A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer

作者：Peng, Shaoliang^*; Cui, Yingbo; Yang, Shunyun; Su, Wenhe; Zhang, Xiaoyu; Zhang, Tenglilang; Liu, Weiguo; Zhao, Xing-Ming

来源：IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, 16(2): 425-433.

DOI：10.1109/TCBB.2017.2713362

• GROMACS
• molecular dynamics simulation
• high performance computing
• parallel framework

Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel (R) Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer. Furthermore, we optimize GROMACS so that it can run on both the CPU and MIC at the same time. In addition, we accelerate multi-node GROMACS so that it can be used in practice. Benchmarking on real data, our accelerated GROMACS performs very well and reduces computation time significantly. Source code: https://github.com/tianhe2/gromacs-mic.

• 出版日期2019-4
• 单位山东大学; 复旦大学; 湖南大学; 中国人民解放军国防科学技术大学; 长沙学院