Job process terminated abnormally-3D flex reconstruction

Dear all,

I was running 3d flex reconstruction job with 60k particles (box size 480). However, the job can not run through and showed error: job process terminated abnormally:

Is this a issue with the box size? I saw a previous discussion with similar error, which bin-2 particle would particle but particle without binning would not work.

Thanks,

Yan

@wangyan16 Please can you let us know

  • your CryoSPARC version
  • the box size of your particles
  • whether additional error messages can be found in the job log (under Metadata|Log)
  • specifications for the CryoSPARC worker computer, via these commands:
    nvidia-smi
    free -h
    

Thanks for your quick reply!

The cryosparc version is 4.5.3. Box size is 460 (pixel size 0.86).

There is an error in the log:

Screenshot 2024-06-27 at 2.36.00 PM
Screenshot 2024-06-27 at 2.36.23 PM

Our work computer: 128 cores, 1032GB memory, 8 GPU (NVIDIA A100 80GB PCIe).

Thanks @wangyan16 The screenshot suggests you looked that the Data tab under Metadata. Please can you also check the Log tab for errors.
image

There is no error in the log. I re-extracted particle with a smaller box size (440) and it worked. So it is something about the computation and pixel size?

What was the original box size with which the job failed?

Sorry for the late reply. It’s 460 vs 440 (pixel size 0.84).

Unfortunately, we do not know what caused the segmentation fault. The log also does not suggest to us how to further debug the error.