GROMACS

GROMACS is a free and open-source molecular dynamics package. Details can be found at the project page:

GROMACS webpage

General documentation can be found at:

GROMACS documentation

Installation

Retrieve and extract the GROMACS source code:

wget https://ftp.gromacs.org/gromacs/gromacs-2024.2.tar.gz
tar xf gromacs-2024.2.tar.gz

Set up a miniconda environment, editing path as required:

setup-miniconda-env /cluster/<group_name>/<your_directory>/gromacs-env
source /cluster/<group_name>/<your_directory>/gromacs-env/activate

Update and install prerequisites:

conda update -n base -c defaults conda
conda config --add channels conda-forge
# Compiler version 10.4.0 required as CUDA-11 does not support GCC > 10
conda install gcc=10.4.0 gxx=10.4.0 cmake

Open an interactive job on a GPU node and reactivate conda:

qrsh -adds l_hard hostname gpu*
source /cluster/<group_name>/<your_directory>/gromacs-env/activate

Set environment variables so CUDA is picked up by GROMACS at configuration time:

export PATH=/usr/local/cuda-11/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-11/lib64:$LD_LIBRARY_PATH

Create the directory where GROMACS is to be installed, editing path as required:

mkdir -p /cluster/<group_name>/<your_directory>/gromacs-install

Perform the build:

cd gromacs-2024.2
mkdir build
cd build

# Set -DCMAKE_INSTALL_PREFIX to the directory where GROMACS is to be installed.
# Adjust this line further to enable/disable features as required.
cmake .. -DGMX_GPU=CUDA -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/cluster/<group_name>/<your_directory>/gromacs-install
make
make install

GROMACS will now be installed in /cluster/<group_name>/<your_directory>/gromacs-install with the gmx binary located in the bin subdirectory.

Usage

Create a job script containing your desired command(s):

nano myjobscript.sh

with contents:

# Job Name
#$ -N GROMACS-Job

# Number of job slots/cores
#$ -pe smp 4
# Number of GPUs
#$ -l gpu=1

# Job class:
# * short (default) - max runtime of 12 hours
# * long - max runtime of 72 hours
# * 4weeks - max runtime of 4weeks
#$ -jc short

# Change to working directory before running script
# i.e. the directory this script is `qsub`-ed from
#$ -cwd

# Activate your Conda environment
source "/cluster/<group_name>/<your_directory>/gromacs-env/bin/activate"
# Add GROMACS install to your PATH
export PATH=/cluster/<group_name>/<your_directory>/gromacs-install/bin:$PATH

# Command(s)
gmx <parameters as required>

Submit the script using qsub:

qsub myjobscript.sh

Standard and error output for the job will be produced in .o and .e files.