Dear all,
we are testing a setup where we mounted a folder with the ‘sshfs’ command and now we wish to use this folder as the source of movies in tif format. CS version 3.2.2. SLURM cluster setup.
I can execute Import movies and the symbolic links are created. The links seem to work fine when I test them in the terminal. The files have read permissions:
stat FoilHole_10182344_Data_10180841_10180843_20191010_130455_Fractions.tif
File: FoilHole_10182344_Data_10180841_10180843_20191010_130455_Fractions.tif
Size: 643139681 Blocks: 1256136 IO Block: 4096 regular file
Device: 47h/71d Inode: 9 Links: 1
Access: (0644/-rw-r--r--) Uid: (383400030/ UNKNOWN) Gid: (383400030/ UNKNOWN)
Access: 2022-09-13 12:16:20.000000000 +0200
Modify: 2022-09-13 12:21:32.000000000 +0200
Change: 2022-09-13 12:21:32.000000000 +0200
But when I setup a Motion correction job I get this error
[CPU: 217.6 MB] Error occurred while processing J97/imported/016082983820181942327_FoilHole_10185797_Data_10180841_10180843_20191010_160357_Fractions.tif
Traceback (most recent call last):
File "/d/hpc/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 60, in exec
return self.process(item)
File "cryosparc_worker/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_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 125, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File "/d/hpc/software/cryosparc/cryosparc_worker/cryosparc_compute/blobio/tiff.py", line 65, in read_tiff
mov = read_tiff_frames_threaded(path, num_threads)
File "/d/hpc/software/cryosparc/cryosparc_worker/cryosparc_compute/blobio/tiff.py", line 44, in read_tiff_frames_threaded
tif = libtiff.TIFF.open(tifpath, mode='r')
File "/d/hpc/software/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/libtiff/libtiff_ctypes.py", line 501, in open
raise TypeError('Failed to open file ' + repr(filename))
TypeError: Failed to open file b'/ab/ab/ab/cryosparc/P4/J97/imported/016082983820181942327_FoilHole_10185797_Data_10180841_10180843_20191010_160357_Fractions.tif'
Marking J97/imported/016082983820181942327_FoilHole_10185797_Data_10180841_10180843_20191010_160357_Fractions.tif as incomplete and continuing...
All the movies fail in this way. These same movies were once before imported and motion corrected on a different cluster so the movies themselves should be OK.
Any ideas? Is it a CS issue?