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Acceleration of cardiac tissue simulation with graphic processing units

Daisuke Sato, Yuanfang Xie, James Weiss, Zhilin Qu, Alan Garfinkel, Allen Sanderson
Cardiovascular Research Laboratory, Departments of Medicine (Cardiology), David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
Medical and Biological Engineering and Computing, Volume 47, Number 9, 1011-1015

@article{sato2009acceleration,

   title={Acceleration of cardiac tissue simulation with graphic processing units},

   author={Sato, D. and Xie, Y. and Weiss, J.N. and Qu, Z. and Garfinkel, A. and Sanderson, A.R.},

   journal={Medical and Biological Engineering and Computing},

   volume={47},

   number={9},

   pages={1011–1015},

   issn={0140-0118},

   year={2009},

   publisher={Springer}

}

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In this technical note we show the promise of using graphic processing units (GPUs) to accelerate simulations of electrical wave propagation in cardiac tissue, one of the more demanding computational problems in cardiology. We have found that the computational speed of two-dimensional (2D) tissue simulations with a single commercially available GPU is about 30 times faster than with a single 2.0 GHz Advanced Micro Devices (AMD) Opteron processor. We have also simulated wave conduction in the three-dimensional (3D) anatomic heart with GPUs where we found the computational speed with a single GPU is 1.6 times slower than with a 32-central processing unit (CPU) Opteron cluster. However, a cluster with two or four GPUs is faster than the CPU-based cluster. These results demonstrate that a commodity personal computer is able to perform a whole heart simulation of electrical wave conduction within times that enable the investigators to interact more easily with their simulations.
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