GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since 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, e.g. polymers.
Useful Links
Using GROMACS on ARCHER2
GROMACS is Open Source software and is freely available to all users. Three versions are available:
- Parallel MPI/OpenMP, single precision:
gmx_mpi
- Parallel MPI/OpenMP, double precision:
gmx_mpi_d
- Serial, single precision:
gmx
Important
The gromacs
modules reset the CPU frequency to the highest possible value
(2.25 GHz) as this generally achieves the best balance of performance to
energy use. You can change this setting by following the instructions in the
Energy use section of the User Guide.
Running parallel GROMACS jobs
Running MPI only jobs
The following script will run a GROMACS MD job using 4 nodes (128x4 cores) with pure MPI.
#!/bin/bash
#SBATCH --job-name=mdrun_test
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --time=00:20:00
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
#SBATCH --partition=standard
#SBATCH --qos=standard
# Setup the environment
module load gromacs
export OMP_NUM_THREADS=1
srun --distribution=block:block --hint=nomultithread gmx_mpi mdrun -s test_calc.tpr
Running hybrid MPI/OpenMP jobs
The following script will run a GROMACS MD job using 4 nodes (128x4 cores) with 6 MPI processes per node (24 MPI processes in total) and 6 OpenMP threads per MPI process.
#!/bin/bash
#SBATCH --job-name=mdrun_test
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=16
#SBATCH --cpus-per-task=8
#SBATCH --time=00:20:00
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
#SBATCH --partition=standard
#SBATCH --qos=standard
# Setup the environment
module load gromacs
export OMP_NUM_THREADS=8
srun --distribution=block:block --hint=nomultithread gmx_mpi mdrun -s test_calc.tpr
Compiling Gromacs
The latest instructions for building GROMACS on ARCHER2 may be found in the GitHub repository of build instructions: