OSError: [Errno 16] Device or resource busy

Particle Picking
1

Dear colleagues,

running the filament tracer I got the following error.

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/run.py”, line 61, in cryosparc_compute.jobs.template_picker_gpu.run.run
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/run.py”, line 250, in cryosparc_compute.jobs.template_picker_gpu.run.do_pick
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/run.py”, line 261, in cryosparc_compute.jobs.template_picker_gpu.run.do_pick
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/run.py”, line 89, in cryosparc_compute.jobs.template_picker_gpu.run.lambda
File “/home/cryosparc_user/software/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py”, line 130, in read_mrc
with open(fname, ‘rb’) as file_obj:
OSError: [Errno 16] Device or resource busy: ‘/data3/20230504_tg_Arf_time_series/CS-arf1p-time-series-4h/J2/motioncorrected/015285281078990338700_FoilHole_3512354_Data_3521227_3521229_20230505_033230_EER_patch_aligned_doseweighted.mrc’

Update:
the file that CS can not see is in the folder - 015285281078990338700_FoilHole_3512354_Data_3521227_3521229_20230505_033230_EER_patch_aligned_doseweighted.mrc

is present in the folder J2/motioncorrected

The TOPAZ also complains about the missing files but they all are in the motion corrected folder

Could you please advice how to fix it?

Thanks in advance.

Sincerely,
Dmitry

2

Maybe another process is accessing the file? What are the outputs of these commands:

stat -f /data3/20230504_tg_Arf_time_series/CS-arf1p-time-series-4h/J2/motioncorrected/
stat /data3/20230504_tg_Arf_time_series/CS-arf1p-time-series-4h/J2/motioncorrected/015285281078990338700_FoilHole_3512354_Data_3521227_3521229_20230505_033230_EER_patch_aligned_doseweighted.mrc
lsof /data3/20230504_tg_Arf_time_series/CS-arf1p-time-series-4h/J2/motioncorrected/015285281078990338700_FoilHole_3512354_Data_3521227_3521229_20230505_033230_EER_patch_aligned_doseweighted.mrc
1 Like
3

Hello @wtempel ,

the issue was solved and it seems to be connected to permission rights

Thank you

Sincerely,
Dmitry

1 Like