A Method to Accelerate GROMACS in Offload Mode on Tianhe-2 Supercomputer

Author

Haiqiang Wang ; Shaoliang Peng ; Xiaoqian Zhu ; Chengkun Wu ; Xin Liu ; Qian Chen ; Weiliang Zhu ; Jinan Wang ; Huaiyu Yang

Author_Institution

Sch. of Comput. Sci., Nat. Univ. of Defense Technol., Changsha, China

fYear

2015

fDate

4-7 May 2015

Firstpage

781

Lastpage

784

Abstract

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.

Keywords

coprocessors; molecular dynamics method; multiprocessing systems; parallel machines; pharmaceutical technology; CPU; GROMACS; Intel Xeon Phi many integrated core; MD; MIC; N-body simulation; Tianhe-2 supercomputer; computer simulation; coprocessors; molecular dynamics; offload mode; pharmaceutical industry; Acceleration; Arrays; Coprocessors; Force; Industries; Microwave integrated circuits; Supercomputers; GROMACS; MIC; Tianhe-2; offload;

fLanguage

English

Publisher

ieee

Conference_Titel

Cluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposium on

Conference_Location

Shenzhen

Type

conf

DOI

10.1109/CCGrid.2015.65

Filename

7152556