Alphafold3 filling up /tmp on compute nodes
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- Dominant language
- Python
- Stars
- 24
- Forks
- 15
- Avg merge
- 10d 3h
- Merged PRs (30d)
- 1
Description
What would you like to see added?
Alphafold3 writes temporary files to /tmp on compute nodes. For very large sequences, this can result in a no space left on device error, which causes Jackhmmer to fail.
Recommended Solution:
Create a directory in your scratch to serve as your TMPDIR, and bind the container's temporaray folder (mnt/tmp_alphafold) to this directory.
- Create the directory
mkdir -p /scratch/$USER/tmp_alphafold - Export the temporary directory path
export TMPDIR=/mnt/tmp_alphafold - Bind your scratch directory to the container's temp path:
--bind /scratch/$USER/tmp_alphafold:/mnt/tmp_alphafold
Contributor guide
No contributing guide indexed for this repository
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
Search the repository documentation for existing AlphaFold3 or Jackhmmer guidance and identify the page covering temporary files or compute-node execution. Add the TMPDIR setup and bind instructions from the issue, then verify that the documented commands clearly direct temporary files to scratch and prevent the reported disk-space failure.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation, hpc
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100