Cluster scripts macros


We are working on a solution that will avoid the need to run all the jobs on a Slurm cluster as a single user.
For that, we have a special user that is running the cryoSPARC server, and has sudo permissions over the Slurm commands.

The batch-related lines in the json file then become:
“qdel_cmd_tpl”: “sudo -u {{ job_creator }} /path/to/scancel {{ cluster_job_id }}”,
“qsub_cmd_tpl”: “sudo -u {{ job_creator }} /path/to/sbatch {{ script_path_abs }}”,


While this works properly for the qsub_cmd_tpl, it does not for the qdel and qstat lines. From the error messages I get afterwards, it looks like what is happening is that {{ job_creator }} is not expanded in these lines (and neither is {{ cryosparc_username }}), while it is for qsub.

Is that expected?

Hi @geraudk,

This behaviour is expected as of v4.0.1. Thank you for bringing this issue to our attention as we look to continue improving cluster integration in CryoSPARC.