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Kernel optimization for short-range molecular dynamics

文献类型：期刊论文

作者Hu Changjun4; Wang Xianmeng4; Li Jianjiang4; He Xinfu1; Li Shigang2; Feng Yangde3; Yang Shaofeng4; Bai He4
刊名COMPUTER PHYSICS COMMUNICATIONS
出版日期2017-02-01
卷号211页码:31-40
关键词Molecular Dynamics OpenMP SIMD MIC
ISSN号0010-4655
DOI10.1016/j.cpc.2016.07.010
英文摘要To optimize short-range force computations in Molecular Dynamics (MD) simulations, multi-threading and SIMD optimizations are presented in this paper. With respect to multi-threading optimization, a Partition-and-Separate-Calculation (PSC) method is designed to avoid write conflicts caused by using Newton's third law. Serial bottlenecks are eliminated with no additional memory usage. The method is implemented by using the OpenMP model. Furthermore, the PSC method is employed on Intel Xeon Phi coprocessors in both native and offload models. We also evaluate the performance of the PSC method under different thread affinities on the MIC architecture. In the SIMD execution, we explain the performance influence in the PSC method, considering the "if-clause" of the cutoff radius check. The experiment results show that our PSC method is relatively more efficient compared to some traditional methods. In double precision, our 256-bit SIMD implementation is about 3 times faster than the scalar version. (C) 2016 Elsevier B.V. All rights reserved.
资助项目Hi-Tech Research and Development Program (863) of China[2015AA01A303] ; Natural Science Foundation of China[61303050] ; Youth Innovation Promotion Association, CAS[2015375] ; National Natural Science Foundation of China[61502450]
WOS研究方向Computer Science ; Physics
语种英语
WOS记录号WOS:000390181300006
出版者ELSEVIER SCIENCE BV
源URL[http://119.78.100.204/handle/2XEOYT63/7759]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Li Jianjiang
作者单位1.China Inst Atom Energy, Beijing, Peoples R China
2.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Syst & Architecture, Beijing, Peoples R China
3.Chinese Acad Sci, Comp Network Informat Ctr, Beijing, Peoples R China
4.Univ Sci & Technol Beijing, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Hu Changjun,Wang Xianmeng,Li Jianjiang,et al. Kernel optimization for short-range molecular dynamics[J]. COMPUTER PHYSICS COMMUNICATIONS,2017,211:31-40.
APA Hu Changjun.,Wang Xianmeng.,Li Jianjiang.,He Xinfu.,Li Shigang.,...&Bai He.(2017).Kernel optimization for short-range molecular dynamics.COMPUTER PHYSICS COMMUNICATIONS,211,31-40.
MLA Hu Changjun,et al."Kernel optimization for short-range molecular dynamics".COMPUTER PHYSICS COMMUNICATIONS 211(2017):31-40.

入库方式： OAI收割

来源：计算技术研究所

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