Question: CWL: SLurm Job Sheduler
0
gravatar for kevin.o.oluoch
2.3 years ago by
Kenya
kevin.o.oluoch70 wrote:

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

cwl slurm • 1.4k views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 2.3 years ago by kevin.o.oluoch70
2
gravatar for Michael R. Crusoe
2.3 years ago by
Common Workflow Language project
Michael R. Crusoe1.7k wrote:

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,

ADD COMMENTlink written 2.3 years ago by Michael R. Crusoe1.7k
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