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Implementation of scalable bidomain-based 3D cardiac simulations on a graphics processing unit cluster

  • Ehsan EsmailiEmail author
  • Ali Akoglu
  • Salim Hariri
  • Talal Moukabary
Article
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Abstract

Computational models of the human cardiac cells provide detailed properties of human ventricular cells. The execution time for a realistic 3D heart simulation based on these models is a major barrier for physicians to study and understand the heart diseases, and evaluate hypotheses rapidly toward developing treatments. Graphics processing unit (GPU)-based parallelization efforts to this date have been shown to be more effective than parallelization efforts on the CPU-based clusters in terms of addressing the 3D cardiac simulation time challenge. In this paper, we review all GPU-based studies and investigate both the cardiac cell models and cardiac tissue models in 3D space. We propose algorithmic optimizations based on red black successive over-relaxation method for reducing the number of simulation iterations and convergence method for dependence elimination between neighboring cells of the heart tissue. We investigate data transfer reduction and 2D mesh partitioning strategies, evaluate their impact on thread utilization, and propose a strongly scalable cardiac simulation. Our implementation results with reducing the execution time by a factor of five compared to the state-of-the-art baseline implementation. More importantly, our implementation is an important step toward achieving real-time cardiac simulations as it achieves the strongest scalability among all other cluster-based implementations.

Keywords

Cardiac simulation Bidomain model Graphics processing unit (GPU) GPU cluster 

Notes

Acknowledgements

This material is based upon the work supported by the National Science Foundation under Grant No. CNS 1624668 I/UCRC: Industry/University Cooperative Research Center for Cloud and Autonomic Computing.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Ehsan Esmaili
    • 1
    Email author
  • Ali Akoglu
    • 1
  • Salim Hariri
    • 1
  • Talal Moukabary
    • 2
  1. 1.Department of Electrical and Computer EngineeringUniversity of ArizonaTucsonUSA
  2. 2.Carondelet Heart and Vascular Institute - Cardiology WestTucsonUSA

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