Breaking Down the Parallel Performance of GROMACS, a High-Performance Molecular Dynamics Software

GROMACS is one of the most widely used HPC software packages using Molecular Dynamics (MD) simulation technique. In this work, we quantify parallel performance different configurations, systems, and FFT libraries (FFTW, Intel MKL FFT, PACK). We break down cost each computational phase identify non-scalable stages, such as MPI communication during 3D computation when a large number processes. show that Particle-Mesh Ewald calculation significantly impact performance. Finally, discuss opportunities with particular interest in developing for calculations.