TY - GEN
T1 - A method to accelerate GROMACS in offload mode on tianhe-2 supercomputer
AU - Wang, Haiqiang
AU - Peng, Shaoliang
AU - Zhu, Xiaoqian
AU - Wu, Chengkun
AU - Liu, Xin
AU - Chen, Qian
AU - Zhu, Weiliang
AU - Wang, Jinan
AU - Yang, Huaiyu
N1 - Publisher Copyright:
© 2015 IEEE.
PY - 2015/7/7
Y1 - 2015/7/7
N2 - 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.
AB - 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.
KW - GROMACS
KW - MIC
KW - Offload
KW - Tianhe-2
UR - https://www.scopus.com/pages/publications/84941193785
U2 - 10.1109/CCGrid.2015.65
DO - 10.1109/CCGrid.2015.65
M3 - 会议稿件
AN - SCOPUS:84941193785
T3 - Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015
SP - 781
EP - 784
BT - Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 15th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015
Y2 - 4 May 2015 through 7 May 2015
ER -