SLURM Pipelines#

Run PhenoTypic batch processing on SLURM-managed clusters.

Automatic SLURM Detection#

When SLURM is available, the CLI automatically submits jobs to the scheduler. To force local execution instead:

python -m phenotypic pipeline.json /plates/ /output/ --force-local

SLURM Arguments#

Pass SLURM parameters with --slurm-args:

python -m phenotypic pipeline.json /plates/ /output/ \
    --slurm-args time=04:00:00 \
    --slurm-args partition=gpu \
    --slurm-args mem=16G

Wait for Completion#

By default, the CLI returns immediately after submitting SLURM jobs. To wait:

python -m phenotypic pipeline.json /plates/ /output/ --wait

Resume on SLURM#

Resume works the same way as local execution:

python -m phenotypic pipeline.json /plates/ /output/ --resume