IEICE TRANSACTIONS on Information
Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing
Summary :
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.
- Publication
- IEICE TRANSACTIONS on Information Vol.E96-D No.12 pp.2587-2595
- Publication Date
- 2013/12/01
- Publicized
- Online ISSN
- 1745-1361
- DOI
- 10.1587/transinf.E96.D.2587
- Type of Manuscript
- Special Section PAPER (Special Section on Parallel and Distributed Computing and Networking)
- Category
Authors
Jun CHAI
National University of Defense Technology
Mei WEN
National University of Defense Technology
Nan WU
National University of Defense Technology
Dafei HUANG
National University of Defense Technology
Jing YANG
National University of Defense Technology
Xing CAI
University of Oslo
Chunyuan ZHANG
National University of Defense Technology
Qianming YANG
National University of Defense Technology
Keyword
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Jun CHAI, Mei WEN, Nan WU, Dafei HUANG, Jing YANG, Xing CAI, Chunyuan ZHANG, Qianming YANG, "Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing" in IEICE TRANSACTIONS on Information,
vol. E96-D, no. 12, pp. 2587-2595, December 2013, doi: 10.1587/transinf.E96.D.2587.
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.
URL: https://global.ieice.org/en_transactions/information/10.1587/transinf.E96.D.2587/_p
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@ARTICLE{e96-d_12_2587,
author={Jun CHAI, Mei WEN, Nan WU, Dafei HUANG, Jing YANG, Xing CAI, Chunyuan ZHANG, Qianming YANG, },
journal={IEICE TRANSACTIONS on Information},
title={Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing},
year={2013},
volume={E96-D},
number={12},
pages={2587-2595},
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.},
keywords={},
doi={10.1587/transinf.E96.D.2587},
ISSN={1745-1361},
month={December},}
Copy
TY - JOUR
TI - Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing
T2 - IEICE TRANSACTIONS on Information
SP - 2587
EP - 2595
AU - Jun CHAI
AU - Mei WEN
AU - Nan WU
AU - Dafei HUANG
AU - Jing YANG
AU - Xing CAI
AU - Chunyuan ZHANG
AU - Qianming YANG
PY - 2013
DO - 10.1587/transinf.E96.D.2587
JO - IEICE TRANSACTIONS on Information
SN - 1745-1361
VL - E96-D
IS - 12
JA - IEICE TRANSACTIONS on Information
Y1 - December 2013
AB - 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.
ER -
English
