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

TL;DR

MD-Bench is a versatile proxy-app for molecular dynamics that combines multiple algorithms from leading MD software, designed for transparency, extensibility, and performance research.

Contribution

It introduces MD-Bench, a new proxy-app that integrates state-of-the-art MD algorithms from multiple applications, unlike existing single-application proxy-benchmarks.

Findings

MD-Bench is understandable and extensible.

It supports teaching, benchmarking, and research.

Demonstrated on three example cases.

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.