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A Comprehensive Comparison of GPU Implementations of Cardiac Electrophysiology Models

  • Abouzar KaboudianEmail author
  • Hector Augusto Velasco-Perez
  • Shahriar Iravanian
  • Yohannes Shiferaw
  • Elizabeth M. Cherry
  • Flavio H. Fenton
Chapter
First Online:
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11500)

Abstract

Cardiac disease is the leading cause of death in developed countries, and arrhythmias, which are disorders in the regular generation and propagation of electrical waves that trigger contraction, form a major class of heart diseases. Computational techniques have proved to be useful in the study and understanding of cardiac arrhythmias. However, the computational cost associated with solving cardiac models makes them especially challenging to solve. Traditionally, hardware available on personal computers has been insufficient for such models; instead, supercomputers have been employed to overcome the computational costs of cardiac simulations. However, in recent years substantial advances in the computational power of graphics processing units (GPUs), combined with their modest prices and widespread availability, have made them an attractive alternative to high-performance computing using supercomputers. With greater use of GPUs, however, new challenges have emerged. GPUs must be programmed using their own languages or extensions of other languages, and, at present, there are a number of languages that support general-purpose GPU codes with substantial differences in programming ease and available levels of optimization. In this work, we present the implementation of cardiac models in several major GPU languages without language-specific optimization and compare their performance for different levels of model complexity and domain sizes.

Keywords

Cardiac electrophysiology GPU MATLAB OpenACC Python Numba TensorFlow WebGL Abubu.js NVIDIA CUDA 
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Notes

Acknowledgements

This work was supported in part by the National Science Foundation under grants CNS-1446312(EMC) and by CMMI-1762553 (FHF and AK). EMC, AK, YS, and FHF, also collaborated while at Kavli Institute for Theoretical Physics (KITP) and thus research was also supported in part by NSF Grant No. PHY-1748958, NIH Grant No. R25GM067110, and the Gordon and Betty Moore Foundation Grant No. 2919.01.

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Abouzar Kaboudian
    • 1
    Email author
  • Hector Augusto Velasco-Perez
    • 1
  • Shahriar Iravanian
    • 2
  • Yohannes Shiferaw
    • 3
  • Elizabeth M. Cherry
    • 1
    • 4
  • Flavio H. Fenton
    • 1
  1. 1.Georgia Institute of TechnologyAtlantaUSA
  2. 2.Emory UniversityAtlantaUSA
  3. 3.California State UniversityNorthridgeUSA
  4. 4.Rochester Institute of TechnologyRochesterUSA

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