Patch Motion Correction error

Motion Correction
1

Hi all,
There is an error messenge when I do the Patch motion correction. Does anyone know what happen?

-----------------------------------------------------------------------------------------------------------------
Error occurred while processing J3/imported/011447104231546704801_20170629_00022_frameImage.tiff
Traceback (most recent call last):
  File "/home/cryosparc/software/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 71, in cryosparc_compute.blobio.prefetch.synchronous_native_read
RuntimeError: Error ocurred (Input/output error) at line 666 in sendfile

IO request details:filename:    /activeEM/data/cyfu/fuchiyu/YC_test2/CS-tutorial-2/J3/imported/011447104231546704801_20170629_00022_frameImage.tiff
filetype:    1
header_only: 0
idx_start:   0
idx_limit:   -1
eer_upsampfactor: 1
eer_numfractions: 40
num_threads: 6
buffer:      (nil)
nx, ny, nz:  0 0 0
dtype:       0
total_time:  -1.000000


Marking J3/imported/011447104231546704801_20170629_00022_frameImage.tiff as incomplete and continuing.
-----------------------------------------------------------------------------------------------------------

Any help is appreciated

2

Looks like a corrupt micrograph. Check your micrographs, check your filesystem for corruption (and/or disks for bad sectors) or a failure in the network connection if a network filesystem.

3

Hi @cafbi,

Is your installation running under docker, or is there anything else in any way peculiar about your installation? Is it a cluster? Also, how much memory does your machine have?

Regardless, though, you can probably avoid this by opening the file /path/to/cryosparc_worker/config.sh and adding the line export CRYOSPARC_TIFF_IO_SHM=false. That will turn off shared-memory I/O, wherein we read an entire TIFF file into memory before decompressing it (rather than decompressing it piece-by-piece directly from disk). We added this as an optimization, and turning this off may have a negative performance impact if you’re using a cluster file system like Lustre.

—Harris