High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer

doi:10.1109/TCBB.2018.2805709

	High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer
	Peng, Shaoliang 2; Zhang, Xiaoyu 3; Lu, Yutong 2; Liao, Xiangke 3; Lu, Kai 4; Yang, Canqun 3; Liu, Jie 5; Zhu, Weiliang3 ; Wei, Dongqing 6
刊名	IEEE/ACM Transactions on Computational Biology and Bioinformatics
	2018-02-12
ISSN号	15455963
DOI	10.1109/TCBB.2018.2805709
文献子类	Article
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 the Tianhe-2 supercomputer. The parallel optimization of AMBER is carried out on three different levels: fine grained OpenMP parallel on a single CPU, single node CPU/MIC 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. IEEE
语种	英语
出版者	Institute of Electrical and Electronics Engineers Inc.
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/266957]
专题	中国科学院上海药物研究所
作者单位	1.College of Life Sciences and Biotechnology and State Key Laboratory of Microbial Metabolism, Shanghai, Shanghai China 2.School of Computer Science, National University of Defense Technology, 58294 Changsha, Hunan China 3.; 4.Computer Science and Technology, National University of Defense Technology, Changsha, Hunan China 410073 5.CSE, NUDT, Changsha, Hunan China 6.School of Computer Science, National University of Defense Technology, 58294 changsha, Hunan China 7.School of Computer Science, National University of Defense Technology, Changsha, Hunan China 8.Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, Shanghai China
推荐引用方式 GB/T 7714	Peng, Shaoliang,Zhang, Xiaoyu,Lu, Yutong,et al. High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics,2018.
APA	Peng, Shaoliang.,Zhang, Xiaoyu.,Lu, Yutong.,Liao, Xiangke.,Lu, Kai.,...&Wei, Dongqing.(2018).High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer.IEEE/ACM Transactions on Computational Biology and Bioinformatics.
MLA	Peng, Shaoliang,et al."High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer".IEEE/ACM Transactions on Computational Biology and Bioinformatics (2018).