CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. 2011; 23:708–720 Published online 7 December 2010 in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/cpe.1683 Accelerating cardiac excitation spread simulations using graphics processing units B. M. Rocha 1, ∗, † , F. O. Campos 2 , R. M. Amorim 3 , G. Plank 2, 5 , R. W. dos Santos 3 , M. Liebmann 4 and G. Haase 4 1 National Laboratory of Scientific Computing, Av. Getúlio Vargas, 333, 25651-075 Petropolis, Brazil 2 Medical University of Graz, Institute of Biophysics, Harrachgasse 21, 8010 Graz, Austria 3 Department of Computer Science and Master Program in Computational Modeling, Federal University of Juiz de Fora, Martelos, 36036-330 Juiz de Fora, Brazil 4 Karl–Franzens-University of Graz, Institute for Mathematics and Scientific Computing, Heinrichstrasse 36, 8010 Graz, Austria 5 Oxford e-Research Centre, University of Oxford, U.K. SUMMARY The modeling of the electrical activity of the heart is of great medical and scientific interest, because it provides a way to get a better understanding of the related biophysical phenomena, allows the development of new techniques for diagnoses and serves as a platform for drug tests. The cardiac electrophysiology may be simulated by solving a partial differential equation coupled to a system of ordinary differential equations describing the electrical behavior of the cell membrane. The numerical solution is, however, computationally demanding because of the fine temporal and spatial sampling required. The demand for real-time high definition 3D graphics made the new graphic processing units (GPUs) a highly parallel, multithreaded, many-core processor with tremendous computational horsepower. It makes the use of GPUs a promising alternative to simulate the electrical activity in the heart. The aim of this work is to study the performance of GPUs for solving the equations underlying the electrical activity in a simple cardiac tissue. In tests on 2D cardiac tissues with different cell models it is shown that the GPU implementation runs 20 times faster than a parallel CPU implementation running with 4 threads on a quad–core machine, parts of the code are even accelerated by a factor of 180. Copyright  2010 John Wiley & Sons, Ltd. Received 19 March 2010; Revised 30 June 2010; Accepted 18 September 2010 KEY WORDS: cardiac electrophysiology; graphic processing units; high performance computing 1. INTRODUCTION The phenomenon of electrical propagation in the heart comprises a set of complex nonlinear biophysical processes. Its multi-scale nature spans from nanometer processes such as ionic move- ments and protein dynamic conformation to centimeter phenomena such as whole heart contrac- tion [1]. Computer models have become valuable tools for the study and comprehension of such complex phenomena, as they allow different information acquired from different physical scales and experiments to be combined in order to generate a better picture of the whole system functionality. There are two components that contribute to the modeling of cardiac electrical propagation [2]. The first is a model of cellular membrane dynamics, describing the flow of ions across the cell membrane. Such models are usually formulated as a system of nonlinear ordinary differential ∗ Correspondence to: B. M. Rocha, LNCC, Av. Getúlio Vargas, 333, 25651-075 Petropolis, Brazil. † E-mail: bernardo@lncc.br Copyright  2010 John Wiley & Sons, Ltd.