Patch motion correction job completed immediately after launching

running patch motion correction job completed right after lunching the job with following message:
License is valid.

Launching job on lane default target Gambit …

Running job on master node hostname Gambit

[CPU: 80.7 MB] Project P6 Job J9 Started

[CPU: 80.8 MB] Master running v3.4.0, worker running v3.4.0

[CPU: 81.2 MB] Working in directory: /mnt/CryoEM/2022-03-08/MS032-2/CS-20220308-ms032-aporad52-tilted/J9

[CPU: 81.2 MB] Running on lane default

[CPU: 81.2 MB] Resources allocated:

[CPU: 81.2 MB] Worker: Gambit

[CPU: 81.2 MB] CPU : [0, 1, 2, 3, 4, 5]

[CPU: 81.2 MB] GPU : [0]

[CPU: 81.2 MB] RAM : [0, 1]

[CPU: 81.2 MB] SSD : False

[CPU: 81.2 MB] --------------------------------------------------------------

[CPU: 81.2 MB] Importing job module for job type patch_motion_correction_multi…

[CPU: 244.8 MB] Job ready to run

[CPU: 244.9 MB] ***************************************************************

[CPU: 248.4 MB] Job will process this many movies: 5688

[CPU: 248.6 MB] parent process is 13190

[CPU: 193.4 MB] Calling CUDA init from 13260

[CPU: 269.9 MB] Child process with PID 13260 terminated unexpectedly with exit code 1.

[CPU: 262.9 MB] --------------------------------------------------------------

[CPU: 262.9 MB] Compiling job outputs…

[CPU: 262.9 MB] Passing through outputs for output group micrographs from input group movies

[CPU: 262.9 MB] This job outputted results [‘micrograph_blob_non_dw’, ‘micrograph_thumbnail_blob_1x’, ‘micrograph_thumbnail_blob_2x’, ‘micrograph_blob’, ‘background_blob’, ‘rigid_motion’, ‘spline_motion’]

[CPU: 262.9 MB] Loaded output dset with 0 items

[CPU: 262.9 MB] Passthrough results [‘movie_blob’, ‘gain_ref_blob’, ‘mscope_params’]

[CPU: 263.0 MB] Loaded passthrough dset with 5688 items

[CPU: 263.0 MB] Intersection of output and passthrough has 0 items

[CPU: 263.0 MB] Passing through outputs for output group micrographs_incomplete from input group movies

[CPU: 263.0 MB] This job outputted results [‘micrograph_blob’]

[CPU: 263.0 MB] Loaded output dset with 5688 items

[CPU: 263.0 MB] Passthrough results [‘movie_blob’, ‘gain_ref_blob’, ‘mscope_params’]

[CPU: 263.0 MB] Loaded passthrough dset with 5688 items

[CPU: 263.6 MB] Intersection of output and passthrough has 5688 items

[CPU: 263.6 MB] Checking outputs for output group micrographs

[CPU: 263.6 MB] Checking outputs for output group micrographs_incomplete

[CPU: 263.6 MB] Updating job size…

[CPU: 263.6 MB] Exporting job and creating csg files…

[CPU: 263.6 MB] ***************************************************************

[CPU: 263.6 MB] Job complete. Total time 30.62s

running uname -a && free -g && lscpu && nvidia-smi shows that:
Linux Gambit 5.15.0-52-generic #58-Ubuntu SMP Thu Oct 13 08:03:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
total used free shared buff/cache available
Mem: 62 3 55 0 4 58
Swap: 1 0 1
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 43 bits physical, 48 bits virtual
Byte Order: Little Endian
CPU(s): 64
On-line CPU(s) list: 0-63
Vendor ID: AuthenticAMD
Model name: AMD Ryzen Threadripper 2990WX 32-Core Processor
CPU family: 23
Model: 8
Thread(s) per core: 2
Core(s) per socket: 32
Socket(s): 1
Stepping: 2
Frequency boost: enabled
CPU max MHz: 3000.0000
CPU min MHz: 2200.0000
BogoMIPS: 5988.10
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fx
sr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid amd_dcm aperfmperf rapl pni pclmulqdq m
onitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm
sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstat
e ssbd ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero
irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold
avic v_vmsave_vmload vgif overflow_recov succor smca sme sev sev_es
Virtualization features:
Virtualization: AMD-V
Caches (sum of all):
L1d: 1 MiB (32 instances)
L1i: 2 MiB (32 instances)
L2: 16 MiB (32 instances)
L3: 64 MiB (8 instances)
NUMA node(s): 4
NUMA node0 CPU(s): 0-7,32-39
NUMA node1 CPU(s): 16-23,48-55
NUMA node2 CPU(s): 8-15,40-47
NUMA node3 CPU(s): 24-31,56-63
Itlb multihit: Not affected
L1tf: Not affected
Mds: Not affected
Meltdown: Not affected
Mmio stale data: Not affected
Retbleed: Mitigation; untrained return thunk; SMT vulnerable
Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Spectre v2: Mitigation; Retpolines, IBPB conditional, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Srbds: Not affected
Tsx async abort: Not affected
Mon Oct 24 21:10:13 2022
| NVIDIA-SMI 515.65.01 Driver Version: 515.65.01 CUDA Version: 11.7 |
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
| 0 NVIDIA GeForce … Off | 00000000:43:00.0 On | N/A |
| 0% 32C P8 27W / 300W | 397MiB / 11264MiB | 38% Default |
| | | N/A |

| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
| 0 N/A N/A 2854 G /usr/lib/xorg/Xorg 258MiB |
| 0 N/A N/A 2989 G /usr/bin/gnome-shell 61MiB |
| 0 N/A N/A 4573 G …512529937732986680,131072 75MiB |

I would appreciate any comments to solve this issue. My current CryoSPARC version is v3.4.0

Thank you,

Hi Ali,

Please post the outputs of

  1. cryosparcm joblog P6 J9

Hi @wtempel

I updated my cryosparc to v4.0.2 and patch motion correction is running now.

Thank you,

1 Like