Cardiac simulation on multi-GPU platform

Authors:
Venkata Krishna Nimmagadda;Ali Akoglu;Salim Hariri;Talal Moukabary
Affiliations:
Department of Electrical and Computer Engineering, University of Arizona, Tucson, USA 85721;Department of Electrical and Computer Engineering, University of Arizona, Tucson, USA 85721;Department of Electrical and Computer Engineering, University of Arizona, Tucson, USA 85721;Sarver Heart Center, College of Medicine, University of Arizona, Tucson, USA 85721
Venue:
The Journal of Supercomputing
Year:
2012

Citing 1
Cited 3

3D finite difference computation on GPUs using CUDA

Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units

A GPU implementation of a structural-similarity-based aerial-image classification

The Journal of Supercomputing
Adaptive step ODE algorithms for the 3D simulation of electric heart activity with graphics processing units

Computers in Biology and Medicine
Recent progress and challenges in exploiting graphics processors in computational fluid dynamics

The Journal of Supercomputing

Quantified Score

Hi-index	0.00

Visualization

Abstract

The cardiac bidomain model is a popular approach to study electrical behavior of tissues and simulate interactions between the cells by solving partial differential equations. The iterative and data parallel model is an ideal match for the parallel architecture of Graphic Processing Units (GPUs). In this study, we evaluate the effectiveness of architecture-specific optimizations and fine grained parallelization strategies, completely port the model to GPU, and evaluate the performance of single-GPU and multi-GPU implementations. Simulating one action potential duration (350 msec real time) for a 256脳256脳256 tissue takes 453 hours on a high-end general purpose processor, while it takes 664 seconds on a four-GPU based system including the communication and data transfer overhead. This drastic improvement (a factor of 2460脳) will allow clinicians to extend the time-scale of simulations from milliseconds to seconds and minutes; and evaluate hypotheses in a shorter amount of time that was not feasible previously.