Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems(General and Mathematical Physics)
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概要
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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 4.7GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93GHz 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.
- 2011-08-25
著者
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Watanabe Hiroshi
Institute for Chemical Research, Kyoto University
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Suzuki Masaru
Department Of Applied Physics And Chemistry The University Of Electro-communications
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Ito Nobuyasu
Department Of Applied Physics Faculty Of Engineering The University Of Tokyo
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Suzuki Masaru
Department Of Applied Quantum Physics And Nuclear Engineering Kyushu University
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Watanabe Hiroshi
Institute For Chemical Research Kyoto University
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Watanabe Hiroshi
Institute for Solid State Physics, The University of Tokyo:Information Technology Center, The University of Tokyo
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Suzuki Masaru
Department of Applied Quantum, Physics and Nuclear Engineering, Kyushu University
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