Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing

Jun CHAI  Mei WEN  Nan WU  Dafei HUANG  Jing YANG  Xing CAI  Chunyuan ZHANG  Qianming YANG  

IEICE TRANSACTIONS on Information and Systems   Vol.E96-D   No.12   pp.2587-2595
Publication Date: 2013/12/01
Online ISSN: 1745-1361
DOI: 10.1587/transinf.E96.D.2587
Print ISSN: 0916-8532
Type of Manuscript: Special Section PAPER (Special Section on Parallel and Distributed Computing and Networking)
GPU cluster,  simulation of cardiac electrophysiology,  high resolution,  monodomain equation,  cardiac cell model,  

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This paper presents a study of the applicability of clusters of GPUs to high-resolution 3D simulations of cardiac electrophysiology. By experimenting with representative cardiac cell models and ODE solvers, in association with solving the monodomain equation, we quantitatively analyze the obtainable computational capacity of GPU clusters. It is found that for a 501×501×101 3D mesh, which entails a 0.1mm spatial resolution, a 128-GPU cluster only needs a few minutes to carry out a 100,000-time-step cardiac excitation simulation that involves a four-variable cell model. Even higher spatial and temporal resolutions are achievable for such simplified mathematical models. On the other hand, our experiments also show that a dramatically larger cluster of GPUs is needed to handle a very detailed cardiac cell model.