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!

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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

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