High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs

Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu
Institute of Computing Technology, Beijing, China
Bioinformatics Research and Applications, Lecture Notes in Computer Science, Volume 6674/2011, 61-72, 2011


   title={High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs},

   author={Wan, X. and Zhang, F. and Chu, Q. and Liu, Z.},

   journal={Bioinformatics Research and Applications},





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Three-dimensional (3D) reconstruction of electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction of ET, but demand huge computational costs. Multiple Graphic processing units (multi-GPUs) offer an affordable platform to meet these demands, nevertheless, are not efficiently used owing to a synchronous communication scheme and the limited available memory of GPUs. We propose a multilevel parallel scheme combined with an asynchronous communication scheme and a blob-ELLR data structure. The asynchronous communication scheme is used to minimize the idle GPU time. The blob-ELLR data structure only needs nearly 1/16 of the storage space in comparison with ELLPACK-R (ELLR) data structure and yields significant acceleration. Experimental results indicate that the multilevel parallel scheme allows efficient implementations of 3D reconstruction of ET on multi-GPUs, without loss any resolution.
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