Running on a SLURM cluster
bin/sbatch_omero_screen.py writes a SLURM job script that runs omero-screen and submits it with sbatch. It is set up for the Sussex HPC (job classes, GPU nodes); other clusters will need its template adjusted.
Note
This is a bin/ utility and still uses argparse, unlike the installed commands. It keeps argparse conventions, including abbreviated options.
python bin/sbatch_omero_screen.py 12345 67890 --env production --stitch --trackBy default it submits one job per plate ID.
Job options
| Option | Default | Effect |
|---|---|---|
--class CLASS |
gpu |
SLURM job class |
-u, --username USER |
current user | Cluster username |
-t, --threads N |
1 | CPU threads; raise it when running without a GPU |
--hours N |
24 | Wall-clock limit in hours |
-m, --memory N |
32 | Memory in GB |
--gpu / --no-gpu |
on | Request a GPU node |
--exec / --no-exec |
on | Execute the generated script statements |
--submit / --no-submit |
on | Submit with sbatch |
--multi-submit / --no-multi-submit |
on | One job per plate ID |
The memory you request becomes the job’s cgroup limit, which the pipeline reads to decide whether to stream the stitch.
Pipeline options
These are forwarded to omero-screen in every job. They mean the same as in the CLI reference.
| Option | Forwarded as |
|---|---|
--env ENV |
--env |
--config PATH |
--config, resolved to an absolute path and checked at submission |
--inference MODEL [MODEL ...] |
--inference |
--segmentation |
--segmentation |
--delete |
--delete |
--cp4, --model MODEL |
--cp4, --model |
--stitch, --stitch-config PATH |
--stitch, --stitch-config |
--stream-stitch / --no-stream-stitch |
the same |
--track [MODEL], --track-mode, --track-device, --track-window, --track-batch-size |
the same |