Algebraic multigrid preconditioner for the cardiac bidomain model.
The bidomain equations are considered to be one of the most complete descriptions of the electrical activity in cardiac tissue, but large scale simulations, as resulting from discretization of an entire heart, remain a computational challenge due to the elliptic portion of the problem, the part associated with solving the extracellular potential. In such cases, the use of iterative solvers and parallel computing environments are mandatory to make parameter studies feasible. The preconditioned conjugate gradient (PCG) method is a standard choice for this problem. Although robust, its efficiency greatly depends on the choice of preconditioner. On structured grids, it has been demonstrated that a geometric multigrid preconditioner performs significantly better than an incomplete LU (ILU) preconditioner. However, unstructured grids are often preferred to better represent organ boundaries and allow for coarser discretization in the bath far from cardiac surfaces. Under these circumstances, algebraic multigrid (AMG) methods are advantageous since they compute coarser levels directly from the system matrix itself, thus avoiding the complexity of explicitly generating coarser, geometric grids. In this paper, the performance of an AMG preconditioner (BoomerAMG) is compared with that of the standard ILU preconditioner and a direct solver. BoomerAMG is used in two different ways, as a preconditioner and as a standalone solver. Two 3-D simulation examples modeling the induction of arrhythmias in rabbit ventricles were used to measure performance in both sequential and parallel simulations. It is shown that the AMG preconditioner is very well suited for the solution of the bidomain equation, being clearly superior to ILU preconditioning in all regards, with speedups by factors in the range 5.9-7.7.
Plank
Gernot
G
Institute of Biophysics, Center for Physiological Medicine, Medical University Graz, Harrachgasse 21, A-8010 Graz, Austria. gernot.plank@meduni-graz.at
Liebmann
Manfred
M
Weber dos Santos
Rodrigo
R
Vigmond
Edward J
EJ
Haase
Gundolf
G
D000200:Action Potentials; D000465:Algorithms; D000818:Animals; D001145:Arrhythmias, Cardiac / Q000503:physiopathology*; D018780:Body Surface Potential Mapping / Q000379:methods*; D003198:Computer Simulation; D003936:Diagnosis, Computer-Assisted / Q000379:methods; D006329:Heart Conduction System / Q000503:physiopathology*; D008955:Models, Cardiovascular; D009716:Numerical Analysis, Computer-Assisted; D011817:Rabbits