CWL: SLurm Job Sheduler

Question

[kevin.o.oluoch]

Does the slurm job scheduler work with Common Workflow Language implementations? How can I use it to run multiple files?

Answer 1

[Michael R. Crusoe]

Hello kevin.o.oluoch & thank you for your question,

At http://www.commonwl.org/ we see both Arvados and Toil listing support for the Slurm Workload Manager. Arvados requires Docker, which you might not have available.

Toil's documentation for running CWL workflows is at https://toil.readthedocs.io/en/releases-3.7.x/running/running.html#running-cwl-workflows

To run using Slurm, try cwltoil --batchSystem slurm --disableCaching my_workflow.cwl my_inputs.yaml

You may need to set additional Slurm options via the TOIL_SLURM_ARGS environment variable, see the first part of https://toil.readthedocs.io/en/releases-3.7.x/batchSystem.html

I hope this was helpful.

Cheers,