Automated Parallel Simulation of Heart Electrical Activity Using Finite Element Method

详细信息    查看全文

• 关键词：Heart simulation ; Finite element method ; Scalability ; Krylov subspace methods ; FEniCS ; Parallel computing
• 刊名：Lecture Notes in Computer Science
• 出版年：2016
• 出版时间：2016
• 年：2016
• 卷：10049
• 期：1
• 页码：365-372
• 丛书名：Algorithms and Architectures for Parallel Processing
• ISBN：978-3-319-49956-7
• 卷排序：10049

文摘

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.