matsunagalab/hpc-run

HPC Run Skill

Read skills/common/preamble.md, skills/common/tool-output.md, and skills/common/node-cli-patterns.md before acting.

Use this skill when the user wants to run equilibration or production nodes on SLURM, submit multiple replicates or systems, monitor/recover jobs, configure cluster policy, or extend production runs.

Structure preparation remains a login-node or interactive step. HPC submission starts after a topo node exists and the next eq or prod node can resolve its inputs from the DAG.

Route To The Right Guidance

• Cluster discovery, resource policy, or packaged runtime setup: skills/hpc-run/discovery-policy.md
• One DAG node as one SLURM job: skills/hpc-run/submit-single.md
• Homogeneous batches or replicate arrays: skills/hpc-run/submit-array.md
• Monitoring, status sync, logs, and recovery: skills/hpc-run/monitor-recover.md
• Extending a completed production node: skills/hpc-run/prod-extension.md
• Multi-system study campaigns: skills/hpc-run/study-campaigns.md

Critical Rules

• Always pass both --job-dir and --node-id when submitting or running a DAG workflow node.
• Do not pass --system-xml-file, --topology-pdb-file, --state-xml-file, or --restart-from in normal DAG SLURM commands; resolver logic handles these.
• COMPLETED SLURM state alone does not mark a node complete. The MDClaw tool running inside the job owns the final complete_node call.
• Use arrays only for homogeneous, low-failure task sets. Use individual jobs with dependencies when failure isolation matters.
• GPU resources stay in sync with the OpenMM platform automatically. When a node's run command uses --platform CUDA (or --platform OpenCL) and you pass neither --gpus nor --gres, submit_job / submit_array_job auto-set --gpus 1 and emit a warning, so a CUDA run never lands on a CPU-only node. On a GPU cluster, default min/eq/prod to --platform CUDA so they request a GPU. Pass --gpus N for multi-GPU, or --gres gpu:<type>:N on clusters that require GRES form (--gres also suppresses the autodetection). --platform auto does NOT trigger a GPU request on HPC: without an allocated GPU it falls back to CPU, so make GPU intent explicit with --platform CUDA.