.. _gromacs:

GROMACS
=======

.. sidebar:: GROMACS

  :URL: http://www.gromacs.org/
  :URL: https://www.nvidia.com/en-us/data-center/gpu-accelerated-applications/gromacs/


GROMACS is a versatile package for molecular dynamics simulations, which solves
the Newtonian equations of motion for systems with hundreds to millions of
particles. Although the software scales well to hundreds of cores for typical
simulations, GROMACS calculations are restricted to at most a single node on
the JADE service.

Job scripts
-----------

GROMACS jobs can run using 1, 4 (half a node), or 8 (full node) GPUs (please see note below regarding job performance). The following SLURM script example is written for one of the regression tests from the installation:


.. code-block:: bash

   #!/bin/bash

   #SBATCH --nodes=1
   #SBATCH --ntasks-per-node=1
   #SBATCH --cpus-per-task=5
   #SBATCH --gres=gpu:1
   #SBATCH --gres-flags=enforce-binding
   #SBATCH --time=10:00:00
   #SBATCH -J testGromacs
   #SBATCH -p small

   module purge
   module use /apps/system/modules
   module use /apps/system/easybuild/modules/all

   module load GROMACS/2024.3-foss-2024a-mpi

   mpirun -np ${SLURM_NTASKS_PER_NODE} --bind-to socket \
          mdrun_mpi -s topol.tpr \
	  -ntomp ${SLURM_CPUS_PER_TASK} &> run-gromacs.out


The example utilises 1 GPU (``--gres=gpu:1``) on a JADE node. GROMACS is started with a number of MPI processes (``--ntasks-per-node=1``) , which must match the number of requested GPUs. Each MPI process will run 5 OMP threads (``--cpus-per-task=5``). The number of requested MPI processes is saved in the environment variable ``SLURM_NTASKS_PER_NODE``, while the number of threads per process is saved in ``SLURM_CPUS_PER_TASK``.

The request ``--bind-to socket`` is specific to OpenMPI, which was used to build GROMACS on JADE. This extra option to the OpenMPI ``mpirun`` is essential in obtaining the optimal run configuration and computational performance.