Package versions

[LeoXue09]

Could anyone provide me a stable virtual env? Or just the versions of each packages?

I'm trying to install colabdesign locally, but facing multiple compatibility issues, with Jax or dm-haiku mostly.

Appreciate it!!!

[reece-maticebio]

ColabDesign Local Installation Setup

This setup worked for me on Ubuntu 22.04 with CUDA 12.4.1 and cuDNN 9.1.

Package Versions

• jax==0.4.29
• jaxlib==0.4.29+cuda12.cudnn91
• py3Dmol==2.4.2
• absl-py
• biopython==1.85
• chex==0.1.86
• dm-haiku==0.0.13
• dm-tree==0.1.8
• immutabledict==4.2.1
• ml-collections==1.0.0
• numpy==1.26.4
• pandas==2.2.3
• scipy==1.15.2
• optax==0.2.2
• joblib==1.4.2
• matplotlib==3.9.1
• ColabDesign==v1.1.3 (installed via GitHub with --no-deps)

Installation Commands

python -m pip install jax==0.4.29 jaxlib==0.4.29+cuda12.cudnn91 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

python -m pip install py3Dmol==2.4.2 absl-py biopython==1.85 chex==0.1.86 \
    dm-haiku==0.0.13 dm-tree==0.1.8 immutabledict==4.2.1 ml-collections==1.0.0 \
    numpy==1.26.4 pandas==2.2.3 scipy==1.15.2 optax==0.2.2 joblib==1.4.2 matplotlib==3.9.1

python -m pip install -q git+https://github.com/sokrypton/ColabDesign.git@v1.1.3 --no-deps