MAMBER: Accelerating explicit solvent molecular dynamic with Intel Xeon Phi many-integrated core coprocessors
文献类型：会议论文
| 作者 | Liu, Xin1; Peng, Shaoliang1; Yang, Canqun1; Wu, Chengkun1; Wang, Haiqiang1; Cheng, Qian1; Zhu, Weiliang2 ; Wang, Jinan2
|
| 出版日期 | 2015-07-07 |
| DOI | 10.1109/CCGrid.2015.66 |
| 页码 | 729-732 |
| 英文摘要 | Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules, which is a very important research technique for the study of biological and chemical systems at micro-scale. Assisted Model Building with Energy Refinement (AMBER) is one of the most commonly used software for MD. However, the microsecond MD simulation of large-scale atom system requires a lot of computation power. In this paper, we propose mAMBER: an Intel Xeon Phi Many-Integrated Core (MIC) Coprocessors accelerated implementation of explicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package. We mAMBER also includes new parallel algorithm using CPUs and MIC coprocessors on Tianhe-2 supercomputer. With several optimizing techniques including CPU/MIC collaborated parallelization, factorization and asynchronous data transfer framework, we can accelerate the sander program of AMBER (version 12) in 'offload' mode, and achieves a 4.17-fold overall speedup compared with the CPU-only sander program. |
| 会议录 | Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015
 |
| 会议录出版者 | Institute of Electrical and Electronics Engineers Inc. |
| 文献子类 | Proceedings Paper |
| 语种 | 英语 |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/266848]  |
| 专题 | 药物发现与设计中心 |
| 通讯作者 | Peng, Shaoliang |
| 作者单位 | 1.School of Computer Science, National University of Defense Technology, Changsha, China; 2.Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China |
| 推荐引用方式 GB/T 7714 | Liu, Xin,Peng, Shaoliang,Yang, Canqun,et al. MAMBER: Accelerating explicit solvent molecular dynamic with Intel Xeon Phi many-integrated core coprocessors[C]. 见:. |
入库方式： OAI收割
来源：上海药物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。