MD-Bench: A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms

Rafael Ravedutti Lucio Machado; Jan Eitzinger; Harald Köstler; Gerhard Wellein

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arXiv · 2207.13094

MD-Bench: A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms

Rafael Ravedutti Lucio Machado·Jan Eitzinger·Harald Köstler·Gerhard Wellein

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Abstract

Proxy-apps, or mini-apps, are simple self-contained benchmark codes with performance-relevant kernels extracted from real applications. Initially used to facilitate software-hardware co-design, they are a crucial ingredient for serious performance engineering, especially when dealing with large-scale production codes. MD-Bench is a new proxy-app in the area of classical short-range molecular dynamics. In contrast to existing proxy-apps in MD (e.g. miniMD and coMD) it does not resemble a single application code, but implements state-of-the art algorithms from multiple applications (currently LAMMPS and GROMACS). The MD-Bench source code is understandable, extensible and suited for teaching, benchmarking and researching MD algorithms. Primary design goals are transparency and simplicity, a developer is able to tinker with the source code down to the assembly level. This paper introduces MD-Bench, explains its design and structure, covers implemented optimization variants, and illustrates its usage on three examples.

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Rafael Ravedutti Lucio Machado, Jan Eitzinger, Harald Köstler, Gerhard Wellein. 2022-07-26. MD-Bench: A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms. https://arxiv.org/abs/2207.13094

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