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SLURM and HPC

trasgu can run on SLURM clusters through Snakemake profiles.

See Snakemake profiles for example profile files and how to use them with a run directory.

Install SLURM support

The SLURM executor plugin is optional:

uv sync --frozen --extra slurm

Packaged SLURM profile

From a run directory:

trasgu_run --profile slurm

This resolves the SLURM profile packaged with trasgu.

Custom Snakemake profile

trasgu_run --profile /path/to/snakemake-profile

Extra Snakemake arguments can be appended:

trasgu_run --profile /path/to/snakemake-profile --printshellcmds

Before submitting

Run a dry run:

trasgu_run --profile slurm --dry-run

Check that:

  • trasgu.yaml points to accessible input data.
  • the chunk work directory (.trasgu_<run> by default, or output_dir if configured) is on storage visible to compute nodes.
  • trasgu_url is reachable from compute nodes, or points to a local Zarr copy.
  • The requested variable size exists in the Chimera Zarr store.