!/usr/bin/env bash

SBGrid RosettaFold-All-Atom example

James Vincent - help@sbgrid.org

May 13, 2024

SLURM

SBATCH --mem=64G

SBATCH -t 0:30:00

SBATCH -p gpu_quad

SBATCH --gres=gpu:1

cd /temp_work/ch199734/114504_rosettafoldaa # BCH E3

cd /home/jjv16/tickets/114504_rosettafoldaa # O2

module load cuda/11.2

Start SBGrid environment

source /programs/sbgrid.shrc

Set version of RFAA

export ROSETTAFOLDAA_X=bf21483

Set critical env variables

export DGLBACKEND=pytorch

export ROSETTAFOLD_DB_PATH=/programs/local/biogrids/rosettafold/ # BCH E3

export ROSETTAFOLD_DB_PATH=/n/scratch/users/j//jjv16/rosettafold # O2 export MY_RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom

Call the correct python bundled with RFAA

python.rfaa --version

Run inference, override hydra parameters from YAML file

python.rfaa -m rf2aa.run_inference \ --config-name sbgrid_example -cd ./ \ checkpoint_path=${MY_RFAA_DIR}/RFAA_paper_weights.pt \ database_params.command=${MY_RFAA_DIR}/make_msa.sh \ database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03