243s Preparing to unpack .../00-libdeflate0_1.23-1_armhf.deb ... 243s Unpacking libdeflate0:armhf (1.23-1) ... 243s Selecting previously unselected package libgomp1:armhf. 243s Preparing to unpack .../01-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 243s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 243s Selecting previously unselected package libfftw3-double3:armhf. 243s Preparing to unpack .../02-libfftw3-double3_3.3.10-2fakesync1build1_armhf.deb ... 243s Unpacking libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 243s Selecting previously unselected package libfftw3-single3:armhf. 243s Preparing to unpack .../03-libfftw3-single3_3.3.10-2fakesync1build1_armhf.deb ... 243s Unpacking libfftw3-single3:armhf (3.3.10-2fakesync1build1) ... 243s Selecting previously unselected package libgfortran5:armhf. 243s Preparing to unpack .../04-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 243s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 243s Selecting previously unselected package libhwloc15:armhf. 244s Preparing to unpack .../05-libhwloc15_2.12.0-1_armhf.deb ... 244s Unpacking libhwloc15:armhf (2.12.0-1) ... 244s Selecting previously unselected package libjpeg-turbo8:armhf. 244s Preparing to unpack .../06-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 244s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 244s Selecting previously unselected package libjpeg8:armhf. 244s Preparing to unpack .../07-libjpeg8_8c-2ubuntu11_armhf.deb ... 244s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 244s Selecting previously unselected package liblerc4:armhf. 244s Preparing to unpack .../08-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 244s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 244s Selecting previously unselected package libsharpyuv0:armhf. 244s Preparing to unpack .../09-libsharpyuv0_1.5.0-0.1_armhf.deb ... 244s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 244s Selecting previously unselected package libslurm42t64. 244s Preparing to unpack .../10-libslurm42t64_24.11.1-1_armhf.deb ... 244s Unpacking libslurm42t64 (24.11.1-1) ... 244s Selecting previously unselected package libjbig0:armhf. 244s Preparing to unpack .../11-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 244s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 244s Selecting previously unselected package libwebp7:armhf. 244s Preparing to unpack .../12-libwebp7_1.5.0-0.1_armhf.deb ... 244s Unpacking libwebp7:armhf (1.5.0-0.1) ... 244s Selecting previously unselected package libtiff6:armhf. 244s Preparing to unpack .../13-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 244s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 244s Selecting previously unselected package hwloc-nox. 244s Preparing to unpack .../14-hwloc-nox_2.12.0-1_armhf.deb ... 244s Unpacking hwloc-nox (2.12.0-1) ... 244s Selecting previously unselected package libmpich12:armhf. 244s Preparing to unpack .../15-libmpich12_4.2.1-5_armhf.deb ... 244s Unpacking libmpich12:armhf (4.2.1-5) ... 244s Selecting previously unselected package mpich. 244s Preparing to unpack .../16-mpich_4.2.1-5_armhf.deb ... 244s Unpacking mpich (4.2.1-5) ... 244s Selecting previously unselected package mpi-default-bin. 244s Preparing to unpack .../17-mpi-default-bin_1.18_armhf.deb ... 244s Unpacking mpi-default-bin (1.18) ... 244s Selecting previously unselected package relion. 244s Preparing to unpack .../18-relion_3.1.3-4build1_armhf.deb ... 244s Unpacking relion (3.1.3-4build1) ... 244s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 244s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 244s Setting up libdeflate0:armhf (1.23-1) ... 244s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 244s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 244s Setting up libslurm42t64 (24.11.1-1) ... 244s Setting up libhwloc15:armhf (2.12.0-1) ... 244s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 244s Setting up libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 244s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 244s Setting up libwebp7:armhf (1.5.0-0.1) ... 244s Setting up libmpich12:armhf (4.2.1-5) ... 244s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 244s Setting up libfftw3-single3:armhf (3.3.10-2fakesync1build1) ... 244s Setting up hwloc-nox (2.12.0-1) ... 244s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 244s Setting up mpich (4.2.1-5) ... 244s update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode 244s update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode 244s Setting up mpi-default-bin (1.18) ... 244s Setting up relion (3.1.3-4build1) ... 244s Processing triggers for libc-bin (2.41-1ubuntu2) ... 244s Processing triggers for man-db (2.13.0-1) ... 253s autopkgtest [16:57:15]: test command1: /usr/bin/relion_refine 253s autopkgtest [16:57:15]: test command1: [----------------------- 254s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 254s ====== General options ===== 254s --i () : Input images (in a star-file) 254s --o () : Output rootname 254s --iter (50) : Maximum number of iterations to perform 254s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 254s --K (1) : Number of references to be refined 254s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 254s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 254s --flatten_solvent (false) : Perform masking on the references as well? 254s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 254s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 254s --lowpass_mask (None) : User-provided mask for low-pass filtering 254s --lowpass (0) : User-provided cutoff for region specified above 254s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 254s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 254s --split_random_halves (false) : Refine two random halves of the data completely separately 254s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 254s ====== Initialisation ===== 254s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 254s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 254s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 254s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 254s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 254s ====== Orientations ===== 254s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 254s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 254s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 254s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 254s --sym (c1) : Symmetry group 254s --relax_sym () : Symmetry to be relaxed 254s --offset_range (6) : Search range for origin offsets (in pixels) 254s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 254s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 254s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 254s --auto_refine (false) : Perform 3D auto-refine procedure? 254s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 254s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 254s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 254s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 254s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 254s --skip_align (false) : Skip orientational assignment (only classify)? 254s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 254s --bimodal_psi (false) : Do bimodal searches of psi angle? 254s ====== Helical reconstruction (in development...) ===== 254s --helix (false) : Perform 3D classification or refinement for helices? 254s --ignore_helical_symmetry (false) : Ignore helical symmetry? 254s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 254s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 254s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 254s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 254s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 254s --helical_rise_initial (0.) : Helical rise (in Angstroms) 254s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 254s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 254s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 254s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 254s --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 254s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 254s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 254s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 254s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 254s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 254s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 254s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 254s ====== Corrections ===== 254s --ctf (false) : Perform CTF correction? 254s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 254s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 254s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 254s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 254s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 254s --norm (false) : Perform normalisation-error correction? 254s --scale (false) : Perform intensity-scale corrections on image groups? 254s --no_norm (false) : Switch off normalisation-error correction? 254s --no_scale (false) : Switch off intensity-scale corrections on image groups? 254s ====== Stochastic Gradient Descent ===== 254s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 254s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 254s --sgd_ini_iter (50) : Number of initial SGD iterations 254s --sgd_fin_iter (50) : Number of final SGD iterations 254s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 254s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 254s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 254s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 254s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 254s --mu (0.9) : Momentum parameter for SGD updates 254s --sgd_stepsize (0.5) : Step size parameter for SGD updates 254s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 254s --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) 254s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 254s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 254s ====== Computation ===== 254s --pool (1) : Number of images to pool for each thread task 254s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 254s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 254s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 254s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 254s --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! 254s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 254s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 254s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 254s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 254s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 254s --gpu (false) : Use available gpu resources for some calculations 254s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 254s ====== Expert options ===== 254s --pad (2) : Oversampling factor for the Fourier transforms of the references 254s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 254s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 254s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 254s --verb (1) : Verbosity (1=normal, 0=silent) 254s --random_seed (-1) : Number for the random seed generator 254s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 254s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 254s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 254s --fix_sigma_noise (false) : Fix the experimental noise spectra? 254s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 254s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 254s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 254s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 254s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 254s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 254s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 254s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 254s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 254s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 254s --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). 254s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 254s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 254s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 254s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 254s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 254s --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 254s --maxsig (-1) : Maximum number of poses & translations to consider 254s --skip_gridding (false) : Skip gridding in the M step 254s --version : Print RELION version and exit 255s autopkgtest [16:57:17]: test command1: -----------------------] 259s autopkgtest [16:57:21]: test command1: - - - - - - - - - - results - - - - - - - - - - 259s command1 PASS (superficial) 262s autopkgtest [16:57:24]: @@@@@@@@@@@@@@@@@@@@ summary 262s command1 PASS (superficial)