scverse / scverse/rapids-singlecell
[BUG] running the Leiden algorithm doesn't support oversubscription
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- Dominant language
- Python
- Stars
- 394
- Forks
- 52
- Avg merge
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- Merged PRs (30d)
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Description
Describe the bug
While running the leiden algorithm rsc.tl.leiden(adata, key_added="leiden_res0_25", resolution=0.25 , I got a "CUDA error encountered 101 cudaErrorInvalidDevice invalid device ordinal"
Just setting rmm.reinitialize managed_memory to False resolved the issue
Expected behavior
Just information for other people running into the same error
Environment details (please complete the following information):
- Environment location: Conda running in WSL2
- Linux Distro/Architecture: Ubuntu 22.04.4 LTS
- GPU Model/Driver: [RTX 3070 and driver 31.0.15.5161]
- CUDA: 12.4
- Method of Rapids install: conda
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the rsc.tl.leiden call and the reported CUDA error in the WSL2, Conda, CUDA 12.4 environment. Check how rmm.reinitialize manages managed_memory and whether the workaround should be documented or the oversubscription behavior fixed. Done should be defined as either a reproducible fix or clear user-facing guidance for this configuration.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100