GROMACS: optimising a versatile molecular dynamics package
GROMACS is a versatile package to perform molecular dynamics.
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.
EPCC was involved in developing and optimising the GROMACS software through a HECToR dCSE project, the CRESTA project and the DiRAC BlueGene/Q facility. The HECToR dCSE project aimed to improve the parallel performance of GROMACS through the use of single-sided communications using the Cray SHMEM library. The CRESTA project profiled the use of OpenMP in GROMACS to understand performance characteristics and provide the information required optimise the code for potential exascale architectures. In partnership with DiRAC we worked to produce an optimised version of GROMACS for the BlueGene/Q architecture.