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Usage

Obtaining model parameters

Prior to running AlphaFold 3, individual researchers must obtain the model parameters. To request access to the AlphaFold 3 model parameters, please complete this form.

Genetic Databases

AlphaFold3 also requires a writable directory of genetic database files. The files can be found in /data/reference/alphafold/3.0.0 but will need to be copied or linked to a user writable directory.

Running AlphaFold

The following commands are adapted from the AlphaFold documentation:

ml alphafold3
export AF_WORKDIR = /blue/mygroup/username/alphafold

apptainer exec \
  --nv \
  --bind /data/reference/alphafold/3.0.0:/root/databases \
  $HPC_ALPHAFOLD_IMG \
  python /app/alphafold/run_alphafold.py \
  --json_path=$AF_WORKDIR/af_input/fold_input.json \
  --model_dir=$AF_WORKDIR/models \
  --db_dir=/root/databases \
  --output_dir=$AF_WORKDIR/af_output

Note: flags to enable shared memory for multi-gpu on B200 nodes: --ipc=host or --bind /dev/shm