Agent-Skills.md

Agent Skills: SLURM Job Script Generator

Generate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when preparing submission scripts, deciding MPI vs MPI+OpenMP layouts, standardizing `#SBATCH` directives, or debugging job launch configuration (`sbatch`/`srun`).

UncategorizedID: HeshamFS/materials-simulation-skills/slurm-job-script-generator

Repository

HeshamFS/materials-simulation-skills
HeshamFSLicense: Apache-2.0
262

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pnpm dlx add-skill https://github.com/HeshamFS/materials-simulation-skills/tree/HEAD/skills/hpc-deployment/slurm-job-script-generator

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skills/hpc-deployment/slurm-job-script-generator/SKILL.md

Skill Metadata

Name
slurm-job-script-generator
Description
Generate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when preparing submission scripts, deciding MPI vs MPI+OpenMP layouts, standardizing `#SBATCH` directives, or debugging job launch configuration (`sbatch`/`srun`).

SLURM Job Script Generator

Goal

Generate a correct, copy-pasteable SLURM job script (.sbatch) for running a simulation, and surface common configuration mistakes (bad walltime format, conflicting memory flags, oversubscription hints).

Requirements

  • Python 3.8+
  • No external dependencies (Python standard library only)
  • Works on Linux, macOS, and Windows (script generation only)

Inputs to Gather

| Input | Description | Example | |-------|-------------|---------| | Job name | Short identifier for the job | phasefield-strong-scaling | | Walltime | SLURM time limit | 00:30:00 | | Partition | Cluster partition/queue (if required) | compute | | Account | Project/account (if required) | matsim | | Nodes | Number of nodes to allocate | 2 | | MPI tasks | Total tasks, or tasks per node | 128 or 64 per node | | Threads | CPUs per task (OpenMP threads) | 2 | | Memory | --mem or --mem-per-cpu (cluster policy dependent) | 32G | | GPUs | GPUs per node (optional) | 4 | | Working directory | Where the run should execute | $SLURM_SUBMIT_DIR | | Modules | Environment modules to load (optional) | gcc/12, openmpi/4.1 | | Run command | The command to launch under SLURM | ./simulate --config cfg.json |

Decision Guidance

MPI vs MPI+OpenMP layout

Does the code use OpenMP / threading?
├── NO  → Use MPI-only: cpus-per-task=1
└── YES → Use hybrid: set cpus-per-task = threads per MPI rank
          and export OMP_NUM_THREADS = cpus-per-task

Rule of thumb: if you see diminishing strong-scaling efficiency at high MPI ranks, try fewer ranks with more threads per rank (and measure).

Memory flag selection

  • Use either --mem (per node) or --mem-per-cpu (per CPU), not both.
  • Follow your cluster’s documentation; some sites enforce one style.
  • SLURM --mem units are integer MB by default, or an integer with suffix K/M/G/T (and --mem=0 commonly means “all memory on node”).

Script Outputs (JSON Fields)

| Script | Key Outputs | |--------|-------------| | scripts/slurm_script_generator.py | results.script, results.directives, results.derived, results.warnings |

Workflow

  1. Gather cluster constraints (partition/account, GPU policy, memory policy).
  2. Choose a process layout (MPI-only vs hybrid MPI+OpenMP).
  3. Generate the script with slurm_script_generator.py.
  4. Inspect warnings (conflicts, suspicious layouts).
  5. Save the generated script as job.sbatch.
  6. Submit with sbatch job.sbatch and monitor with squeue.

CLI Examples

# Preview a job script (prints to stdout)
python3 skills/hpc-deployment/slurm-job-script-generator/scripts/slurm_script_generator.py \
  --job-name phasefield \
  --time 00:10:00 \
  --partition compute \
  --nodes 1 \
  --ntasks-per-node 8 \
  --cpus-per-task 2 \
  --mem 16G \
  --module gcc/12 \
  --module openmpi/4.1 \
  -- \
  ./simulate --config config.json

# Write to a file and also emit structured JSON
python3 skills/hpc-deployment/slurm-job-script-generator/scripts/slurm_script_generator.py \
  --job-name phasefield \
  --time 00:10:00 \
  --nodes 1 \
  --ntasks 16 \
  --cpus-per-task 1 \
  --out job.sbatch \
  --json \
  -- \
  /bin/echo hello

Conversational Workflow Example

User: I need an sbatch script for my MPI simulation. I want 2 nodes, 64 ranks per node, 2 OpenMP threads per rank, and 2 hours.

Agent workflow:

  1. Confirm partition/account and whether GPUs are needed.
  2. Generate a hybrid job script: 
    python3 scripts/slurm_script_generator.py --job-name run --time 02:00:00 --nodes 2 --ntasks-per-node 64 --cpus-per-task 2 -- -- ./simulate
  3. Explain the mapping:
    • Total ranks = 128
    • Threads per rank = 2 (OMP_NUM_THREADS=2)
  4. If the user provides node core counts, sanity-check oversubscription using --cores-per-node.

Error Handling

| Error | Cause | Resolution | |-------|-------|------------| | time must be HH:MM:SS or D-HH:MM:SS | Bad walltime format | Use 00:30:00 or 1-00:00:00 | | nodes must be positive | Non-positive nodes | Provide --nodes >= 1 | | Provide either --mem or --mem-per-cpu, not both | Conflicting memory directives | Choose one memory style | | Provide a run command after -- | Missing launch command | Add -- ./simulate ... |

Limitations

  • Does not query cluster hardware or site policies; it can only validate internal consistency.
  • SLURM installations vary (GPU directives, QoS rules, partitions). Adjust directives for your site.

References

  • references/slurm_directives.md - Common #SBATCH directives and mapping tips

Version History

  • v1.0.0 (2026-02-25): Initial SLURM job script generator