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.pht-pipe --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 starts a short local submitter that calls phenotypic … --slurm key=value … against your cluster. The run registry allocates a durable generation before submission. Recent Runs then follows generation-bound scheduler, controller, and finalizer evidence through queued, reconciling, running, terminal, and cancelling states. This works for ordinary arrays and staged GPU controller lifecycles without confusing an older attempt with a new one.

Warning

This page captures a fully selected pipeline, input, and output plus form-valid SLURM fields. The capture does not launch a dry-run generation or submit to a scheduler. 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, click Validate (dry-run): the dry-run validates the selected paths and prints the argv the hub would pass to phenotypic. Once you’re satisfied, click Run.

What SLURM submission writes

A successful submission writes lifecycle evidence under the output directory. The submit script uses sbatch --export=ALL. PhenoTypic also snapshots the caller’s PYTHONPATH internally as PHENOTYPIC_SLURM_PYTHONPATH; generated ordinary, staged, and recovery scripts restore that snapshot before starting Python on clusters that filter PYTHONPATH. Users set PYTHONPATH normally and do not set the internal variable themselves.

An explicit GUI cancellation remains authoritative until it settles, even if publication becomes visible. When there was no explicit cancellation, an ordinary run whose scheduler fence is inactive but whose successful publication is visible reconciles through the finalizer and is never autonomously reported as cancelled.

Key artifacts are:

• <output_dir>/.phenotypic/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, published by the normal or staged finalizer once the run is complete.

Operational restart guidance

Restarting the GUI does not cancel submitted work. On startup it rehydrates durable output records and reattaches only when it can prove the matching generation. If a restart occurs during submission, wait for scheduler metadata and use Refresh rather than launching the same output again. Keep .phenotypic/progress/ and staged-controller ledgers intact when redeploying the hub.

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

Next: View Results.