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Slurm job array starter

Skill ma-compbio-lab/SkillFoundry/skills/hpc/slurm-job-array-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill slurm-job-array-starter

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SKILL.md

1.1 KB, 273 tokens by cl100k_base, as published. Nobody here has run it

Slurm Job Array Starter

Use this skill to submit a tiny real Slurm job array, wait for terminal accounting, and summarize per-task outputs in compact JSON.

What it does

  • Renders and submits a minimal sbatch --array script on the live cluster.
  • Polls queue state with squeue and waits for terminal task accounting with sacct.
  • Reads each task's stdout and stderr logs and exports a per-task summary.

When to use it

  • You need a verified starter for the job arrays leaf.
  • You want a minimal example of per-task output capture and accounting on the current Slurm cluster.
  • You need deterministic JSON for tests before scaling to larger batched workloads.

Example

python3 skills/hpc/slurm-job-array-starter/scripts/run_slurm_job_array.py \
  --partition cpu \
  --array-spec 0-1 \
  --sleep 1 \
  --out scratch/slurm-array/summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/hpc/slurm-job-array-starter/tests -p 'test_*.py'
  • Expected summary: task_count == 2 and all task states are COMPLETED with ExitCode 0:0

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