New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Can someone show the command to run on SLURM GRID? #310

Closed

Isoris opened this issue Dec 19, 2024 · 1 comment

Isoris commented Dec 19, 2024

Hello, I read the tutorial but I didn't get it to work. I am not sure on how to pass the arguments in the slurm.

For instance I have access at multiple nodes but its 126 CPU and 237 GB ram. Also we have to use the partition ( compute ) and the account number -A

Could someone copy and paste their command to show how to make it run.

Thank you very much.

Member

skoren commented Dec 19, 2024

You just need to add --slurm, see the README: https://github.com/marbl/verkko/tree/master?tab=readme-ov-file#running-on-a-grid for how you customize the request to include account/partition, in particular "customizing grid requests". Memory/threads is handled by snakemake. Something like:

--snakeopts '--cluster "./slurm-sge-submit.sh {threads} {resources.mem_gb} {resources.time_h} {rulename} {resources.job_id} --partition=compute --account=yourNumber"'

should work

skoren closed this as completed

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment