FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations

doi:10.1007/s11227-019-02860-3

	FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations
	Li, Kun 1,2; Li, Shigang 1; Huang, Shan 1,2; Chen, Yifeng 3; Zhang, Yunquan 1
	2020-07-01
发表期刊	JOURNAL OF SUPERCOMPUTING
ISSN	0920-8542
卷号	76 期号:7 页码:5501-5520
摘要	In the molecular dynamics simulation, an important step is the establishment of neighbor list for each particle, which involves the distance calculation for each particle pair in the simulation space. However, the distance calculation will cause costly floating-point operations. In this paper, we propose a novel algorithm, called Fast Neighbor List, which establishes the neighbor lists mainly using the bitwise operations. Firstly, we design a data layout, which uses an integer value to represent the three-dimensional coordinates of a particle. Then, a bunch of bitwise operations and two subtraction operations are used to judge whether the distance between a pair of particles is within the cutoff radius. We demonstrate that our algorithm can deal with the periodic boundary seamlessly. We also use single instruction multiple data (SIMD) instructions to further improve the performance. We implement our algorithm on Intel Xeon E5-2670, ARM v8, and Sunway many-core processors, respectively. Compared with the traditional method, our algorithm achieves on average 1.79x speedup on Intel Xeon E5-2670 processor, 3.43x speedup on ARM v8 processor, and 4.03x speedup on Sunway many-core processor. After using SIMD instructions, our algorithm achieves on average 2.64x speedup and 14.43x speedup on Intel Xeon E5-2670 and ARM v8 processors, respectively.
关键词	Neighbor list Bitwise operations SIMD Molecular dynamics
DOI	10.1007/s11227-019-02860-3
收录类别	SCI
语种	英语
WOS研究方向	Computer Science ; Engineering
WOS类目	Computer Science, Hardware & Architecture ; Computer Science, Theory & Methods ; Engineering, Electrical & Electronic
WOS记录号	WOS:000538267400033
出版者	SPRINGER
引用统计	被引频次：1[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/2XEOYT63/15256
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, Shigang
作者单位	1.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Sch Comp & Control Engn, Beijing, Peoples R China 3.Peking Univ, Sch EECS, HCST Key Lab, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Li, Kun,Li, Shigang,Huang, Shan,et al. FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations[J]. JOURNAL OF SUPERCOMPUTING,2020,76(7):5501-5520.
APA	Li, Kun,Li, Shigang,Huang, Shan,Chen, Yifeng,&Zhang, Yunquan.(2020).FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations.JOURNAL OF SUPERCOMPUTING,76(7),5501-5520.
MLA	Li, Kun,et al."FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations".JOURNAL OF SUPERCOMPUTING 76.7(2020):5501-5520.