AutoDock-GPU¶

Description¶

AutoDock-GPU is developed by the Forli lab at Scripps Research. OpenCL and Cuda accelerated version of AutoDock4.2.6. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. The OpenCL version was developed in collaboration with TU-Darmstadt and is able to target CPU, GPU, and FPGA architectures. The Cuda version was developed in collaboration with Nvidia to run AutoDock-GPU on the Oak Ridge National Laboratory's (ORNL) Summit, and it included a batched ligand pipeline developed by Aaron Scheinberg from Jubilee Development.

Environment Modules¶

Run module spider autodock-gpu to find out what environment modules are available for this application.

Environment Variables¶

HPC_AUTODOCK_GPU_DIR - installation directory
HPC_AUTODOCK_GPU_BIN - executable directory

Additional Usage Information¶

See Job Script Examples.

Job Script Examples¶

Job script used for testing application installation¶

#!/bin/bash
#SBATCH --job-name=autodock-gpu_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=4gb
#SBATCH --partition=gpu
#SBATCH --gres=gpu:a100:1
#SBATCH --time=24:00:00
#SBATCH --output=autodock-gpu_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/autodock-gpu/1.5.3
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}
module load autodock-gpu/1.5.3

# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}

echo "Starting test run at $(date) on $(hostname)..."

###################################
autodock_gpu_64wi \
    --ffile ${TEST_DATADIR}/input/1stp/derived/1stp_protein.maps.fld \
    --lfile ${TEST_DATADIR}/input/1stp/derived/1stp_ligand.pdbqt \
    --resnam ${TEST_WORKDIR}/dock_gpu_test.dlg
    #--devnum $(echo ${SLURM_STEP_GPUS:-$SLURM_JOB_GPUS} | awk -F, '{print $1 + 1}')
###################################

# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR} -type f ! -empty -ls

echo "Test complete at $(date)."

Citation¶

If you publish research that uses AutoDock-GPU you have to cite it as follows:

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search, J. Chem. Theory Comput. 2021, 10.1021/acs.jctc.0c01006

Categories¶

chemistry