Introduction

This is a convinience Alphafold3 batch execution pipeline using Nextflow. optimized for the Unity HPC cluster. The main optimizations are listed below;

• Splits MSA (CPU-heavy) and structure prediction (GPU-heavy) steps and submits jobs accordingly

• GPU jobs will be batched for efficiency. 20 predictions will be run on each GPU.

• Parallel execution and checkpointing

• Smart resource usage. Failed jobs will be automatically submitted again with higher resources including better GPUs when neccessary.

• The pipeline will use GPUs with GPU compute capability > 8 to prevent problems.

Usage

Mandatory arguments

• --json_dir: Path to the directory that contains the input JSON files for Alphafold3. Make sure that the JSON files have the correct structure as described here.

• --output_dir: Path to the output directory for the results.

• --model_dir: Path to the directory that contains the model paramaters for Alphafold3. Check here to learn how to obtain the model paramaters.

Optional arguments

• #SBATCH paramaters can be adjusted as desired. The main one to adjust is the --time paramater. Increase or decrease as desired. Rest of the paramaters do not need adjusting.

Example slurm script

Example script provided below. Assuming the name of the script is main.sh, it can be submitted with sbatch main.sh on the Unity cluster.

main.sh

#!/usr/bin/bash
#SBATCH --job-name=af3_batch                # Job name
#SBATCH --partition=workflow,cpu            # Partition (queue) name
#SBATCH -c 2                                # Number of CPUs
#SBATCH --nodes=1                           # Number of nodes
#SBATCH --mem=10gb                          # Job memory request
#SBATCH --time=1-00:00:00                   # Time limit days-hrs:min:sec
#SBATCH --output=logs/af3_batch_%j.log

module load nextflow/24.10.3

export NXF_OPTS="-Xms1G -Xmx8G"

nextflow run UnityHPC/alphafold3-batch -r v0.2.0 \
    --json_dir /path/to/json_dir \
    --output_dir /path/to/results \
    --model_dir /path/to/model/dir \
    -profile unity \
    -resume