af-mmr-singularity_large.sb

#!/bin/bash
#SBATCH --job-name af232-mmer
#SBATCH --time=48:00:00
#SBATCH --gres=gpu:4
#SBATCH -C [nvf|nal|nif]
#SBATCH --cpus-per-task=20
#SBATCH --mem=100G
#SBATCH -o af232-mmer-%x.%j.log
#SBATCH --error=af232-mmer-%x.%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=aimerdiaz.evo@gmail.com

module load GCC/6.4.0-2.28  OpenMPI/2.1.2 Python/3.6.4
module load alphafold/2.3.2
## SBATCH -C [nvf|nal|nif|nvl]
echo $HOSTNAME
echo "Export AlphaFold variables"
# These variables are now set by the module
echo INFO: ALPHAFOLD_DIR=$ALPHAFOLD_DIR
echo INFO: ALPHAFOLD_DATADIR=$ALPHAFOLD_DATADIR

export output_dir=$SLURM_SUBMIT_DIR/$2 # you chnage this to whatever path you like

cd $SLURM_SUBMIT_DIR
mkdir -p $output_dir
timestamp=$(date)
echo "Starting AlphaFold at $timestamp"

python3 ${ALPHAFOLD_DIR}/run_singularity.py \
    --use_gpu \
    --output_dir=$output_dir \
    --data_dir=${ALPHAFOLD_DATADIR} \
    --fasta_paths=$1 \
    --max_template_date=2023-08-01 \
    --model_preset=multimer \
    --db_preset=reduced_dbs

#    --model_preset=monomer \
#    --db_preset=reduced_dbs
echo INFO: AlphaFold returned $?

timestamp=$(date)
echo "Finishing AlphaFold at $timestamp"

#https://docs.icer.msu.edu/2023-11-10_LabNotebook_AlphaFold2.3.2/