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Evaluating the use of GPUs in liver image segmentation and HMMER database searches

J. P. Walters, V. Balu, S. Kompalli, V. Chaudhary
Department of Computer Science and Engineering, University at Buffalo, SUNY, Buffalo, NY
Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on In IEEE International Symposium on Parallel & Distributed Processing (IPDPS’09) (2009), pp. 1-12

@conference{walters2009evaluating,

   title={Evaluating the use of GPUs in liver image segmentation and HMMER database searches},

   author={Walters, J.P. and Balu, V. and Kompalli, S. and Chaudhary, V.},

   booktitle={Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on},

   pages={1–12},

   issn={1530-2075},

   year={2009},

   organization={IEEE}

}

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In this paper we present the results of parallelizing two life sciences applications, Markov random fields-based (MRF) liver segmentation and HMMER’s Viterbi algorithm, using GPUs. We relate our experiences in porting both applications to the GPU as well as the techniques and optimizations that are most beneficial. The unique characteristics of both algorithms are demonstrated by implementations on an NVIDIA 8800 GTX Ultra using the CUDA programming environment. We test multiple enhancements in our GPU kernels in order to demonstrate the effectiveness of each strategy. Our optimized MRF kernel achieves over 130times speedup, and our hmmsearch implementation achieves up to 38times speedup. We show that the differences in speedup between MRF and hmmsearch is due primarily to the frequency at which the hmmsearch must read from the GPU’s DRAM.
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