sokrypton / sokrypton/ColabFold
LLVM ERROR: pthread_create failed when using colabfold_batch
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Description
Hello,
When executing the following command:
colabfold_batch <directory_with_fasta_files> <result_dir>
I'm getting following error:
2023-02-23 20:14:06,281 Running on GPU
2023-02-23 20:14:10,601 Found 4 citations for tools or databases
2023-02-23 20:14:10,602 Query 1/2: input_short1 (length 36)
2023-02-23 20:14:10,923 Sleeping for 8s. Reason: PENDING
COMPLETE: 100%|█████████████████████| 150/150 [elapsed: 00:08 remaining: 00:00]
2023-02-23 20:14:19,544 Padding length to 38
Instructions for updating:
Lambda fuctions will be no more assumed to be used in the statement where they are used, or at least in the same block. https://github.com/tensorflow/tensorflow/issues/56089
LLVM ERROR: pthread_create failed: Resource temporarily unavailable
Aborted (core dumped)
This error always occurs when processing the second query, how can I solve this problem?
I hope a help!
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 by reproducing the colabfold_batch <directory_with_fasta_files> <result_dir> command and inspect why the second query reaches LLVM ERROR: pthread_create failed: Resource temporarily unavailable. Confirm completion of multiple queries without the process aborting; the issue names no source file or test to guide further investigation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, tensorflow
- Domain
- bioinformatics, cli, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100