High-performance Blob-based iterative reconstruction of electron tomography on multi-GPUs
Institute of Computing Technology, Beijing, China
Bioinformatics Research and Applications, Lecture Notes in Computer Science, Volume 6674/2011, 61-72, 2011
@article{wan2011high,
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},
pages={61–72},
year={2011},
publisher={Springer}
}
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.
November 15, 2011 by hgpu
