Patch motion correction error v4.2.0

Motion Correction
1

Dear all,

While I am running the Patch Motion Correction job, for every single imported movies from the previous job, I am getting this error message:

“Error occurred while processing J4/imported/XXX.tif
Traceback (most recent call last):
File “/home/XXX/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 60, in exec
return self.process(item)
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py”, line 117, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File “cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py”, line 132, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File “cryosparc_master/cryosparc_compute/blobio/prefetch.py”, line 68, in cryosparc_compute.blobio.prefetch.synchronous_native_read
RuntimeError: Error ocurred (Input/output error) at line 720 in sendfile”
I even re import movies but it didn’t fix the issue.
Can someone advise how to interpret this error message and where the issue came from?

2

Hi @arazi,

Have a look at this forum thread, in which another user encountered a similar issue and a functional workaround was found: RuntimeError: sendfile582: Input/output error.

We still don’t really know why this happens on some users’ systems, but the workaround in the above thread does work, to the best of our knowledge. It would be helpful to know the details of your computational setup:

  • what Linux distro are you running?
  • is this a cluster or a single workstation, etc?
  • is there anything “interesting” or off-script going on with your computational infrastructure (docker, etc)?

– Harris

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3

Hello Harris,

Thank you for your reply. Our IT specialist could fix it by increasing the shared memory for the associated docker container. For reference, all jobs are managed within a kubernetes/slurm framework.

Thanks again.
Aida

1 Like