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Automated Parallel Simulation of Heart Electrical Activity Using Finite Element Method

  • Andrey SozykinEmail author
  • Timofei Epanchintsev
  • Vladimir Zverev
  • Svyatoslav Khamzin
  • Aleksandr Bersenev
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10049)

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.

Keywords

Heart simulation Finite element method Scalability Krylov subspace methods FEniCS Parallel computing 

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Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  • Andrey Sozykin
    • 1
    • 2
    • 3
    Email author
  • Timofei Epanchintsev
    • 1
    • 2
    • 3
  • Vladimir Zverev
    • 1
    • 3
  • Svyatoslav Khamzin
    • 2
    • 3
  • Aleksandr Bersenev
    • 1
    • 3
  1. 1.Krasovskii Institute of Mathematics and MechanicsEkaterinburgRussia
  2. 2.Institute of Immunology and Physiology UrB RASEkaterinburgRussia
  3. 3.Ural Federal UniversityEkaterinburgRussia

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