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Implementation and performance evaluation of reconstruction algorithms on graphics processors

D. Castanodiez, H. Mueller, A. Frangakis
European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
Journal of Structural Biology, Vol. 157, No. 1. (January 2007), pp. 288-295

@article{castano2007implementation,

   title={Implementation and performance evaluation of reconstruction algorithms on graphics processors},

   author={Casta{~n}o D{‘i}ez, D. and Mueller, H. and Frangakis, A.S.},

   journal={Journal of structural biology},

   volume={157},

   number={1},

   pages={288–295},

   issn={1047-8477},

   year={2007},

   publisher={Elsevier}

}

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The high-throughput needs in electron tomography and in single particle analysis have driven the parallel implementation of several reconstruction algorithms and software packages on computing clusters. Here, we report on the implementation of popular reconstruction algorithms as weighted backprojection, simultaneous iterative reconstruction technique (SIRT) and simultaneous algebraic reconstruction technique (SART) on common graphics processors (GPUs). The speed gain achieved on the GPUs is in the order of sixty (60x) to eighty (80x) times, compared to the performance of a single central processing unit (CPU), which is comparable to the acceleration achieved on a medium-range computing cluster. This acceleration of the reconstruction is caused by the highly specialized architecture of the GPU. Further, we show that the quality of the reconstruction on the GPU is comparable to the CPU. We present detailed flow-chart diagrams of the implementation. The reconstruction software does not require special hardware apart from the commercially available graphics cards and could be easily integrated in software packages like SPIDER, XMIPP, TOM-Package and others.
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