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Hybrid Parallelization of a Large-Scale Heart Model

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Part of the Lecture Notes in Computer Science book series (LNTCS,volume 7174)

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.

Keywords

  • Communication Time
  • Multiple Thread
  • Strong Scaling
  • Bidomain Model
  • Implicit Time Discretizations

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Bordas, R., Carpentieri, B., Fotia, G., Maggio, F., Nobes, R., Pitt-Francis, J., Southern, J.: Simulation of cardiac electrophysiology on next-generation high-performance computers. Phil. Trans. Roy. Soc. A. 367, 1951–1969 (2009)

    CrossRef  MathSciNet  MATH  Google Scholar 

  2. Desplantez, T., Dupont, E., Severs, N.J., Weingart, R.: Gap junction channels and cardiac impulse propagation. J. Membrane Biol. 218, 13–28 (2007)

    CrossRef  Google Scholar 

  3. Ethier, S., Tang, W.M., Lin, Z.: Gyrokinetic particle-in-cell simulations of plasma microturbulence on advanced computing platforms. J. Phys. Conf. Ser. 16(1), 1–15 (2005)

    CrossRef  Google Scholar 

  4. Henriquez, C.S.: Simulating the electrical behavior of cardiac tissue using the bidomain model. CRC Crit. Rev. Biomed. Eng. 21, 1–77 (1993)

    MathSciNet  Google Scholar 

  5. Hille, B.: Ion Channels of Excitable Membranes. Sinauer Associates, Inc., Sunderland (2001)

    Google Scholar 

  6. Hoogendijk, M.G., et al.: Mechanism of right precordial ST-segment elevation in structural heart disease: Excitation failure by current-to-load mismatch. Heart Rhythm 7, 238–248 (2010)

    CrossRef  Google Scholar 

  7. Hooke, N., Henriquez, C.S., Lanzkron, P., Rose, D.: Linear algebraic transformations of the bidomain equations: Implications for numerical methods. Math. Biosci. 120(2), 127–145 (1994)

    CrossRef  MathSciNet  MATH  Google Scholar 

  8. Hutter, J., Curioni, A.: Dual-level parallelism for ab initio molecular dynamics: Reaching teraflop performance with the CPMD code. Parallel Comput. 31(1), 1–17 (2005)

    CrossRef  MathSciNet  Google Scholar 

  9. IPM Homepage (2009), http://ipm-hpc.sourceforge.net/

  10. Kaeppeli, R., Whitehouse, S.C., Scheidegger, S., Pen, U.L., Liebendörfer, M.: FISH: A 3D parallel MHD code for astrophysical applications. Technical Report arXiv:0910.2854 (2009)

    Google Scholar 

  11. Karypis, G., Kumar, V.: A coarse-grain parallel formulation of multilevel k-way graph partitioning algorithm. In: Parallel Processing for Scientific Computing. SIAM (1997)

    Google Scholar 

  12. Kléber, A., Rudy, Y.: Basic mechanisms of cardiac impulse propagation and associated arrhythmias. Physiol. Rev. 84, 431–488 (2004)

    CrossRef  Google Scholar 

  13. Loft, R., Thomas, S., Dennis, J.: Terascale spectral element dynamical core for atmospheric general circulation models. In: ACM/IEEE 2001 Conference on Supercomputing (2001)

    Google Scholar 

  14. Mahinthakumar, G., Saied, F.: A hybrid MPI-OpenMP implementation of an implicit finite-element code on parallel architectures. Int. J. High Perform. C. 16(4), 371–393 (2002)

    Google Scholar 

  15. Mitchell, L., Bishop, M., Hötzl, E., Neic, A., Liebmann, M., Haase, G., Plank, G.: Modeling cardiac electrophysiology at the organ level in the peta flops computing age. In: AIP Conference Proceedings, vol. 1281(1), pp. 407–410 (2010)

    Google Scholar 

  16. Niederer, S., Mitchell, L., Smith, N., Plank, G.: Simulating a human heart beat with near-real time performance. Front. Physio. 2, 14 (2011)

    CrossRef  Google Scholar 

  17. Noble, D., Rudy, Y.: Models of cardiac ventricular action potentials: Iterative interaction between experiment and simulation. Phil. Trans. Roy. Soc. London; Phys. Sc. 359, 1127–1142 (2001)

    CrossRef  Google Scholar 

  18. PARAllel Total Energy Code, http://www.nersc.gov/projects/paratec

  19. Potse, M., Dubé, B., Richer, J., Vinet, A., Gulrajani, R.M.: A comparison of monodomain and bidomain reaction-diffusion models for action potential propagation in the human heart. IEEE Trans. Biomed. Eng. 53, 2425–2435 (2006)

    CrossRef  Google Scholar 

  20. Potse, M., Dubé, B., Vinet, A.: Cardiac anisotropy in boundary-element models for the electrocardiogram. Med. Biol. Eng. Comput. 47, 719–729 (2009)

    CrossRef  Google Scholar 

  21. Rabenseifner, R., Hager, G., Jost, G.: Hybrid MPI/OpenMP parallel programming on clusters of multi-core SMP nodes. In: 17th Euromicro International Conference on Parallel, Distributed and Network-based Processing, pp. 427–436 (2009)

    Google Scholar 

  22. Sahni, O., Zhou, M., Shephard, M.S., Jansen, K.E.: Scalable implicit finite element solver for massively parallel processing with demonstration to 160k cores. In: ACM/IEEE 2009 Conference on Supercomputing (2009)

    Google Scholar 

  23. ten Tusscher, K.H., Panfilov, A.V.: Alternans and spiral breakup in a human ventricular tissue model. Am. J. Physiol. 291(3), H1088–H1100 (2006)

    Google Scholar 

  24. Trayanova, N., Aguel, F.: Computer simulations of cardiac defibrillation: A look inside the heart. Comput. Vis. Sci. 4, 259–270 (2002)

    CrossRef  MATH  Google Scholar 

  25. Vigmond, E.J., Aguel, F., Trayanova, N.A.: Computational techniques for solving the bidomain equations in three dimensions. IEEE Trans. Biomed. Eng. 49, 1260–1269 (2002)

    CrossRef  Google Scholar 

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Krause, D., Potse, M., Dickopf, T., Krause, R., Auricchio, A., Prinzen, F. (2012). Hybrid Parallelization of a Large-Scale Heart Model. In: Keller, R., Kramer, D., Weiss, JP. (eds) Facing the Multicore - Challenge II. Lecture Notes in Computer Science, vol 7174. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30397-5_11

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  • DOI: https://doi.org/10.1007/978-3-642-30397-5_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30396-8

  • Online ISBN: 978-3-642-30397-5

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