sokrypton / sokrypton/ColabFold

Jax error AF2 batch notebook.

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Jupyter Notebook
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Description

Expected Behavior

run batch predictions from google drive - used to work just fine.

Current Behavior

When running now getting this error:

AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
Seems like something is changed in the JAX version or so ?
Could reproduce error on 3 different google accounts.

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used
  • If you run it on a local system. Please add the server specifications
  • Operating system and version:

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the batch notebook and the colabfold_batch entry point mentioned in the report. Reproduce the error after a Colab Factory Reset, recording the complete output and environment details, then investigate the reported JAX/JAXlib mismatch. Done means batch predictions from Google Drive run successfully and the reproduction details are documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
bioinformatics, 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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