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Use of Multiple GPUs to Speedup the Execution of a Three-Dimensional Computational Model of the Innate Immune System

M. P. Xavier, T. M. do Nascimento, R. W. dos Santos, M. Lobosco
FISIOCOMP Lab, Federal University of Juiz de Fora, Brazil
Journal of Physics: Conference Series 490, 012075, 2014

@article{1742-6596-490-1-012075,

   author={M P Xavier and T M do Nascimento and R W dos Santos and M Lobosco},

   title={Use of Multiple GPUs to Speedup the Execution of a Three-Dimensional Computational Model of the Innate Immune System},

   journal={Journal of Physics: Conference Series},

   volume={490},

   number={1},

   pages={012075},

   url={http://stacks.iop.org/1742-6596/490/i=1/a=012075},

   year={2014}

}

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The development of computational systems that mimics the physiological response of organs or even the entire body is a complex task. One of the issues that makes this task extremely complex is the huge computational resources needed to execute the simulations. For this reason, the use of parallel computing is mandatory. In this work, we focus on the simulation of temporal and spatial behaviour of some human innate immune system cells and molecules in a small three-dimensional section of a tissue. To perform this simulation, we use multiple Graphics Processing Units (GPUs) in a shared-memory environment. Despite of high initialization and communication costs imposed by the use of GPUs, the techniques used to implement the HIS simulator have shown to be very effective to achieve this purpose.
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