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GPU Enhanced Simulation of Angiogenesis

Marcin Worecki, Rafal Wcislo
AGH University of Science and Technology, Department of Computer Science, Krakow, Poland
Computer Science, 13 (1). pp. 35-48. ISSN 1508-2806, 2012

@article{worecki2012gpu,

   title={GPU ENHANCED SIMULATION OF ANGIOGENESIS},

   author={Worecki, M. and Wcislo, R.},

   journal={Computer},

   volume={13},

   pages={1},

   year={2012}

}

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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.
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