MAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer

doi:10.1109/BIBM.2016.7822595

CORC > 上海药物研究所 > 中国科学院上海药物研究所 > 药物发现与设计中心

	MAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer
	Peng, Shaoliang 1; Zhang, Xiaoyu 1; Lu, Yutong 1; Liao, Xiangke 1; Lu, Kai 1; Yang, Canqun 1; Liu, Jie 1; Zhu, Weiliang2 ; Wei, Dongqing 3
	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
内容类型	会议论文
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:.