AuthorsJ. Chai, J. E. Hake, N. Wu, M. Wen, X. Cai, G. T. Lines, J. Yang, H. Su, C. Zhang and X. Liao
TitleTowards Simulation of Subcellular Calcium Dynamics at Nanometre Resolution
AfilliationCardiac Modeling, High Performance Computing, Center for Biomedical Computing (SFF), Scientific Computing
StatusPublished
Publication TypeJournal Article
Year of Publication2015
JournalInternational Journal of High Performance Computing Applications
Volume29
Issue1
Pagination51-63
PublisherSAGE
Abstract

Numerical simulation of subcellular  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.

DOI10.1177/1094342013514465

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