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. (Summary from the program web page.)

The official web page: http://www.gromacs.org/

Notes:

The package supports sequential, parallel execution and execution using GPUs (see manual for details). The mdrun program was updated so it should automatically select the number of CPUs and GPUs according to psubmit command. However, an optimal choice of the parallelization setup strongly depends both on the properties of the simulated system and on hardware configuration. You are thus strongly advised to try changing e.g. the -ntomp parameter of mdrun to get better performance. This is especially important when using GPUs, where an optimal choice of -ntomp is often several times faster than the default setting.

Consult the official guide for more details: Acceleration and parallelization

Example script

#!/usr/bin/env infinity-env

module add gromacs

# automatic configuration
mdrun -s md1.tpr
## OR
## automatic configuration with custom options
# mdrun -ntomp 4 -s md1.tpr
## OR
## fully manual control (for :para builds)
# mpirun -np 2 mdrun_mpi -ntomp 4 -s md1.tpr

Job submission as a single CPU job

$ psubmit normal test_me             # gromacs mdrun execution on 1 CPU

Job submission as a parallel job

$ psubmit normal test_me ncpus=8           # gromacs mdrun execution on 8 CPUs

Job submission as a parallel job using GPUs

$ psubmit normal test_me ncpus=8 ngpus=1   # gromacs mdrun execution on 8 CPUs and 1 GPUs