Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
复制标题
Lennard-Jones 系统分子动力学模拟的高效实现
DOI：
10.1143/ptp.126.203
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发表时间：
2011
期刊：
影响因子：
--
通讯作者：
and N. Ito
中科院分区：
文献类型：
--
作者：
H. Watanabe;M. Suzuki;and N. Ito
考虑了 Lennard-Jones 粒子系统的经典分子动力学 (MD) 方法的有效实现。不仅介绍了通用算法，还介绍了对某些特定 CPU 架构有效的技术。采用简单的基于空间分解的策略进行并行化。利用开发的代码，在国立融合科学研究所 (NIFS) 的由 IBM POWER6 处理器组成的 HITACHI SR16000/J2 系统（主频为 4.7 GHz）和东京大学固体物理研究所 (ISSP) 的由 Intel Xeon 处理器组成的 SGI Altix ICE 8400EX 系统（主频为 2.93 GHz）上进行了基准模拟。最大运行（由 41 亿个粒子和 8192 个 MPI 进程组成）的并行化效率相对于 NIFS 上具有 128 个 MPI 进程的最小运行的并行化效率约为 73%，相对于 ISSP 上具有 4 个 MPI 进程的最小运行的并行化效率约为 66%。研究了导致并行开销的因素。研究发现，每个进程执行时间的波动会降低并行效率。这些波动可能是由于操作系统的干扰造成的，这就是所谓的OS Jitter。
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatial-decomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.