MAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer
文献类型：会议论文
| 作者 | Peng, Shaoliang1; Zhang, Xiaoyu1; Lu, Yutong1; Liao, Xiangke1; Lu, Kai1; Yang, Canqun1; Liu, Jie1; Zhu, Weiliang2 ; Wei, Dongqing3
|
| 出版日期 | 2017-01-17 |
| DOI | 10.1109/BIBM.2016.7822595 |
| 页码 | 651-657 |
| 英文摘要 | Molecular dynamics (MD) is a computer simulation method of studying physical movements of atoms and molecules that provide detailed microscopic sampling on molecular scale. With the continuous efforts and improvements, MD simulation gained popularity in materials science, biochemistry and biophysics with various application areas and expanding data scale. Assisted Model Building with Energy Refinement (AMBER) is one of the most widely used software packages for conducting MD simulations. However, the speed of AMBER MD simulations for system with millions of atoms in microsecond scale still need to be improved. In this paper, we propose a parallel acceleration strategy for AMBER on Tianhe-2 supercomputer. The parallel optimization of AMBER is carried out on three different levels: fine grained OpenMP parallel on a single MIC, single-node CPU/MIC collaborated parallel optimization and multi-node multi-MIC collaborated parallel acceleration. By the three levels of parallel acceleration strategy above, we achieved the highest speedup of 25-33 times compared with the original program. Source Code: https://github.com/tianhe2/mAMBER. |
| 会议录 | Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
 |
| 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/2S10ELR8/266847]  |
| 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; 3.College of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China |
| 推荐引用方式 GB/T 7714 | Peng, Shaoliang,Zhang, Xiaoyu,Lu, Yutong,et al. MAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer[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。