Bus error (core dumped) during non-uniform refinement

gogo_science · January 3, 2023, 9:46pm

hi all,

We have the same problem with NUR in CS v4.1.1.
Not sure what is going on because homo refine works for the same particle stack.
job.log output says:
"/cryosparc/software/cryosparc_worker/bin/cryosparcw: line 163: 56545 Bus error (core dumped) python -c “import cryosparc_compute.run as run; run.run()” “$@”

wtempel · January 4, 2023, 2:10pm

Welcome to the forum @gogo_science.
Please can you check /var/log/messages or /var/log/syslog for entries that coincide with the Bus error and post what you find.

gogo_science · January 4, 2023, 6:35pm

Thanks!
No messages that coincide with the job.

gogo_science · January 6, 2023, 5:44pm

It’s interesting that it always fails when it starts the cross validation of the second half-set.

wtempel · January 16, 2023, 9:59pm

@gogo_science Is this the only job type and/or dataset where you observed a Bus error?
Does the error also occur when you run the benchmark workflow with Run all job types enabled?

gogo_science · March 14, 2023, 5:30pm

The error occurs only with this dataset and only at full pixel size.
We tested a few things and it turned out the job was requiring a lot more memory than permitted on our HPC system. We’ve resolved it now, so in case anyone else notices this, check your memory usage.