Towards simulation of subcellular calcium dynamics at nanometre resolution. (February 2015)

• Record Type: Journal Article
• Authors: Chai, Jun; Hake, Johan; Wu, Nan; Wen, Mei; Cai, Xing; Lines, Glenn T; Yang, Jing; Su, Huayou; Zhang, Chunyuan; Liao, Xiangke
• Is Part Of: International journal of high performance computing applications. Volume 29:Number 1(2015:Spring)
• Page Start: 51
• Page End: 63
• Publication Date: 2015-02
• Subjects: numerical simulation -- subcellular Ca2+ dynamics -- nano-resolution -- hybrid cluster -- Tianhe-2 -- Intel Xeon Phi; High performance computing -- Periodicals; Supercomputers -- Periodicals; 004.1105
• DOI: 10.1177/1094342013514465
• Languages: English
• ISSNs: 1094-3420

Abstract

Numerical simulation of subcellularCa 2 + dynamics with a resolution down to one nanometre can be an important tool for discovering the physiological cause of many heart diseases. The requirement of enormous computational power, however, has made such simulations prohibitive so far. By using up to 12, 288 Intel Xeon Phi 31S1P coprocessors on the new hybrid cluster Tianhe-2, which is the new number one supercomputer of the world, we have achieved 1.27 Pflop/s in double precision, which brings us much closer to the nanometre resolution. This is the result of efficiently using the hardware on different levels: (1) a single Xeon Phi (2) a single compute node that consists of a host and three coprocessors, and (3) a huge number of interconnected nodes. To overcome the challenge of programming Intel's new many-integrated core (MIC) architecture, we have adopted techniques such as vectorization, hierarchical data blocking, register data reuse, offloading computations to the coprocessors, and pipelining computations with intra-/inter-node communications.