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Automated Parallel Simulation of Heart Electrical Activity Using Finite Element Method

  • Conference paper
  • First Online:
Algorithms and Architectures for Parallel Processing (ICA3PP 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10049))

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Abstract

In this paper we present an approach to the parallel simulation of the heart electrical activity using the finite element method with the help of the FEniCS automated scientific computing framework. FEniCS allows scientific software development using the near-mathematical notation and provides automatic parallelization on MPI clusters. We implemented the ten Tusscher–Panfilov (TP06) cell model of cardiac electrical activity. The scalability testing of the implementation was performed using up to 240 CPU cores and the 95 times speedup was achieved. We evaluated various combinations of the Krylov parallel linear solvers and the preconditioners available in FEniCS. The best performance was provided by the conjugate gradient method and the biconjugate gradient stabilized method solvers with the successive over-relaxation preconditioner. Since the FEniCS-based implementation of TP06 model uses notation close to the mathematical one, it can be utilized by computational mathematicians, biophysicists, and other researchers without extensive parallel computing skills.

The work is supported by the RAS Presidium grant I.33P “Fundamental problems of mathematical modeling,” project no. 0401-2015-0025. Our study was performed using the Uran supercomputer of the Krasovskii Institute of Mathematics and Mechanics and computational cluster of the Ural Federal University.

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References

  1. Alnæs, M.S., Logg, A., Ølgaard, K.B., Rognes, M.E., Wells, G.N.: Unified form language. ACM Trans. Math. Softw. 40(2), 1–37 (2014)

    Article  MATH  Google Scholar 

  2. Geuzaine, C., Remacle, J.F.: Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities. Int. J. Numer. Methods Eng. 79(11), 1309–1331 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  3. Jansson, N.: Optimizing sparse matrix assembly in finite element solvers with one-sided communication. In: Daydé, M., Marques, O., Nakajima, K. (eds.) VECPAR 2012. LNCS, vol. 7851, pp. 128–139. Springer, Heidelberg (2013). doi:10.1007/978-3-642-38718-0_15

    Chapter  Google Scholar 

  4. Kirby, R.C., Logg, A.: A compiler for variational forms. ACM Trans. Math. Softw. 32(3), 417–444 (2006)

    Article  MathSciNet  Google Scholar 

  5. Li, Y., Chen, C.: An efficient split-operator scheme for 2-D advection-diffusion simulations using finite elements and characteristics. Appl. Math. Model. 13(4), 248–253 (1989)

    Article  MATH  Google Scholar 

  6. Logg, A., Mardal, K.A., Wells, G.: Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book. Springer Science & Business Media, Heidelberg (2012)

    Book  MATH  Google Scholar 

  7. Logg, A., Wells, G.N.: DOLFIN: automated finite element computing. ACM Trans. Math. Softw. (TOMS) 37(2), 1–28 (2010)

    Article  MathSciNet  Google Scholar 

  8. Pravdin, S.F., Berdyshev, V.I., Panfilov, A.V., Katsnelson, L.B., Solovyova, O., Markhasin, V.S.: Mathematical model of the anatomy and fibre orientation field of the left ventricle of the heart. Biomed. Eng. Online 54(12), 21 (2013)

    Google Scholar 

  9. Kerckhos, R.C.P., Healy, S.N., Usyk, T.P., McCulloch, A.D.: Computational methods for cardiac electromechanics. Proc. IEEE 94, 769–783 (2006)

    Article  Google Scholar 

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

    Article  Google Scholar 

  11. Ten Tusscher, K.H., Panfilov, A.V., et al.: Organization of ventricular fibrillation in the human heart. Circulation Res. 100(12), e87–e101 (2007)

    Article  Google Scholar 

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Authors and Affiliations

  1. Krasovskii Institute of Mathematics and Mechanics, Ekaterinburg, Russia

    Andrey Sozykin, Timofei Epanchintsev, Vladimir Zverev & Aleksandr Bersenev

  2. Institute of Immunology and Physiology UrB RAS, Ekaterinburg, Russia

    Andrey Sozykin, Timofei Epanchintsev & Svyatoslav Khamzin

  3. Ural Federal University, Ekaterinburg, Russia

    Andrey Sozykin, Timofei Epanchintsev, Vladimir Zverev, Svyatoslav Khamzin & Aleksandr Bersenev

Authors
  1. Andrey Sozykin
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  2. Timofei Epanchintsev
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  3. Vladimir Zverev
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  4. Svyatoslav Khamzin
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  5. Aleksandr Bersenev
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Corresponding author

Correspondence to Andrey Sozykin .

Editor information

Editors and Affiliations

  1. Carlos III University of Madrid, Getafe, Spain

    Jesus Carretero

  2. Carlos III University of Madrid, Getafe, Spain

    Javier Garcia-Blas

  3. Mathematical Support for Computers, N. I. Lobachevsky State University of Nizhny Novgorod, Nizhniy Novgorod, Russia

    Victor Gergel

  4. Research Computing Center (RCC), Moscow State University, Moscow, Russia

    Vladimir Voevodin

  5. Research Computing Center (RCC), Moscow State University, Moscow, Russia

    Iosif Meyerov

  6. E.U. Politécnica, Universidad de Extremaddura, Cáceres, Spain

    Juan A. Rico-Gallego

  7. Ingenieria de Sistemas Informáticos, Universidad de Extremaddura, Cáceres, Spain

    Juan C. Díaz-Martín

  8. Universitat Politécnica de València, Valencia, Spain

    Pedro Alonso

  9. Distributed and Parallel Systems Group, Institute for Computer Science, Innsbruck, Austria

    Juan Durillo

  10. Carlos III University of Madrid, Getafe, Spain

    José Daniel Garcia Sánchez

  11. UCD School of Computer Science, University College Dublin, Dublin, Ireland

    Alexey L. Lastovetsky

  12. University of Calabria, Rende (CS), Italy

    Fabrizio Marozzo

  13. Information Science and Engineering, Central South University, Changsha, Hunan, China

    Qin Liu

  14. Information Science and Engineering, Central South University, Changsha, Hunan, China

    Zakirul Alam Bhuiyan

  15. Ludwig Maximilian University of Munich, Munich, Germany

    Karl Fürlinger

  16. Informatik 10 - Rechnertechnik, Technische Universität München, Munich, Germany

    Josef Weidendorfer

  17. High Performance Computing Center (HLRS), Stuttgart, Germany

    José Gracia

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Sozykin, A., Epanchintsev, T., Zverev, V., Khamzin, S., Bersenev, A. (2016). Automated Parallel Simulation of Heart Electrical Activity Using Finite Element Method. In: Carretero, J., et al. Algorithms and Architectures for Parallel Processing. ICA3PP 2016. Lecture Notes in Computer Science(), vol 10049. Springer, Cham. https://doi.org/10.1007/978-3-319-49956-7_29

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  • DOI: https://doi.org/10.1007/978-3-319-49956-7_29

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-49955-0

  • Online ISBN: 978-3-319-49956-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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