diffdock

DiffDock Example Mar. 9, 2023

Version 73ef67f

#!/usr/bin/env bash

## DiffDock example
## Args: none
##
## James Vincent  - help@sbgrid.org
## Mar 9, 2023

# ACKNOWLEDGE

# If your use of SBGrid compiled software was an important element in
# your publication, please include the following statement in your work:
# "Software used in the project was installed and configured by SBGrid
# (cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)



# Load cuda
module load cuda/11.5.2
gpu_out=gpu_load.out   # for monitoring gpu use

# Verify we have a working GPU
echo -e "hostname: $HOSTNAME \n\n"
echo -e "nvidia-smi output \n\n"
nvidia-smi

# Start nvidia-smi monitor of gpu
nvidia-smi --query-gpu=timestamp,name,utilization.gpu,utilization.memory,memory.total,memory.free,memory.used --format=csv -l 5 >& ${gpu_out} &


# Activate SBGrid env
source /programs/sbgrid.shrc

# Copy sample data
cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/data ./
cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/workdir ./
mkdir results

out_dir="./results/user_predictions_small"
input_csv="./data/protein_ligand_example_csv.csv"

# Run job
python.diffdock -m inference --protein_ligand_csv ${input_csv} --out_dir ${out_dir} \
	       --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise