Thanks @wtempel, I can submit my jobs now, but not able to run. cryosparc user not able to get the “sbatch” command. Even though it is available in the user path.
Cluster script submission for P1 J4 failed with exit code 127
/bin/sh: sbatch: command not found
I can add the absolute path in below file, then it is working, but I would like to fix this issue as well.
cluster_info.json: “qsub_cmd_tpl” : “sbatch {{script_path_abs }}”,
Did this happen for a patch motion correction job?
If this error occurred on AWS parallelcluster, this might be a question for an AWS forum. Afair, when I encountered this same error, I hypothesized that parallelcluster configuration was still in progress, restarted CryoSPARC, cloned the job and re-submitted. The job then started properly.
I am still curious about the actual cause of this error.
It is happening with import movies job itself. Yes this error is on AWS parallelcluster. I will try to get some more details and will see.
In your slurm submission script, are you using “sh” or “bash”? AWS ParallelCluster does not setup the correct paths to the slurm commands unless you are using bash. So in your cluster_info.json, you should have for example:
“script_tpl”: “#!/usr/bin/env bash\n#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}\n#other SBATCH directives”
@vmdri, I have used bash, still it is not working, now currently I am using absolute path for all the slum and other binaries. Thanks.