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Numerical Performance for CUDA Capability 7.x GPUs

All CUDA Capability 7.x GPUs (e.g. V100) produce obviously bad output, with lots of clashing residues.

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Issue Description

When running AlphaFold 3 on CUDA Capability 7.x GPUs (such as the V100), the model produces poor quality predictions with:
  • Lots of clashing residues
  • Ranking scores of -99 or lower
  • Generally unusable output

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Workaround

Set the XLA_FLAGS environment variable to include the following flag: 
export XLA_FLAGS="--xla_disable_hlo_passes=custom-kernel-fusion-rewriter"
When running with Docker, pass this environment variable: 
docker run -it \
    --env XLA_FLAGS="--xla_disable_hlo_passes=custom-kernel-fusion-rewriter" \
    --volume $HOME/af_input:/root/af_input \
    --volume $HOME/af_output:/root/af_output \
    --volume <MODEL_PARAMETERS_DIR>:/root/models \
    --volume <DATABASES_DIR>:/root/public_databases \
    --gpus all \
    alphafold3 \
    python run_alphafold.py \
    --json_path=/root/af_input/fold_input.json \
    --model_dir=/root/models \
    --output_dir=/root/af_output

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Affected Hardware

  • NVIDIA V100 GPUs
  • All other CUDA Capability 7.x GPUs

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Incorrect Handling of Two-Letter Atoms in SMILES Ligands

This issue was fixed in commit 4e4023c.

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Issue Description

Between commits f8df1c7 and 4e4023c, AlphaFold 3 handled incorrectly any two-letter atoms in ligands defined using SMILES strings.

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Affected Atoms

Two-letter atoms such as:
  • Chlorine (Cl)
  • Bromine (Br)
  • Other two-letter atomic symbols

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Resolution

This issue has been resolved in the current version. If you are using an older version of AlphaFold 3, please update to the latest version or ensure you are using a commit after 4e4023c.

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Reporting New Issues

If you encounter an issue not listed here, please check the GitHub issues tracker first.
To report a new issue:
  1. Check if the issue already exists in the issues tracker
  2. If not found, create a new issue
  3. Provide detailed information about:
    • Your hardware configuration
    • AlphaFold 3 version
    • Input JSON structure
    • Error messages or unexpected behavior
    • Steps to reproduce
For additional support, contact the AlphaFold team at [email protected].

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