Kernel optimization for short-range molecular dynamics

doi:10.1016/j.cpc.2016.07.010

	Kernel optimization for short-range molecular dynamics
	Hu Changjun 1; Wang Xianmeng 1; Li Jianjiang 1; He Xinfu 2; Li Shigang 3; Feng Yangde 4; Yang Shaofeng 1; Bai He 1
	2017-02-01
发表期刊	COMPUTER PHYSICS COMMUNICATIONS
ISSN	0010-4655
卷号	211 页码:31-40
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.
关键词	Molecular Dynamics OpenMP SIMD MIC
DOI	10.1016/j.cpc.2016.07.010
收录类别	SCI
语种	英语
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
WOS类目	Computer Science, Interdisciplinary Applications ; Physics, Mathematical
WOS记录号	WOS:000390181300006
出版者	ELSEVIER SCIENCE BV
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/7760
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.Univ Sci & Technol Beijing, Beijing, Peoples R China 2.China Inst Atom Energy, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Syst & Architecture, Beijing, Peoples R China 4.Chinese Acad Sci, Comp Network Informat Ctr, 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.