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The CUBLAS and CULA based GPU acceleration of adaptive finite element framework for bioluminescence tomography

Bo Zhang, Xiang Yang, Fei Yang, Xin Yang, Chenghu Qin, Dong Han, Xibo Ma, Kai Liu, Jie Tian
Sino-Dutch Biomedical and Information Engineering School of Northeastern University, Shenyang, 110004, China
Opt. Express, Vol. 18, No. 19. (13 September 2010), pp. 20201-20214.

@article{zhang2010cublas,

   title={The CUBLAS and CULA based GPU acceleration of adaptive finite element framework for bioluminescence tomography},

   author={Zhang, B. and Yang, X. and Yang, F. and Yang, X. and Qin, C. and Han, D. and Ma, X. and Liu, K. and Tian, J.},

   journal={Optics Express},

   volume={18},

   number={19},

   pages={20201–20214},

   issn={1094-4087},

   year={2010},

   publisher={Optical Society of America}

}

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In molecular imaging (MI), especially the optical molecular imaging, bioluminescence tomography (BLT) emerges as an effective imaging modality for small animal imaging. The finite element methods (FEMs), especially the adaptive finite element (AFE) framework, play an important role in BLT. The processing speed of the FEMs and the AFE framework still needs to be improved, although the multi-thread CPU technology and the multi CPU technology have already been applied. In this paper, we for the first time introduce a new kind of acceleration technology to accelerate the AFE framework for BLT, using the graphics processing unit (GPU). Besides the processing speed, the GPU technology can get a balance between the cost and performance. The CUBLAS and CULA are two main important and powerful libraries for programming on NVIDIA GPUs. With the help of CUBLAS and CULA, it is easy to code on NVIDIA GPU and there is no need to worry about the details about the hardware environment of a specific GPU. The numerical experiments are designed to show the necessity, effect and application of the proposed CUBLAS and CULA based GPU acceleration. From the results of the experiments, we can reach the conclusion that the proposed CUBLAS and CULA based GPU acceleration method can improve the processing speed of the AFE framework very much while getting a balance between cost and performance.
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