Research Article

Accelerating cardiac excitation spread simulations using graphics processing units

  1. B. M. Rocha1,*,
  2. F. O. Campos2,
  3. R. M. Amorim3,
  4. G. Plank2,5,
  5. R. W. dos Santos3,
  6. M. Liebmann4,
  7. G. Haase4

Article first published online: 7 DEC 2010

DOI: 10.1002/cpe.1683

Issue

Concurrency and Computation: Practice and Experience

Concurrency and Computation: Practice and Experience

Special Issue: GPU computing

Volume 23, Issue 7, pages 708–720, May 2011

Additional Information

How to Cite

Rocha, B. M., Campos, F. O., Amorim, R. M., Plank, G., Santos, R. W. d., Liebmann, M. and Haase, G. (2011), Accelerating cardiac excitation spread simulations using graphics processing units. Concurrency Computat.: Pract. Exper., 23: 708–720. doi: 10.1002/cpe.1683

Author Information

  1. 1

    National Laboratory of Scientific Computing, Av. Getúlio Vargas, 333, 25651-075 Petropolis, Brazil

  2. 2

    Medical University of Graz, Institute of Biophysics, Harrachgasse 21, 8010 Graz, Austria

  3. 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. 4

    Karl–Franzens-University of Graz, Institute for Mathematics and Scientific Computing, Heinrichstrasse 36, 8010 Graz, Austria

  5. 5

    Oxford e-Research Centre, University of Oxford, U.K.

*LNCC, Av. Getúlio Vargas, 333, 25651-075 Petropolis, Brazil

Publication History

  1. Issue published online: 30 MAR 2011
  2. Article first published online: 7 DEC 2010
  3. Manuscript Accepted: 18 SEP 2010
  4. Manuscript Revised: 30 JUN 2010
  5. Manuscript Received: 19 MAR 2010

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Keywords:

  • cardiac electrophysiology;
  • graphic processing units;
  • high performance computing

Abstract

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.

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