We recently upgraded to ver 4.6.2. There were Anaconda issues which is still not fully resolved. However we noticed that cryosparc does indeed install and can be opened. I can run simple jobs such as importing mics or movies, but when I try to run anything other than this I encounter errors. For example when I import micrographs and try to run CTF estimation I encounter this error. Another error I will describe below.
I have tried importing .tiff (50 frames, K3) or .eer (falcon 4i) movies and the same problem happens. I can import the movies without issue. When I try to align using patch motion I get the error below. Note that I am submitting jobs to a cluster setup. It shows several incomplete micrograph and 0 successful.
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Running on lane slurmcluster
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Resources allocated:
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Worker: slurmcluster
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CPU : [0, 1, 2, 3, 4, 5]
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GPU : [0]
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RAM : [0, 1]
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SSD : False
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Importing job module for job type patch_motion_correction_multi...
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Job ready to run
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[CPU: 249.5 MB]
Transparent hugepages are enabled. You may encounter stalls or performance problems with CryoSPARC jobs.
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Job will process this many movies: 1
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Job will output denoiser training data for this many movies: 1
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Random seed: 848562516
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parent process is 591487
[CPU: 167.0 MB]
Calling CUDA init from 591846
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Child process with PID 591846 terminated unexpectedly with exit code 1.
[CPU: 250.2 MB]
['uid', 'movie_blob/path', 'movie_blob/shape', 'movie_blob/psize_A', 'movie_blob/is_gain_corrected', 'movie_blob/format', 'movie_blob/has_defect_file', 'movie_blob/import_sig', 'micrograph_blob/path', 'micrograph_blob/idx', 'micrograph_blob/shape', 'micrograph_blob/psize_A', 'micrograph_blob/format', 'micrograph_blob/is_background_subtracted', 'micrograph_blob/vmin', 'micrograph_blob/vmax', 'micrograph_blob/import_sig', 'micrograph_blob_non_dw/path', 'micrograph_blob_non_dw/idx', 'micrograph_blob_non_dw/shape', 'micrograph_blob_non_dw/psize_A', 'micrograph_blob_non_dw/format', 'micrograph_blob_non_dw/is_background_subtracted', 'micrograph_blob_non_dw/vmin', 'micrograph_blob_non_dw/vmax', 'micrograph_blob_non_dw/import_sig', 'micrograph_blob_non_dw_AB/path', 'micrograph_blob_non_dw_AB/idx', 'micrograph_blob_non_dw_AB/shape', 'micrograph_blob_non_dw_AB/psize_A', 'micrograph_blob_non_dw_AB/format', 'micrograph_blob_non_dw_AB/is_background_subtracted', 'micrograph_blob_non_dw_AB/vmin', 'micrograph_blob_non_dw_AB/vmax', 'micrograph_blob_non_dw_AB/import_sig', 'micrograph_thumbnail_blob_1x/path', 'micrograph_thumbnail_blob_1x/idx', 'micrograph_thumbnail_blob_1x/shape', 'micrograph_thumbnail_blob_1x/format', 'micrograph_thumbnail_blob_1x/binfactor', 'micrograph_thumbnail_blob_1x/micrograph_path', 'micrograph_thumbnail_blob_1x/vmin', 'micrograph_thumbnail_blob_1x/vmax', 'micrograph_thumbnail_blob_2x/path', 'micrograph_thumbnail_blob_2x/idx', 'micrograph_thumbnail_blob_2x/shape', 'micrograph_thumbnail_blob_2x/format', 'micrograph_thumbnail_blob_2x/binfactor', 'micrograph_thumbnail_blob_2x/micrograph_path', 'micrograph_thumbnail_blob_2x/vmin', 'micrograph_thumbnail_blob_2x/vmax', 'background_blob/path', 'background_blob/idx', 'background_blob/binfactor', 'background_blob/shape', 'background_blob/psize_A', 'rigid_motion/type', 'rigid_motion/path', 'rigid_motion/idx', 'rigid_motion/frame_start', 'rigid_motion/frame_end', 'rigid_motion/zero_shift_frame', 'rigid_motion/psize_A', 'spline_motion/type', 'spline_motion/path', 'spline_motion/idx', 'spline_motion/frame_start', 'spline_motion/frame_end', 'spline_motion/zero_shift_frame', 'spline_motion/psize_A']
[CPU: 250.3 MB]
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Compiling job outputs...
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Passing through outputs for output group micrographs from input group movies
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This job outputted results ['micrograph_blob_non_dw', 'micrograph_blob_non_dw_AB', 'micrograph_thumbnail_blob_1x', 'micrograph_thumbnail_blob_2x', 'movie_blob', 'micrograph_blob', 'background_blob', 'rigid_motion', 'spline_motion']
[CPU: 250.3 MB]
Loaded output dset with 0 items
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Passthrough results ['gain_ref_blob', 'mscope_params']
[CPU: 250.3 MB]
Loaded passthrough dset with 1 items
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Intersection of output and passthrough has 0 items
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Output dataset contains: ['gain_ref_blob', 'mscope_params']
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Outputting passthrough result gain_ref_blob
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Outputting passthrough result mscope_params
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Passing through outputs for output group micrographs_incomplete from input group movies
[CPU: 250.3 MB]
This job outputted results ['micrograph_blob']
[CPU: 250.3 MB]
Loaded output dset with 1 items
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Passthrough results ['movie_blob', 'gain_ref_blob', 'mscope_params']
[CPU: 250.3 MB]
Loaded passthrough dset with 1 items
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Intersection of output and passthrough has 1 items
[CPU: 250.3 MB]
Output dataset contains: ['movie_blob', 'gain_ref_blob', 'mscope_params']
[CPU: 250.3 MB]
Outputting passthrough result movie_blob
[CPU: 250.3 MB]
Outputting passthrough result gain_ref_blob
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Outputting passthrough result mscope_params
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Checking outputs for output group micrographs
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Checking outputs for output group micrographs_incomplete
[CPU: 250.4 MB]
Updating job size...
[CPU: 250.4 MB]
Exporting job and creating csg files...
[CPU: 250.5 MB]
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Job complete. Total time 30.52s