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Proxy-apps, or mini-apps, are simple self-contained benchmark codes withperformance-relevant kernels extracted from real applications. Initially usedto facilitate software-hardware co-design, they are a crucial ingredient forserious performance engineering, especially when dealing with large-scaleproduction codes. MD-Bench is a new proxy-app in the area of classicalshort-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 implementsstate-of-the art algorithms from multiple applications (currently LAMMPS andGROMACS). The MD-Bench source code is understandable, extensible and suited forteaching, benchmarking and researching MD algorithms. Primary design goals aretransparency and simplicity, a developer is able to tinker with the source codedown to the assembly level. This paper introduces MD-Bench, explains its designand structure, covers implemented optimization variants, and illustrates itsusage on three examples.

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