Alphafold3

[WilleBell]

• link to support ticket: VUB request, Other request (KUL?)
• website: https://github.com/google-deepmind/alphafold3
• installation docs:
• toolchain:
• easyblock to use:
• required dependencies:
  • absl-py
  • chex
  • dm-haiku==0.0.13
  • dm-tree
  • jax==0.4.34
  • jax[cuda12]==0.4.34
  • jax-triton==0.2.0
  • jaxtyping
  • numpy
  • rdkit==2024.3.5
  • triton==3.1.0
  • tqdm
  • zstandard
• optional dependencies:
  • CUDA: 12.6
• notes:
  • We might want to land this in 2024a ?
  • They provide a dockerfile (see below)
• effort: (TBD)
• other install methods
  • conda: no
  • container image: yes (https://github.com/google-deepmind/alphafold3/tree/v3.0.0/docker)
  • pre-built binaries (RHEL8 Linux x86_64): no
  • easyconfig outside EasyBuild: no

[lexming]

Updated the dependencies based on what is in its pyproject.toml. The file requirements.txt has a more exhaustive list with all the versions pinned to what they probably use internally for testing.

[boegel]

We'll probably get attacked from multiple angles again for this one, so perhaps it's worth setting up a "task force" and having a dedicated short meeting to discuss how to quickly get this supported into EasyBuild?

Other people outside of VSC (like @ThomasHoffmann77) may be interested in helping out here...

[ThomasHoffmann77]

@jpecar

[jpecar]

Yes, 2024a seems like a proper toolchain for this. However it will need some work, first major one will be SciPy-bundle. See https://github.com/easybuilders/easybuild-easyblocks/issues/3508 Jax and Triton are also potential pain points, others look doable at this stage.

[lexming]

I would focus first on Jax/Triton and try to use the already available SciPy-bundle-2024.05-gfbf-2024a.eb with numpy==1.26.4. Neither Jax or AlphaFold3 have a requirement on numpy>=2.0 in their pyproject.toml, so they might work with 1.26.4.

[jpecar]

What about requirements.txt and dev-requirements.txt ? Are these still relevant?

[lexming]

Those are used to populate the container and I guess it also reflects what is used internally for testing. So I agree that it would be nice if we can stick to those same versions, but IMO not mandatory if the code works with what we already have.

[WilleBell]

There's a WIP PR for AlphaFold3 in 2024a.