Simulating cardiac electrophysiology in the era of GPU-cluster computing
J Chai, M Wen, N Wu, D Huang, J Yang… - … on Information and …, 2013 - search.ieice.org
J Chai, M Wen, N Wu, D Huang, J Yang, X Cai, C Zhang, Q Yang
IEICE TRANSACTIONS on Information and Systems, 2013•search.ieice.orgThis 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 0.1 mm spatial resolution, a 128-GPU cluster
only needs a few minutes to carry out a 100,000-time-step cardiac excitation simulation that …
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 0.1 mm spatial resolution, a 128-GPU cluster
only needs a few minutes to carry out a 100,000-time-step cardiac excitation simulation that …
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.
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