Alphafold

AlphaFold is an artificial intelligence program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure.

Available modules

Alphafold2 is available as modules on Midway3 that you can check via module avail alphafold. The training data sets are accessible under /software/alphafold-data/ and /software/alphafold-data-2.2/.

Example job script

Typically, Alphafold2 uses OpenMM as backend which requires the CUDA toolkit to run on a GPU node. You can run the job on a CPU-only node without the relaxation run for the candidate protein (by adding -r false to the run_alphafold command).

#!/bin/bash
#SBATCH --job-name=alphafold2
#SBATCH --account=[your-accountname]
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --time=00:30:00
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=16
#SBATCH --gres=gpu:2
#SBATCH --constraint=v100
#SBATCH --mem=64G

module load alphafold/2.2.0 cuda/11.3

cd $SLURM_SUBMIT_DIR

echo "GPUs available: $CUDA_VISIBLE_DEVICES"
echo "CPU cores: $SLURM_CPUS_PER_TASK"

nvidia-smi

echo "Using `which run_alphafold`"

run_alphafold -o /project/rcc/trung/test/alphafold -f /path/to/your-fasta/T1083.fasta -t 2020-07-24 -g true -u true