⚠ INFORMATION
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Alphafold 2 on Jean Zay

Useful links

• 🌐 Official website: https://github.com/deepmind/alphafold
• 📘 Documentation: https://github.com/deepmind/alphafold
• 🧬 Git repository: https://github.com/deepmind/alphafold

Usage tips

Sequence alignments

Sequence alignment tools are not ported to GPU. As this phase can be quite long, it is recommended not to use a GPU partition to avoid wasting resources. You can request an allocation on the CPU partition or use the prepost partition.

Management of temporary files

The Alphafold procedure writes temporary files in the /tmp directory of the compute node. This directory is very small and this can create errors of the type No space left on device. You need to add the following line to the submission script:

export TMPDIR=$JOBSCRATCH

Submission file examples

V100 Partition

#!/usr/bin/env bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=1 # Number of MPI tasks per node
#SBATCH --cpus-per-task=10 # Number of core for each MPI task
#SBATCH --gpus-per-node=1 # Number of GPU per node
#SBATCH --hint=nomultithread
#SBATCH --job-name=alphafold
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@v100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load alphafold/2.3.2

export TMPDIR=$JOBSCRATCH
export ALPHAFOLDDB=$DSDIR/Alphafold-2024-04

python $(which run_alphafold.py) \
  --fasta_paths=<list_of fasta files> \
  --nobenchmark \
  --data_dir=$ALPHAFOLDDB \
  --uniref90_database_path=${ALPHAFOLDDB}/uniref90/uniref90.fasta \
  --mgnify_database_path=${ALPHAFOLDDB}/mgnify/mgy_clusters_2022_05.fa \
  --template_mmcif_dir=${ALPHAFOLDDB}/pdb_mmcif/mmcif_files \
  --obsolete_pdbs_path=${ALPHAFOLDDB}/pdb_mmcif/obsolete.dat \
  --pdb_seqres_database_path=${ALPHAFOLDDB}/pdb_seqres/pdb_seqres.txt \
  --bfd_database_path=${ALPHAFOLDDB}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
  --uniref30_database_path=${ALPHAFOLDDB}/uniref30/UniRef30_2021_03 \
  --uniprot_database_path=${ALPHAFOLDDB}/uniprot/uniprot.fasta \
  --db_preset=full_dbs \
  --output_dir=./outputs \
  --max_template_date=2023-12-12 \
  --model_preset=multimer \
  --num_multimer_predictions_per_model=1 \
  --models_to_relax=best \
  --random_seed=424242 \
  --use_gpu_relax

A100 Partition

#!/usr/bin/env bash
#SBATCH --nodes=1 # Number of nodes
#SBATCH --ntasks-per-node=1 # Number of MPI tasks per node
#SBATCH --cpus-per-task=8 # Number of core for each MPI task
#SBATCH --gpus-per-node=1 # Number of GPU per node
#SBATCH --hint=nomultithread # Disable hyperthreading
#SBATCH --constraint=a100 # Aim A100 partition
#SBATCH --job-name=alphafold
#SBATCH --output=%x.%j # output in <job-name>.<jobid>
#SBATCH --error=%x.%j # errors <job-name>.<jobid>
#SBATCH --account=<project_id>@a100 # project_id available with idracct
#SBATCH --time=02:00:00

module purge
module load arch/a100
module load alphafold/2.3.2

export TMPDIR=$JOBSCRATCH
export ALPHAFOLDDB=$DSDIR/Alphafold-2024-04

python $(which run_alphafold.py) \
  --fasta_paths=<list_of fasta files> \
  --nobenchmark \
  --data_dir=$ALPHAFOLDDB \
  --uniref90_database_path=${ALPHAFOLDDB}/uniref90/uniref90.fasta \
  --mgnify_database_path=${ALPHAFOLDDB}/mgnify/mgy_clusters_2022_05.fa \
  --template_mmcif_dir=${ALPHAFOLDDB}/pdb_mmcif/mmcif_files \
  --obsolete_pdbs_path=${ALPHAFOLDDB}/pdb_mmcif/obsolete.dat \
  --pdb_seqres_database_path=${ALPHAFOLDDB}/pdb_seqres/pdb_seqres.txt \
  --bfd_database_path=${ALPHAFOLDDB}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
  --uniref30_database_path=${ALPHAFOLDDB}/uniref30/UniRef30_2021_03 \
  --uniprot_database_path=${ALPHAFOLDDB}/uniprot/uniprot.fasta \
  --db_preset=full_dbs \
  --output_dir=./outputs \
  --max_template_date=2023-12-12 \
  --model_preset=multimer \
  --num_multimer_predictions_per_model=1 \
  --models_to_relax=best \
  --random_seed=424242 \
  --use_gpu_relax