Hi
I’d like to report an error when I run the Patch CTF Estimation.
An error of ‘Child process with PID 42472 terminated unexpectedly with exit code 1’ showed up and all my micrographs went to “incomplete” group.
I’ve tried my old dataset which worked well with cryoSPARC v3, but I encountered the same error.
Seems like a new bug in cryoSPARC v4.1.1?
Hi, here is the log:
--------------------
License is valid.
Launching job on lane default target syrah.qb3.berkeley.edu ...
Running job on master node hostname syrah.qb3.berkeley.edu
[CPU: 194.7 MB]
Job J63 Started
[CPU: 194.7 MB]
Master running v4.1.1+230110, worker running v4.1.1+230110
[CPU: 194.8 MB]
Working in directory: /mount/local4/minghao/XXX_processing/XXX/J63
[CPU: 194.8 MB]
Running on lane default
[CPU: 194.8 MB]
Resources allocated:
[CPU: 194.8 MB]
Worker: syrah.qb3.berkeley.edu
[CPU: 194.8 MB]
CPU : [0, 1, 2, 3, 4, 5, 6, 7]
[CPU: 194.8 MB]
GPU : [0, 1, 2, 3]
[CPU: 194.8 MB]
RAM : [0]
[CPU: 194.8 MB]
SSD : False
[CPU: 194.8 MB]
--------------------------------------------------------------
[CPU: 194.8 MB]
Importing job module for job type patch_ctf_estimation_multi...
[CPU: 231.1 MB]
Job ready to run
[CPU: 231.1 MB]
***************************************************************
[CPU: 234.1 MB]
Job will process this many micrographs: 5383
[CPU: 234.1 MB]
parent process is 42432
[CPU: 178.9 MB]
Calling CUDA init from 42472
[CPU: 178.9 MB]
Calling CUDA init from 42473
[CPU: 178.9 MB]
Calling CUDA init from 42475
[CPU: 178.9 MB]
Calling CUDA init from 42476
[CPU: 252.8 MB]
Child process with PID 42472 terminated unexpectedly with exit code 1.
[CPU: 252.8 MB]
Child process with PID 42473 terminated unexpectedly with exit code 1.
[CPU: 252.8 MB]
Child process with PID 42475 terminated unexpectedly with exit code 1.
[CPU: 252.9 MB]
Child process with PID 42476 terminated unexpectedly with exit code 1.
[CPU: 235.8 MB]
--------------------------------------------------------------
[CPU: 235.8 MB]
Compiling job outputs...
[CPU: 235.8 MB]
Passing through outputs for output group exposures from input group exposures
[CPU: 235.8 MB]
This job outputted results ['ctf', 'ctf_stats']
[CPU: 235.8 MB]
Loaded output dset with 0 items
[CPU: 235.8 MB]
Passthrough results ['micrograph_blob_non_dw', 'micrograph_blob', 'mscope_params']
[CPU: 238.0 MB]
Loaded passthrough dset with 5383 items
[CPU: 235.8 MB]
Intersection of output and passthrough has 0 items
[CPU: 235.8 MB]
Passing through outputs for output group exposures_incomplete from input group exposures
[CPU: 237.0 MB]
This job outputted results ['ctf']
[CPU: 237.0 MB]
Loaded output dset with 5383 items
[CPU: 237.0 MB]
Passthrough results ['micrograph_blob_non_dw', 'micrograph_blob', 'mscope_params']
[CPU: 238.8 MB]
Loaded passthrough dset with 5383 items
[CPU: 238.8 MB]
Intersection of output and passthrough has 5383 items
[CPU: 236.6 MB]
Checking outputs for output group exposures
[CPU: 236.6 MB]
Checking outputs for output group exposures_incomplete
[CPU: 240.9 MB]
Updating job size...
[CPU: 240.9 MB]
Exporting job and creating csg files...
[CPU: 241.1 MB]
***************************************************************
[CPU: 241.1 MB]
Job complete. Total time 30.81s
What is inside
/mount/local4/minghao/XXX_processing/XXX/J63/job.log
?
Sorry for sending the wrong info.
The job.log file is too long to paste in here (4.6 MB). Could you please give me a link to upload?
Your job.log includes an
undefined symbol: cuDevicePrimaryCtxRelease_v2
error.
If you haven’t already, you may try if
/path/to/cryosparc_worker/bin/cryosparcw install-3dflex
fixes this problem, but only after ensuring all the prerequisites (docs).
Hi, I’d like to report that this problem was solved by updating the nvidia driver.
Thank you very much for the help!
Best,
Minghao