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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Acknowledgments
Financial support was provided by the SeRC Exascale Simulation Software Initiative (SESSI) and the DEEP-SEA project. The DEEP-SEA project has received funding from the European Union’s Horizon 2020/EuroHPC research and innovation program under grant agreement No 955606. National VR contribution from Sweden matches the EuroHPC funding. The computations of this work were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at HPC2N, partially funded by the Swedish Research Council through grant agreement no. 2018-05973.
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Andersson, M.I., Murugan, N.A., Podobas, A., Markidis, S. (2023). Breaking Down the Parallel Performance of GROMACS, a High-Performance Molecular Dynamics Software. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds) Parallel Processing and Applied Mathematics. PPAM 2022. Lecture Notes in Computer Science, vol 13826. Springer, Cham. https://doi.org/10.1007/978-3-031-30442-2_25
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