Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing

Abstract

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.