Homogenous refinement Job process terminated abnormally

[abasle]

Hi,

I have homogenous refinement jobs failing abnormally and I have not found why.

It does not seem to be a memory problem as the server(s) had plenty free and:
[CPU: 228.9 MB Avail: 246.45 GB] ====== Job process terminated abnormally.

The particles are in box size of 1200. Is that the problem? I thought cryosparc and dependencies would work with 1200 pixels box sizes.

Cheers,
Arnaud

[rbs_sci]

1100 pixels seems to be the maximum right now.

Support for box sizes above 1100 pixels

Hi @sarulthasan, THP “sort of” helped - the timing isn’t so asymmetric any more. Haven’t run more than 2 NU Refines in parallel yet to really stress it for that (waiting on RBMC!) Wanted to query about something else, though… Per here, box sizes seem to top out around 1100 pixels. Can confirm with latest CryoSPARC… 1200 pixel box fails to both refine or to reconstruct - even on 48GB GPUs. 1150 fails too. 1100 works. Anything you can suggest to push into 1200/1400 pixel boxes? 1480 fits (just,…

[hsnyder]

Hi @abasle. @rbs_sci is correct. However, I’d be interested to see the job (text) log. You can find it by going to the metadata tab in the job window and then choosing “log” on the line underneath. The last few lines may contain more information about the error.

[LeoTR]

We are having similar problem when trying to refine a virus with pixel size 1.1 and box size 1200. Memory, cache and scratch space are not an issue, yet it interrupts abnormally.

[rbs_sci]

There is currently no way to fix that. A workaround is downsampling to <1,100 pixel boxes.