Jobs still continue running in queue after being killed from cryoSPARC interface

Troubleshooting
1

Hi,

When I kill a running job from the cryoSPARC interface, it turns orange and says killed - but the job nonetheless keeps running in the SLURM queue. They are proving impossible to kill even though they have disappeared from cryoSPARC GUI.

I only have privileges to kill a cryoSPARC job from within, so scancel followed by job-ID doesn’t work.

Can you tell me what might be going on?

Taha

2

Here is my output of cryosparcm status:

3

And of cryosparcm log database:

4

@tahashahid Please can you paste the contents of your cluster_info.json file, omitting information that you don’t want to share with the forum.

5

Hello. Thank you. Here it is:

6

Hello.

It appears I had used cryosparcm command as myself rather than as the lab-user, which badly messed up the permissions.

Our brilliant scientific computation officer managed to resolve it, so this thread may be closed. I have removed the CRYOSPARC_FORCE_USER=true assertion from config.sh to prevent me from doing this again.

Thanks a lot nonetheless for getting back to me so swiftly.

Taha

7

@tahashahid Your update is much appreciated and may help in the future resolution of similar problems.