Specific jaxlib version?
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
Research direction
Start with the colabfold_batch entry point and reproduce the reported command after the listed pip and conda installation steps. Compare the installed JAX 0.3.13, jaxlib 0.3.10, CUDA 11.1.1, and cuDNN 8.4.1.50 versions with the command-line behavior; done means the documented local installation produces a functioning GPU workflow without the unrecognized-argument error.
Written by the indexing model from the issue text.
Description
Expected Behavior
Fully functioning colab_batch with GPU.
Current Behavior
colabfold_batch: error: unrecognized arguments: --use-gpu-relax
Steps to Reproduce (for bugs)
Install as described for local installation:
./pip install --upgrade pip
./pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
./pip install "jax[cuda111]>=0.3.8,<0.4" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
./conda install -y cudatoolkit=11.1.1 cudnn=8.4.1.50
./conda install -y -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0
./conda install -y -c conda-forge openmm=7.5.1 pdbfixer
ColabFold Output (for bugs)
usage: colabfold_batch [-h] [--stop-at-score STOP_AT_SCORE]
[--num-recycle NUM_RECYCLE] [--num-models {1,2,3,4,5}]
[--recompile-padding RECOMPILE_PADDING]
[--model-order MODEL_ORDER] [--host-url HOST_URL]
[--data DATA]
[--msa-mode {MMseqs2 UniRef+Environmental),MMseqs2 (UniRef only,single_sequence}]
[--model-type {auto,AlphaFold2-ptm,AlphaFold2-multimer}]
[--amber] [--templates] [--env] [--cpu]
[--rank {auto,plddt,ptmscore,multimer}]
[--pair-mode {unpaired,paired,unpaired+paired}]
[--recompile-all-models]
[--sort-queries-by {none,length,random}]
[--save-single-representations]
[--save-pair-representations] [--zip]
[--overwrite-existing-results]
input results
colabfold_batch: error: unrecognized arguments: --use-gpu-relax
Context
Resulting installation contains:
cudatoolkit 11.1.1 ha002fc5_10 conda-forge
cudnn 8.4.1.50 hed8a83a_0 conda-forge
jax 0.3.13
jaxlib 0.3.10
Your Environment
Local install
CentOS Linux release 7.9.2009 (Core)
NVIDIA-SMI 460.39 Driver Version: 460.39 CUDA Version: 11.2
GeForce GTX 108
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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