论文标题
MD板凳：用于最先进的分子动力学算法的通用代理应用工具箱
MD-Bench: A generic proxy-app toolbox for state-of-the-art molecular dynamics algorithms
论文作者
论文摘要
代理应用程序或迷你应用是简单的独立基准代码，并具有从真实应用中提取的性能与性能相关的内核。它们最初用于促进软件硬件共同设计，是严重性能工程的关键成分，尤其是在处理大型生产代码时。 MD基座是经典短距离分子动力学领域的新代理应用。与MD中的现有代理应用（例如Minimd和COMD）相反，它与单个应用程序代码不类似，而是从多个应用程序（当前LAMMPS和GROMACS）实现最先进的算法。 MD基础源代码是可以理解的，可扩展的，并且适合教学，基准测试和研究MD算法。主要的设计目标是透明性和简单性，开发人员能够将源代码降低到组装级别。本文介绍了MD板凳，解释其设计和结构，涵盖了实施的优化变体，并在三个示例中说明了其用法。
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.
