ThreeDFSC Failure

Troubleshooting
1

I’m trying to run a ThreeDFSC job on a project. I’m attaching the Volume from the last refinement I did, but after a period of time running I’m getting the following message:

[CPU: 865.5 MB]  Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/run.py", line 90, in cryosparc_compute.run.main
  File "/gs1/RTS/EM/Software/CryoSPARCv2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py", line 965, in create_summary_from_job
    output_group_dataset = load_output_group_direct(_project_uid, _job_uid, output_group_name)
  File "/gs1/RTS/EM/Software/CryoSPARCv2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py", line 499, in load_output_group_direct
    d = load_output_result_dset(project_uid, output_result, version, slot_name)
  File "/gs1/RTS/EM/Software/CryoSPARCv2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py", line 473, in load_output_result_dset
    d.from_file(abspath)
  File "/gs1/RTS/EM/Software/CryoSPARCv2/cryosparc2_worker/cryosparc_compute/dataset.py", line 547, in from_file
    indata = n.load(file, allow_pickle=False)
  File "/gs1/RTS/EM/Software/CryoSPARCv2/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/lib/npyio.py", line 444, in load
    raise ValueError("Cannot load file containing pickled data "
ValueError: Cannot load file containing pickled data when allow_pickle=False

Is there another step between refinement and ThreeDFSC that I’m forgetting? Thanks for any tips

Bryan

2

Hi @hansenbry, what version of cryoSPARC are you running? Can you share a screenshot of the Outputs tab on the failed job?

3

Hi @nfrasser We’re currently running 3.2.0 and here’s my output tab

ThreeDfsc
ThreeDfsc1867×333 53 KB

4

@hansenbry Would it be possible for you to update your cryoSPARC installation and re-run the job?

5

@wtempel It’s on our HPC teams todo list to update to 3.3, but not sure when it’ll happen. I’ll update here if I’m still having issues after the upgrade to 3.3.0

6

@hansenbry Please ask your HPC admins to update to the then-latest version when they get to it (3.3.1 as of now).