Slurm and cryoSPARC

Install, Configure and Update
1

Hi - We are transitioning our cryoSPARC functionality to our HPC environment. Our HPC uses slurm for job management. Slurm isn’t something that I’m familiar with so I was curious if anyone could help me understand how cryoSPARC and slurm work together and how I would go about making some of the files that are needed for cryoSPARC to use slurm. I don’t see anything obvious in the UI that would be what I need. Thanks for any and all tips.

Bryan

2

This part of the guide is actually quite detailed on how to setup the commands needed for use in a cluster. Unfortunately you have to do it via command-line rather than using the GUI.
https://cryosparc.com/docs/reference/install/#installation-cluster

3

Sorry to revive an old discussion, but at the time I am writing this, the submission script generated by cryosparcm cluster example slurm does not work by default.

The reason is that this template script contains these two lines:

#SBATCH -o {{ job_dir_abs }}
#SBATCH -e {{ job_dir_abs }}

So the job then tries to write messages and errors to a directory, which cannot work. I could fix this by editing these two lines as follows:

#SBATCH -o {{ job_dir_abs }}/job.log
#SBATCH -e {{ job_dir_abs }}/job.log

And then running cryosparcm cluster connect again to update the cluster configuration.

Maybe the @team could update the documentation and the template script generated by cryosparcm cluster example slurm?

Thanks!

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4

Thank you @Guillaume for your contribution to the forum. We have recorded the issue for consideration in a future cryoSPARC release.

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5

Yesterday’s patch addresses this issue.

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