GROMACS is a versatile package for performing molecular dynamics, for example, simulating the Newtonian equations of motion for systems with hundreds to millions of particles.

GROMACS is primarily designed for biochemical molecules like proteins, lipids, and nucleic acids that have a lot of complicated bonded interactions. Because GROMACS is extremely fast at calculating the nonbonded interactions that usually dominate simulations, many groups are also using it for research on non-biological systems, for example, polymers.

GROMACS modules on Setonix

Gromacs is compiled with the GNU programming environment.

There are several GROMACS versions and configurations installed on Setonix as modules. 

---------------------------- /software/setonix/2023.08/modules/zen3/gcc/12.2.0/applications --------------------------
   gromacs-amd-gfx90a/2023    gromacs/2022.5    gromacs/2023 (D)

Modules with the -amd-gfx90a suffix support GPU offloading and are meant to be used within the gpu partition.

Example: Running GROMACS on CPU

This is an example of a GROMACS job queueing script.

#!/bin/bash --login
#SBATCH --nodes=1
#SBATCH --ntasks=128
#SBATCH --exclusive
#SBATCH --time=00:05:00
#SBATCH --account=[your-project]


module load gromacs/2023
export OMP_NUM_THREADS=1
srun -N 1 -n 128 gmx_mpi_d mdrun -s ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile

Running GROMACS on GPUs

GROMACS supports GPU offloading of some of the operations to GPU. Acceleration is officially supported using the SYCL standard. Additionally, AMD staff maintains its own GROMACS GPU implementation using HIP. However, while significantly more performant, AMD implementation is not officially endorsed by the GROMACS developers. The version currently installed on Setonix, gromacs-amd-gfx90a/2023, is the AMD port. We will eventually switch to the SYCL implementation, or provide both.

GPU offloading can be enabled with the following options:

• -npme 1 -pme gpu: compute long-range interactions on GPU, using a single task. 
• -nb gpu: compute non bonded interactions on GPUs.
• -bonded gpu: compute bonded interactions on GPUs.
• -update gpu: compute constraints and update on GPUs. This option is not always available, GROMACS will print an error message when the operation cannot be performed on GPU.

More information can be found in Running mdrun with GPUs (external site).

As an example, we used the benchMEM.tpr benchmark case that can be found at the following page: A free GROMACS benchmark set (external site). Here is a very simple submission script.

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=02:00:00
#SBATCH --partition=gpu
#SBATCH --account=[your-project]-gpu



module load gromacs-amd-gfx90a/2023

srun gmx_mpi mdrun -nb gpu -bonded gpu -ntomp 8 -s benchMEM.tpr

External links

• Getting good performance from mdrun (external site)

• Running mdrun with GPUs (external site)
• A free GROMACS benchmark set (external site)