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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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)
Desplantez, T., Dupont, E., Severs, N.J., Weingart, R.: Gap junction channels and cardiac impulse propagation. J. Membrane Biol. 218, 13–28 (2007)
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)
Henriquez, C.S.: Simulating the electrical behavior of cardiac tissue using the bidomain model. CRC Crit. Rev. Biomed. Eng. 21, 1–77 (1993)
Hille, B.: Ion Channels of Excitable Membranes. Sinauer Associates, Inc., Sunderland (2001)
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)
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)
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)
IPM Homepage (2009), http://ipm-hpc.sourceforge.net/
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)
Karypis, G., Kumar, V.: A coarse-grain parallel formulation of multilevel k-way graph partitioning algorithm. In: Parallel Processing for Scientific Computing. SIAM (1997)
Kléber, A., Rudy, Y.: Basic mechanisms of cardiac impulse propagation and associated arrhythmias. Physiol. Rev. 84, 431–488 (2004)
Loft, R., Thomas, S., Dennis, J.: Terascale spectral element dynamical core for atmospheric general circulation models. In: ACM/IEEE 2001 Conference on Supercomputing (2001)
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)
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)
Niederer, S., Mitchell, L., Smith, N., Plank, G.: Simulating a human heart beat with near-real time performance. Front. Physio. 2, 14 (2011)
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)
PARAllel Total Energy Code, http://www.nersc.gov/projects/paratec
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)
Potse, M., Dubé, B., Vinet, A.: Cardiac anisotropy in boundary-element models for the electrocardiogram. Med. Biol. Eng. Comput. 47, 719–729 (2009)
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)
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)
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)
Trayanova, N., Aguel, F.: Computer simulations of cardiac defibrillation: A look inside the heart. Comput. Vis. Sci. 4, 259–270 (2002)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
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
Download citation
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
eBook Packages: Computer ScienceComputer Science (R0)