| Kernel optimization for short-range molecular dynamics | |
| Hu Changjun1; Wang Xianmeng1; Li Jianjiang1; He Xinfu2; Li Shigang3; Feng Yangde4; Yang Shaofeng1; Bai He1 | |
| 刊名 | Computer physics communications
 |
| 2017-02-01 | |
| 卷号 | 211页码:31-40 |
| 关键词 | Molecular dynamics Openmp Simd Mic |
| ISSN号 | 0010-4655 |
| DOI | 10.1016/j.cpc.2016.07.010 |
| 通讯作者 | Li jianjiang(lijianjiang@ustb.edu.cn) |
| 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. |
| WOS关键词 | EMBEDDED-ATOM-METHOD ; EFFICIENT ; METALS |
| WOS研究方向 | Computer Science ; Physics |
| WOS类目 | Computer Science, Interdisciplinary Applications ; Physics, Mathematical |
| 语种 | 英语 |
| 出版者 | ELSEVIER SCIENCE BV |
| WOS记录号 | WOS:000390181300006 |
| 内容类型 | 期刊论文 |
| URI标识 | http://www.corc.org.cn/handle/1471x/2374194 |
| 专题 | 计算机网络信息中心 |
| 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. |
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