Hybrid parallelization of a large-scale heart model

Authors:
Dorian Krause;Mark Potse;Thomas Dickopf;Rolf Krause;Angelo Auricchio;Frits Prinzen
Affiliations:
Institute of Computational Science, University of Lugano, Switzerland;Cardiovascular Research Institute, Maastricht University, The Netherlands;Institute of Computational Science, University of Lugano, Switzerland;Institute of Computational Science, University of Lugano, Switzerland;Fondazione Cardiocentro Ticino, Lugano, Switzerland;Cardiovascular Research Institute, Maastricht University, The Netherlands
Venue:
Facing the Multicore-Challenge II
Year:
2012

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Abstract

The simulation of the electrophysiology of the heart is challenging due to its multiscale nature requiring the use of high spatial resolutions. Hence, it is important to efficiently utilize large parallel machines. In this article, we present a code designed to meet these scalability challenges on contemporary multicore-based massively parallel architectures. It is based on a well-established model originally designed for shared-memory systems. To improve scalability and extend support to distributed-memory architectures, we developed a hybrid OpenMP-MPI code. The new code shows excellent scalability up to 8448 cores with both explicit and implicit time discretizations. We present an in-depth analysis of the advantages of hybrid parallelization for this type of application.