Breaking down the parallel performance of GROMACS, a high-performance molecular dynamics software

DOI10.1007/978-3-031-30442-2_25MaRDI QIDQ6135469zbMATH OpenOpenAlexFDO

Authors Måns I. Andersson, Natarajan Arul Murugan, Artur Podobas, S. Markidis

Publication date 25 August 2023

Published in Parallel Processing and Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2208.13658

zbMATH Keywords

fast Fourier transformmolecular dynamicsParticle-Mesh Ewald calculations

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Research exposition (monographs, survey articles) pertaining to numerical analysis (65-02) Numerical methods for discrete and fast Fourier transforms (65T50) Research exposition (monographs, survey articles) pertaining to fluid mechanics (76-02)

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

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