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Running on Bodhi

pixi run run-bodhi --configfile config/my-project.yml

Profile: cluster/bodhi/config.yaml. CPU rules go to rna (account rbi), GPU rules (basecall, basecall_run, dnascent_detect) to gpu (account gpu_rbi, 3 nodes × 4 A30, 3-day limit). No QOS is needed.

  • Launch the controller from a login shell or an sinteractive session (it only submits and polls). slurm-status-command: squeue is set because a controller inside a compute-node session cannot always reach slurmdbd.
  • pixi run setup once, from one node, before the first submission. The downloads go to resources/tools and resources/models on /beevol.
  • output_directory anywhere under /beevol/home/$USER. Node-local /tmp is used for sort scratch (TMPDIR).
  • Before a long basecall: scontrol show reservation. Bodhi has a monthly all-node maintenance window; a job whose walltime crosses it is deferred until after it, silently.
  • DNAscent: the cluster image /cluster/singularity_images/DNAscent.sif (4.1.1) can be used directly via dnascent.sif, or pull the pinned 4.2.1 with pixi run install-dnascent. singularity is on PATH.
  • Modules also exist for dorado/2.0.0, modkit/0.5.1, minimap2/2.30, samtools/1.22.1; the pipeline does not use them (pixi pins its own), but they are handy for ad-hoc checks.