AuthorsJ. Langguth, Q. Lan, N. Gaur, X. Cai and M. Wen
EditorsC. Zhang
TitleEnabling Tissue-Scale Cardiac Simulations Using Heterogeneous Computing on Tianhe-2
AfilliationScientific Computing
Project(s)User-friendly programming of GPU-enhanced clusters, Center for Cardiological Innovation (SFI), Center for Biomedical Computing (SFF)
StatusPublished
Publication TypeProceedings, refereed
Year of Publication2016
Conference NameIEEE 22nd International Conference on Parallel and Distributed Systems (ICPADS)
Pagination843-852
Date Published12/2016
PublisherACM/IEEE
ISSN Number1521-9097
KeywordsCalcium handling, multiscale cardiac tissue simulation, supercomputing, Xeon Phi
Abstract

We develop a simulator for 3D tissue of the human cardiac ventricle with a physiologically realistic cell model and deploy it on the supercomputer Tianhe-2. In order to attain the full performance of the heterogeneous CPU-Xeon Phi design, we use carefully optimized codes for both devices and combine them to obtain suitable load balancing. Using a large number of nodes, we are able to perform tissue-scale simulations of the electrical activity and calcium handling in millions of cells, at a level of detail that tracks the states of trillions of ryanodine receptors. We can thus simulate arrythmogenic spiral waves and other complex arrhythmogenic patterns which arise from calcium handling deficiencies in human cardiac ventricle tissue. Due to extensive code tuning and parallelization via OpenMP, MPI, and SCIF/COI, large scale simulations of 10 heartbeats can be performed in a matter of hours. Test results indicate excellent scalability, thus paving the way for detailed whole-heart simulations in future generations of leadership class supercomputers.

DOI10.1109/ICPADS.2016.0114
Citation Key25016

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