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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.

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

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 --tasks-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
#!/bin/bash

#SBATCH --job-name=mdrun_test
#SBATCH --nodes=4
#SBATCH --tasks-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 epcc-job-env
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 --tasks-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
#!/bin/bash
#SBATCH --job-name=mdrun_test
#SBATCH --nodes=4
#SBATCH --tasks-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 epcc-job-env
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: