GPU enhanced simulation of angiogenesis

• Autorzy: Worecki M. , Wcisło R.
• Języki publikacji: EN

Abstrakty

EN

In the paper we present the use of graphic processor units to accelerate the most time-consuming stages of a simulation of angiogenesis and tumor growth. By the use of advanced CUDA mechanisms such as shared memory, textures and atomic operations, we managed to speed up the CUDA kernels by a factor of 57x. However, in our simulation we used the GPU as a co-processor and data from CPU was copied back and forth in each phase. It decreased the speedup of rewritten stages by 40%. We showed that the performance of the entire simulation can be improved by a factor of 10 up to 20.

Słowa kluczowe

EN

GPU; angiogenesis; tumor

• Wydawca: Wydawnictwa AGH
• Czasopismo: Computer Science
• Rocznik: 2012
• Tom: Vol. 13 (1)
• Strony: 35--48
• Opis fizyczny: Bibliogr. 9 poz., rys., wykr.

Twórcy

autor

Worecki M.

• AGH University of Science and Technology, Department of Computer Science, Krakow, Poland

autor

Wcisło R.

• AGH University of Science and Technology, Department of Computer Science, Krakow, Poland

Bibliografia

• [1] Anderson J. A., Lorenz C. D., Travesset A.: General purpose molecular dynamics simulations fully implemented on graphics processing units. Journal of Computational Physics February, 2008.
• [2] Aubert M., Chaplain M. A., McDougall S.R., Devlin A., Mitchell C.A.: A Continuum Mathematical Model of the Developing MurineRetinal Vasculature. Bulletin of Mathematical Biology, 2011.
• [3] Green S.: Particle Simulation using CUDA. NVIDIA, 2010.
• [4] Li W., Hutnik M., Smith R., Li V.: Understanding angiogenesis. [online], 2011. http://www.angio.org/ua.php
• [5] Nguyen H.: GPU Gems 3. Addison-Wesley Professional, 2007. Chapter 31, Fast N-Body Simulation with CUDA.
• [6] NVIDIA.: CUDA C Programming Guide. NVIDIA, 2010.
• [7] Shirinifard A., Gens J. S., Zaitlen B. L., Popawski N. J., Swat M., Glazier J. A.:. 3D Multi-Cell Simulation of Tumor Growth and Angiogenesis. Public Library of Science, 2009.
• [8] van Meel J. A., Arnold A., Frenkel D., Zwart S .F.P., Belleman R.G.: Harvesting graphics power for MD simulations. Molecular Simulation, 34: 3, pp. 259–266, 2008.
• [9] Wcislo R., Dzwinel W., Yuen D. A., Dudek, A. Z.: A 3-D model of tumor progression based on complex automata driven by particle dynamics. Journal of Molecular Modeling, 2009.