Kill/delete job that is not anymore in PBS/Slurm scheduler job list

I would like to delete/kill some jobs that had issues with scheduler. The jobs are not anymore in the scheduler list and therefore cannot killed/deleted them

I get

Command [‘qdel’ , '4406.ims ']'returned non-zero exit status 153 (as the job does not exist from the scheduler side)

Can I delete those jobs directly from mongodb? Can I delete all resources associated to a user as well?

Thanks you for any info



HI @jcducom,

This seems to be a bug- the kill command shouldn’t fail if the cluster command fails. We’ve recorded this issue and we’ll update you when it’s fixed. For the time being, you can manually “kill” the job by running the command:
cryosparcm cli "set_job_status('<project_uid>', '<job_uid>', 'killed')"

1 Like

Thank you so much for your quick reply and sorry my late reply! It did fix the issue.
Thanks again

@stephan I am having a very similar issue using on an LSF cluster. I tried to run the command you gave above and received the following error:

[stae8w@bmi-r740-05 bin]$ /usr/local/cryosparc/cryosparc_master/bin/cryosparcm cli “set_job_status(’’, ‘’, ‘killed’)”
Traceback (most recent call last):
File “/usr/local/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/”, line 193, in _run_module_as_main
main”, mod_spec)
File “/usr/local/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/”, line 85, in _run_code
exec(code, run_globals)
File “/usr/local/cryosparc/cryosparc_master/cryosparc_compute/”, line 89, in
File “”, line 1, in
File “/usr/local/cryosparc/cryosparc_master/cryosparc_compute/”, line 62, in func
assert False, res[‘error’]
AssertionError: {‘code’: 500, ‘data’: None, ‘message’: “OtherError: argument of type ‘NoneType’ is not iterable”, ‘name’: ‘OtherError’}

Here is a screenshot of what happens when I try to kill the job.

It looks like you forgot to enter Project ID and Job ID in the command
cryosparcm cli "set_job_status('<project_uid>', '<job_uid>', 'killed')"

Yes, I saw that after posting and forgot to come back here. Total noob mistake!