chore(workflow): gres GPU request, ignore runtime dirs, example config - #32
Merged
Conversation
Stop tracking Snakemake's .snakemake state (iocache/metadata) and the pixi env dir; they are per-machine runtime artefacts. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Use the slurm plugin's `gres: "gpu:1"` (emits --gres=gpu:1) instead of `gpu: 1` (emits --gpus), which left scicore jobs without a bound CUDA device. Clarify the comment. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Update the example: nuclei Cellpose model, label_name cellpose_labels, reuse_pyramid false (rebuild instead of copying the input's pyramid). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Three atomic commits:
.snakemake/.pixi— stop tracking Snakemake state + pixi env (per-machine runtime artefacts).gresGPU request —gres: "gpu:1"(→--gres=gpu:1) instead ofgpu: 1(→--gpus), which left scicore jobs without a bound CUDA device.label_name: cellpose_labels,reuse_pyramid: false.🤖 Generated with Claude Code