Run on SLURM

The same Run console form submits to SLURM when you toggle Mode from Local to SLURM. The hub shells out to the existing phenotypic._cli._cli_slurm_submission pathway — the same code path used by phenotypic --pipeline pipeline.json --input input/ -o output/ --slurm partition=general --slurm time=240.

Switch to SLURM mode

Click the SLURM radio in the form. The SLURM config collapse opens with the typed common fields:

Field	Maps to	Notes
Partition	--slurm partition=…	Required. Use the partition your cluster admin assigned.
Time (HH:MM:SS)	--slurm time=…	SLURM walltime cap.
Memory	--slurm mem=…	Per-node memory (e.g. 16G, 64G).
CPUs / task	--slurm cpus_per_task=…	Maps to --cpus-per-task in sbatch.
GPUs	--slurm gpus=…	Set to 0 unless your pipeline needs a GPU detector.
Extra SLURM (one key=value per line)	repeated --slurm key=value	Free-form pass-through for anything not in the common fields (account, qos, mail-user, etc.). The example screenshot uses account=lab and qos=normal.

Submit

Clicking Run while SLURM mode is active does not spawn a local subprocess. Instead it hands the form values to a background thread that calls phenotypic … --slurm key=value … against your SLURM cluster. The hub waits for the submission to finish (typically <1 s for small arrays), then registers the returned array primary job id with the run registry. The Recent Runs panel surfaces the row as Mode: slurm-<job-id> with status pulled from the manifest as the array chunks finish.

Warning

This page captures the form filled out, not a successful submission. Submitting requires sbatch on PATH and a real SLURM cluster — neither exists on the workstation that captured these screenshots. To verify your form values translate to the right CLI invocation, switch back to Local mode and click Validate (dry-run): the dry-run prints the argv the hub would pass to phenotypic. Once you’re satisfied, switch back to SLURM and click Run.

What SLURM submission writes

A successful submission writes:

• <output_dir>/progress/job_metadata.json with the array primary job id and per-chunk job ids. The hub reads this file to surface the slurm-<id> row in Recent Runs — it does not parse Rich-formatted stdout (locale and terminal-width fragile).

• <output_dir>/deliverables/dashboard.html (written by the CLI submission flow), so the iframe panel can point at the dashboard before any chunk completes.

For deeper SLURM operational detail (chunk sizing, recompile-on-resume, per-chunk cgroups), see SLURM Pipelines.

Next: View Results.