updated gpu profile to support process labels#1134
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JohannesKersting merged 2 commits intoJul 3, 2026
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Pull request overview
Updates the DaiSyBio nf-core profile to support GPU scheduling via process labels, so only GPU-capable steps are dispatched to the GPU queue while the rest remain on CPU resources.
Changes:
- Documented how to keep work directories and how to request GPU execution using the
process_gpulabel. - Updated the
gpuprofile to target the GPU queue only for processes labeledprocess_gpu.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| docs/daisybio.md | Adds guidance for keeping work directories and using process_gpu labels for GPU execution. |
| conf/daisybio.config | Changes GPU scheduling from “all processes on GPU queue” to label-based GPU queue routing. |
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| docker.runOptions = '-u $(id -u):$(id -g) --gpus all' | ||
| apptainer.runOptions = '--nv' | ||
| singularity.runOptions = '--nv' | ||
| process.queue = 'shared-gpu' | ||
| process.clusterOptions = '--qos=limitgpus --gpus=a40:1 --exclude compms-gpu-1.exbio.wzw.tum.de' | ||
| executor.queueSize = 5 | ||
| process{ | ||
| withLabel:process_gpu { |
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This is not actually a problem, as the respective flags are without effect if not GPU is present
nictru
approved these changes
Jul 3, 2026
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name: Update daisybio.config
about: Submit only processes labeled with ´process_gpu´ to the GPU slurm queue
Please follow these steps before submitting your PR:
[WIP]in its titlemasterbranchSteps for adding a new config profile:
conf/directorydocs/directorynfcore_custom.configfile in the top-level directoryprofile:scope in.github/workflows/main.yml.github/CODEOWNERS(**/<custom-profile>** @<github-username>)