GROMACS
GROMACS is a free and open-source software suite for high-performance molecular dynamics and output analysis.
Keywords: biology, physics, chemistry, molecular dynamics
Available modules
There are several GROMACS modules on Midway2 and Midway3 that you can check via module avail gromacs:
---------------------------- /software/modulefiles2 ----------------------------
gromacs/5.0.7-cuda+intelmpi-5.1+intel-16.0
gromacs/5.1.4-cuda-7.5+intelmpi-5.1+intel-16.0
gromacs/2019.2+intelmpi-2018.2.199+intel-18.0
gromacs/2019.3+intelmpi-2018.2.199+intel-18.0
gromacs/2021.1+intelmpi-2019.up7+intel-19.1.1
---------------------------- /software/modulefiles -----------------------------
gromacs/2020.4(default) gromacs/2021.5 gromacs/2022.4 gromacs/2022.4-colvars
You can then show the dependency of individual modules, for example,
module show gromacs/2021.5
-------------------------------------------------------------------
/software/modulefiles/gromacs/2021.5:
module-whatis {setup gromacs 2021.5 compiled with the system compiler}
conflict gromacs
module load gcc/7.4.0 openmpi/4.1.2+gcc-7.4.0 cuda/11.2 plumed/2.7.3
prepend-path PATH /software/gromacs-2021.5-el8-x86_64/bin
prepend-path LD_LIBRARY_PATH /software/gromacs-2021.5-el8-x86_64/lib64
prepend-path LIBRARY_PATH /software/gromacs-2021.5-el8-x86_64/lib64
prepend-path PKG_CONFIG_PATH /software/gromacs-2021.5-el8-x86_64/lib64/pkgconfig
prepend-path CPATH /software/gromacs-2021.5-el8-x86_64/include
prepend-path MANPATH /software/gromacs-2021.5-el8-x86_64/share/man
In this case you can see this module was compiled with openmpi/4.1.2+gcc-7.4.0, cuda/11.2 and plumed/2.7.3. As a result, this version supports GPU acceleration and should be used on GPU nodes.
Note
GROMACS is under active development. You are encouraged to build the latest stable version from source code in your own space using the provided compilers.
The GROMACS documentation contain useful information for improving performance of your specific calculations:
https://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html
Example job script
An example batch script to run GROMACS for Midway3 is given as below
!/bin/bash
#SBATCH --job-name=gmx-bench
#SBATCH --account=pi-[cnetid]
#SBATCH --time=01:00:00
#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
#SBATCH --constraint=v100
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
module load gromacs/2021.5
cd $SLURM_SUBMIT_DIR
export GMX_PATH=/software/gromacs-2021.5-el8-x86_64/bin
source $GMX_PATH/GMXRC
ntasks_per_node=$SLURM_NTASKS_PER_NODE
numnodes=$SLURM_JOB_NUM_NODES
n=$(( ntasks_per_node * numnodes ))
t=1000
mpirun -np $n gmx_mpi mdrun -ntomp 1 -pin on -nb gpu -nsteps $t \
-v -s init.tpr
init.tpr is an existing portable binary run input file.