JUPITER Benchmark Suite: GROMACS

This benchmark is part of the JUPITER Benchmark Suite. See the repository of the suite for some general remarks.

This repository contains the GROMACS benchmark. DESCRIPTION.md contains details for compilation, execution, and evaluation.

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.

Quickstart

Compilation

The JUBE script automatically downloads GROMACS from the official website, and the input for the two possible runs from the PRACE Unified European Applications Benchmark Suite. It's just a matter of using the following commands:

module load JUBE
jube run jube_gromacs_build.xml

This should take about an hour.

Execution

In similar fashion, execute the two sub-benchmarks with the according JUBE scripts:

jube run jube_gromacs_STMV_bench.xml
jube run jube_gromacs_ionchannel_bench.xml

JUBE sample output

ionchannel_run (CPU)

Nodes	MPI tasks	Threads per Task	Performance [ns/d]	Wall t[s]	MFLOPs
64	256	6	354.035	15.253	136650833.463

STMV_run (GPU)

Nodes	MPI tasks	Threads per Task	GPUs per Node	Performance [ns/d]	Wall t[s]	MFLOPs	Version	Compiler
256	1024	6	4	72.172	23.945	43979566371.330	2023RC1	NVHPC