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研究生: 呂金勳
Lu, Chin-Hsun
論文名稱: 顯卡加速技術於單域心電波方程模擬之應用
GPU Acceleration on the Cardiac Monodomain Simulations
指導教授: 陳旻宏
Chen, Min-Hung
學位類別: 碩士
Master
系所名稱: 理學院 - 數學系應用數學碩博士班
Department of Mathematics
論文出版年: 2018
畢業學年度: 106
語文別: 中文
論文頁數: 30
中文關鍵詞: 單域心電波方程擴散反應方程LR91有限體積法熱方程CUDA平行計算
外文關鍵詞: monodomain electrocardiac wave equation, reaction-diffusion equation, LR91, finite volume method, heat equation, CUDA, parallel computing
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  • 在本篇文章考慮在二維數值格式上模擬心臟細胞組織上的波傳問題並使用平行計算的技術做計算效能的提升,我們考慮的單域心電波方程是一條擴散反應方程,其中闡述心臟細胞離子電流的反應項是以CH Luo和Y Rudy在1991發表的心臟細胞模型所包含的許多條常微分方程式。在建構數值方法時,我們使用二維有限體積法,以三角形網格的中心點為計算單位,用顯示算法去求解。在模型實現上,我們會先使用熱方程作為我們的測試問題並檢驗我們使用的二維有限體積法,再運用CUDA加速計算的技術提升效能,最後實行在單域心電波方程上,並比對其結果與加速效能。

    In this paper, we consider the simulation of wave propagation on cardiac tissue in a two-dimensional numerical format and use parallel computing techniques to improve computational efficiency. The monodomain electrocardiac wave equation we consider is a reaction-diffusion equation. The reaction term of the ionic current is a number of ordinary differential equations contained in the cardiac cell model published by CH Luo and Y Rudy in 1991. When constructing the numerical method, we use the two-dimensional finite volume method, taking the center point of the triangle mesh as the unit of calculation, and using forward Euler method to solve. In the model implementation, we will first use the heat equation as our test problem and test the two-dimensional finite volume method we use, and then use the CUDA to improve the performance, and finally implement the monodomain electrocardiac wave equation and compare it with serial.

    摘要 i 英文延伸摘要 ii 致謝 vi 1 簡介 1 2 心臟細胞膜型與單域心電波方程 3 2.1 Hodgkin-Huxley模型 3 2.2 LR91心臟細胞膜型 3 2.3 單域心電波方程 5 3 有限體積法 6 3.1 熱方程 6 3.2 單域心電波方程 9 4 平行計算與CUDA技術 10 4.1 加速比 10 4.2 CUDA 12 4.3 多卡計算 19 5 數值結果 23 5.1 誤差、收斂階數以及網格 23 5.2 熱方程 24 5.3 LR91 26 5.4 多卡計算 26 6 結論 28 7 參考資料 29

    [1] CH Luo and Y Rudy, "A model of the ventricular cardiac action potential. Depolarization,repolarization,
    and their interaction" Circ. Res. 1991;68;1501-1526
    [2] "A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator."
    https://www.cs.cmu.edu/~quake/triangle.html
    [3] F.Moukalled, L.Mangani and M.Darwish, "The Finite Volume Method in Computational
    Fluid Dynamics, OpenFOAM
    R and Matlab
    R ", Springer 2015
    [4] David M. Harrild and Cralg S. Henriquez, "A Finite Volume Model of Cardiac
    Propagation", Annals of Biomedical Engineering, Vol. 25, pp. 315-334, 1997
    [5] Mark Trew, Ian Le Grice, Bruce Smaill, and Andrew Pullan, "A Finite Volume
    Method for Modeling Discontinuous Electrical Activation in Cardiac Tissue", Annals
    of Biomedical Engineering, Vol. 33, No. 5, May 2005 (
    c 2005) pp. 590–602
    [6] Vincent Jacquemet and Craig S. Henriquez, "Finite Volume Stiffness Matrix for
    Solving Anisotropic Cardiac Propagation in 2-D and 3-D Unstructured Meshes", Ieee
    Transactions On Biomedical Engineering, Vol. 52, No. 8, August 2005
    [7] Yves Coudiere, Charles Pierre, Rodolphe Turpault, "A 2D/3D Finite Volume Method
    used to solve the bidomain equations of electrocardiology", Proceedings of Algoritmy
    2009 pp. 1–10
    [8] Mostafa Bendahmane, Raimund Bürger, Ricardo Ruiz-Baier, "A finite volume
    scheme for cardiac propagation in media with isotropic conductivities", Mathematics
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    [9] A. L. Hodgkin and A. F. Huxley, "A quantitative description of membrane current
    29
    and its application to conduction and excitation in nerve", J Physiol. 1952 Aug 28;
    117(4): 500–544.
    [10] MPI Tutorial
    http://mpitutorial.com/
    [11] cellML
    https://www.cellml.org/
    [12] CUDA Toolkit Documentation
    https://docs.nvidia.com/cuda/

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