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feat: Enables running snakemake job within a slurm cluster reservation. #285

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feat: Enables running snakemake job within a slurm cluster reservation. #285

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5 changes: 5 additions & 0 deletions snakemake_executor_plugin_slurm/submit_string.py
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Expand Up @@ -50,6 +50,11 @@ def get_submit_command(job, params):
if job.resources.get("nodes", False):
call += f" --nodes={job.resources.get('nodes', 1)}"

# Specify reservation for job if any. Reservation name is in
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is this is a resource per job, users would need to alter workflows or write a default resource in their workflow profiles. Both scenarios not really desirable, when wanting to stay as generic as possible. See the comment thread for alternatives.

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Hi Christian,
I hadn't considered relying on the magnetic attribute of a reservation. I agree, this would be best as a default resource for a workflow, or passed on the command line, and not a per job resource. This capability is something we would use during post-downtime cluster testing. I'll discuss use of magnetic reservations with our sys admins.
Thanks,
Brett

# single quotes since reservation names may include spaces.
if job.resources.get("reservation"):
call += f" --reservation='{job.resources.reservation}'"

# fixes #40 - set ntasks regardless of mpi, because
# SLURM v22.05 will require it for all jobs
gpu_job = job.resources.get("gpu") or "gpu" in job.resources.get("gres", "")
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