A method to accelerate GROMACS in offload mode on tianhe-2 supercomputer

doi:10.1109/CCGrid.2015.65

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

	A method to accelerate GROMACS in offload mode on tianhe-2 supercomputer
	Wang, Haiqiang 1; Peng, Shaoliang 1; Zhu, Xiaoqian 1; Wu, Chengkun 1; Liu, Xin 1; Chen, Qian 1; Zhu, Weiliang2 ; Wang, Jinan 2; Yang, Huaiyu 2
	2015-07-07
DOI	10.1109/CCGrid.2015.65
页码	781-784
英文摘要	Molecular Dynamics(MD) is a computer simulation of physical movements of atoms and molecules in the context of N-body simulation, and is an important part of pharmaceutical industry. GROMACS, which is the most popular software for MD, could not perform satisfactorily with large-scale for the limit of computing resources. In this paper, we proposed a method to accelerate GROMACS with offload mode. In this mode, GROMACS could be arranged efficiently with CPU and the Intel® Xeon PhiTM Many Integrated Core (MIC) coprocessors at the same time, making the full use of Tianhe-2 supercomputer resources. To promote the efficiency of GROMACS, we proposed a series of methods, such as synchronization, data reassemble and array reuse. As we known, we are the first to accelerate GROMACS in offload mode on MIC.
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
内容类型	会议论文
源URL	[http://119.78.100.183/handle/2S10ELR8/266845]
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	Wang, Haiqiang,Peng, Shaoliang,Zhu, Xiaoqian,et al. A method to accelerate GROMACS in offload mode on tianhe-2 supercomputer[C]. 见:.