Unknown Error in this Book (ColabFold v1.5.5: AlphaFold2 w/ MMseqs2 BATCH)

[Itsyaboiihartojo]

Dear ColabFold team,

I encountered this issue just 2 hours ago whilst trying to start another batch of prediction using this program.

It was working well just last night and was able to predict ~40 structures before the run ended due to maxed GPU RAM overtime.

Installation step worked fine when the error occured. The, once I click run prediction it gives that error.

When I then try to reinstall, the 2nd error appeared:

Any ideas on how to fix and work around this?

[ababaian]

Looks like there's a dependency issue with jaxlib I'm getting the same issue in the AlphaFold2 Advanced notebook.

[milot-mirdita]

Thanks for notifying us. Should work again. We are now using the new Colab runtimes feature to stick to a stable set of packages. We'll have to investigate the actual jax issue at a later point

[sokrypton]

The main and advanced notebook have been fixed. The other notebooks we'll test more, but in meantime, we changed default runtime.

What we changed to fix: pip install dm-haiku==0.0.14 https://github.com/steineggerlab/alphafold/commit/32f9669eff169cb946d898e0353bdc5b75c5eb31

[Itsyaboiihartojo]

Awesome! Thanks for the help.