Efficient implementations of molecular dynamics simulations for Lennard-Jones systems

DOI10.1143/PTP.126.203MaRDI QIDQ3106472zbMATH OpenOpenAlexFDO

Authors Hiroshi Watanabe, Masaru Suzuki, Nobuyasu Ito

Publication date 28 December 2011

Published in Progress of Theoretical Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1012.2677

Mathematics Subject Classification ID

Computational methods for problems pertaining to quantum theory (81-08) Molecular physics (81V55)

Abstract: 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.

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