AlphaFold3¶

Please refer to the official AlphaFold3 GitHub documentation for more in-depth information.

This page documents how to use AF3 on the UTHPC cluster.

When encountering any issues or have ideas for improvements, please let us know at support@hpc.ut.ee

Databases and model parameters¶

Databases¶

The databases have been installed centrally at /gpfs/space/databases/alphafold3 that you can use.

Model parameters¶

Due to the licensing of model parameters, we are not able to provide them centrally for all users. Every user or user group needs to request their own parameters from Google for which you need to fill out a form described in the github documentation

Singularity usage¶

AF3 on UTHPC is provided as a Singularity image located at /gpfs/space/software/cluster_software/containers/alphafold3/alphafold3-3.0.1.sif. To use it you need to load the singularity module with module load singularity.

Singularity binds¶

Singularity containers usually are not aware of most of the filesystem underneath. This means that you need to "bind" the relevant directories for them to be available. This is accomplished with the --bind flag and will be demonstrated in the example job script below.

Running AF3¶

The following is an example Slurm job script for AF3

#!/bin/bash

#SBATCH -J jobname
#SBATCH -p gpu
#SBATCH -t 1:00:00
#SBATCH --cpus-per-task=8
#SBATCH --mem=64G
#SBATCH --gres=gpu:a100-80g:2

export MODEL_PARAMETERS_DIR=/path/to/params
export DB_DIR=/gpfs/space/databases/alphafold3
export AF_INPUT=/path/to/input
export AF_OUTPUT=/path/to/output

module load singularity
singularity exec \
     --nv \
     --bind $AF_INPUT:/root/af_input \
     --bind $AF_OUTPUT:/root/af_output \
     --bind $MODEL_PARAMETERS_DIR:/root/models \
     --bind $DB_DIR:/root/public_databases \
     /gpfs/space/software/cluster_software/containers/alphafold3/alphafold3-3.0.1.sif \
     python /app/alphafold/run_alphafold.py \
     --json_path=/root/af_input/fold_input.json \
     --model_dir=/root/models \
     --db_dir=/root/public_databases \
     --db_dir=/root/public_databases_fallback \
     --output_dir=/root/af_output

This script has the most important directories set as variables and you should customize those as needed. The Singularity binds have been done afterwards and the app should run.