Scaling of GROMACS Molecular Dynamics Code on HPC Cluster

This technical report presents the benchmarking results of the GROMACS 2024 molecular dynamics code on a high-performance computing (HPC) cluster utilizing AMD CPUs, specifically focusing on scaling up to 65,536 CPU cores. The study evaluates five distinct molecular dynamics systems, with atom counts ranging from approximately 82,000 to 204 million. Performance metrics were assessed using two Message Passing Interface (MPI) libraries, Intel-MPI and Open-MPI. The findings indicate that the largest system achieved near-perfect strong scaling up to 512 nodes, maintaining a parallel efficiency above 0.9. The report details the energy efficiency and peak performances for each system, demonstrating the capability of optimized software on advanced HPC hardware to simulate complex biomolecular systems. Additionally, the document outlines the methodologies employed for benchmarking, including the configuration of the AMD-based supercomputer and the specific parameters used during the simulations. The results serve as reference performance numbers for future large-scale molecular dynamics simulations.