Abstract
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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Wan, X., Zhang, F., Chu, Q., Liu, Z. (2011). High-Performance Blob-Based Iterative Reconstruction of Electron Tomography on Multi-GPUs. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_10
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DOI: https://doi.org/10.1007/978-3-642-21260-4_10
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-21259-8
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