High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs

doi:10.1186/1471-2105-13-S10-S4

	High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs
	Wan,Xiaohua 1,2; Zhang,Fa 1; Chu,Qi 1,2; Liu,Zhiyong 1
	2012-06-25
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	13 期号:Suppl 10
摘要	AbstractBackgroundThree-dimensional (3D) reconstruction in 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 in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a synchronous communication scheme between multi-GPUs leads to idle GPU time, and a weighted matrix involved in iterative methods cannot be loaded into GPUs especially for large images due to the limited available memory of GPUs.ResultsIn this paper we propose a multilevel parallel strategy combined with an asynchronous communication scheme and a blob-ELLR data structure to efficiently perform blob-based iterative reconstructions on multi-GPUs. The asynchronous communication scheme is used to minimize the idle GPU time so as to asynchronously overlap communications with computations. 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.ConclusionsExperimental results indicate that the multilevel parallel scheme combined with the asynchronous communication scheme and the blob-ELLR data structure allows efficient implementations of 3D reconstruction in ET on multi-GPUs.
DOI	10.1186/1471-2105-13-S10-S4
语种	英语
WOS记录号	BMC:10.1186/1471-2105-13-S10-S4
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4012
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhang,Fa; Liu,Zhiyong
作者单位	1.Institute of Computing Technology and Key Lab of Intelligent Information Processing 2.Graduate University; Chinese Academy of Sciences
推荐引用方式 GB/T 7714	Wan,Xiaohua,Zhang,Fa,Chu,Qi,et al. High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs[J]. BMC Bioinformatics,2012,13(Suppl 10).
APA	Wan,Xiaohua,Zhang,Fa,Chu,Qi,&Liu,Zhiyong.(2012).High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs.BMC Bioinformatics,13(Suppl 10).
MLA	Wan,Xiaohua,et al."High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs".BMC Bioinformatics 13.Suppl 10(2012).