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Please use this identifier to cite or link to this item: http://hdl.handle.net/10119/8504

Title: Performance Evaluation of Parallel Processing Environment for Molecular Dynamics
Authors: Satou, Kenji
Konno, Kenri
Ohta, Osamu
Mikami, Kazunori
Teranishi, Keita
Yamada, Yoichi
Ohki, Shin-Ya
Keywords: Molecular dynamics software
Computer architecture
Parallel processing
Optimization
Issue Date: 2008-07
Publisher: World Scientific and Engineering Academy and Society
Magazine name: WSEAS Transactions on Biology and Biomedicine
Volume: 5
Number: 7
Start page: 173
End page: 182
Abstract: Molecular dynamics (MD) is one of the popular applications in the research field of high performance computing. Since it requires large amount of CPU time basically proportional to the square of the number of atoms simulated, acceleration of MD is essential to simulation of large biomolecules like proteins. Therefore, parallelization of MD has been actively studied long time. However, most of the studies of parallel MD report modified or newly developed algorithms specialized to some computer architectures like vector-parallel supercomputer, and an end-user of MD software cannot implement them to popular MD software developed by other ones. In this study, we evaluated performance of four kinds of computer architectures: 1) vector-parallel supercomputer, 2) multi-processor machine with shared memory, 3) multi-processor machine with distributed memory, and 4) PC cluster. Various compiler options for parallelization and optimization were tested. Experimental results revealed that if MD software is not parallelized nor vectorized in source level, use of normal PC cluster with maximum use of optimization options in compilation is the best way.
Rights: Copyright (C) 2008 World Scientific and Engineering Academy and Society. Kenji Satou, Kenri Konno, Osamu Ohta, Kazunori Mikami, Keita Teranishi, Yoichi Yamada, Shin-Ya Ohki, WSEAS Transactions on Biology and Biomedicine, 5(7), 2008, 173-182.
URI: http://hdl.handle.net/10119/8504
Material Type: publisher
Appears in Collections:f10-1. 雑誌掲載論文 (Journal Articles)

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