Crewster

crewster CLI

HPC workflow automation tool for file sync and scheduler job management (Slurm/PJM).

CLI Reference

!`crewster --skill`

Getting Started

If crewster.toml does not exist in the project, run crewster init to create it, then ask the user to edit it with their cluster settings (host, workdir, scheduler, etc.) before proceeding.

Typical Workflow

1. crewster sync - Sync files to remote cluster (--dry-run to preview)
2. crewster exec "command" - Run setup on the login node (package installs, configure, etc.)
3. crewster submit "command" or crewster submit -s script.sh - Submit a job
4. crewster status <id> - Check job status (accepts run_id or job_id)
5. crewster job-output <id> - View stdout (-e for stderr)
6. crewster wait <id> - Wait for completion

Key Concepts

• Project root: crewster walks up from CWD to find crewster.toml (like git finds .git). All commands work from any subdirectory. --project-dir <path> overrides the derived project root (for configs kept outside the working tree); it requires an explicit config (--config or $CREWSTER_CONFIG), and metadata-reading commands (status, list, job-output, wait) must be re-invoked with the same --project-dir the run was submitted with.
• run_id vs job_id: crewster submit returns both. Either can be used with status, job-output, wait.
• Default working directory: crewster submit runs the job with its PWD set to the resolved [cluster].workdir from crewster.toml. Scripts passed via -s therefore do not need to cd to the project root — they start there. Adding a manual cd (or relying on $SLURM_SUBMIT_DIR, which may not be propagated to the job's environment) can move the job to the wrong directory.
• Multi-setup runs: Submit from subdirectories to set the job's remote working directory accordingly (e.g., cd runs/setup-a && crewster submit "python main.py" runs in /remote/project/runs/setup-a).
• Config resolution: --config / -c (given after the subcommand, e.g. crewster sync -c ~/my.toml) > $CREWSTER_CONFIG > walk-up discovery > ./crewster.toml. A legacy $HPC_CONFIG / hpc.toml is still read as a deprecated fallback (prints a warning; removed in v1.0).
• Sync scope: crewster sync always syncs the entire project root (the --project-dir override when given), regardless of CWD.

Writing scripts for crewster submit -s

• Start from the assumption that PWD is already [cluster].workdir. No cd needed for the common case.
• If you genuinely need a different working directory, prefer an explicit absolute path or a WORKDIR env-var override; do not rely on $SLURM_SUBMIT_DIR (the scheduler does not always propagate it into the job's shell env).
• The script's stdout/stderr land in the scheduler's job-output files, retrievable via crewster job-output <id>.
• #SBATCH / #PJM directives at the top of the script (column-zero, before the first executable line) are honored: crewster hoists them into the rendered job-script prologue. On conflict with the corresponding config entry ([slurm.options] for Slurm, the pjm.options array for PJM), the script's value wins.

Common pitfalls

• Adding cd "$HOME/path/to/project" to a submitted script: The job already starts in workdir; the manual cd is redundant and silently incorrect if the path doesn't exactly match the deployed one.
• Hardcoding deployment-specific paths in repo-tracked scripts: Use a WORKDIR env override or script-relative resolution; deployment paths belong in crewster.toml, not script source.