HPC & SLURM (consolidated)¶

The standalone HPC subsystem (target files, site registry, sbatch generation) is gone. SLURM execution is now handled by Dask: when lc run is invoked inside an existing SLURM allocation, the cluster manager launches one dask worker per allocated node via srun and Snakemake dispatches each rule across them.

For the user-facing flow, see Running on a Cluster.

For maintainer detail:

• api/dask_cluster — the three-branch decision (existing scheduler / SLURM allocation / local).
• api/dask_executor — the Snakemake executor plugin that turns each rule into a client.submit(...) call.
• api/container — podman-hpc build & migrate.