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

bmilash · 2025-05-15T17:10:44Z

This change lets the plugin start a slurm job using a reservation resource provided within a profile or on the command line.

Summary by CodeRabbit

New Features
- Added support for specifying a SLURM job reservation when submitting jobs. If a reservation is provided, it will be included in the job submission command.

coderabbitai · 2025-05-15T17:10:51Z

Walkthrough

Support for specifying a SLURM job reservation has been added to the submit command string generator. When a reservation is defined in the job's resources, a --reservation='...' argument is included in the sbatch command. No other logic or public interfaces were changed.

Changes

File(s)	Change Summary
snakemake_executor_plugin_slurm/submit_string.py	Added logic to append a `--reservation='...'` option to the sbatch command when specified in job resources.

Poem

In the warren of SLURM, a new path appears,
Reservations now honored, no need for cheers.
With a dash and a quote, the command grows strong,
Jobs find their place, where they truly belong.
🐇✨

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Reviewing files that changed from the base of the PR and between 8568780 and bbe459d.

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snakemake_executor_plugin_slurm/submit_string.py (1 hunks)

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🧠 Learnings (1)

📓 Common learnings

Learnt from: cmeesters
PR: snakemake/snakemake-executor-plugin-slurm#0
File: :0-0
Timestamp: 2025-01-13T09:54:22.950Z
Learning: PR #173 (adding gres resource specification) depends on PR #28 in snakemake-executor-plugin-slurm-jobstep repository, as changes were required in the cpu-settings function of the jobstep-Executor module.

🔇 Additional comments (1)

snakemake_executor_plugin_slurm/submit_string.py (1)

53-57: Nicely implemented SLURM reservation support!

The implementation correctly adds the --reservation flag to the SLURM submission command when a reservation is specified in the job resources. The use of single quotes around the reservation name is appropriate to handle potential spaces in reservation names.

The placement of this code block is logical - after nodes specification and before task count configuration, following the same pattern as other resource parameters.

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cmeesters · 2025-05-15T19:09:07Z

Thank you for your contribution!

Honestly? I thought about that flag, too. Then I learned about the magnetic flag for reservations and as I only use reservations during courses, adding something to the executor did not seem necessary any longer. Is there a need for this flag? I am a little bit concerned about adding too many resources, let alone adding flags to the executor. Here, though, this should not be a property of a rule/job, but rather a default resource or a flag passed to snakemake like --slurm-reservation=<name>.

cmeesters · 2025-05-15T19:15:00Z

snakemake_executor_plugin_slurm/submit_string.py

@@ -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


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.

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

Enables running snakemake job with slurm cluster reservation.

bbe459d

cmeesters changed the title ~~Enables running snakemake job within a slurm cluster reservation.~~ feat: Enables running snakemake job within a slurm cluster reservation. May 15, 2025

cmeesters self-requested a review May 15, 2025 19:13

cmeesters reviewed May 15, 2025

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