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

Xiaohua Wan*, Fa Zhang, Qi Chu, Zhiyong Liu

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Citations (Scopus)

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.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings
Pages61-72
Number of pages12
DOIs
Publication statusPublished - 2011
Externally publishedYes
Event7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011 - Changsha, China
Duration: 27 May 201129 May 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6674 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011
Country/TerritoryChina
CityChangsha
Period27/05/1129/05/11

Keywords

  • blob
  • electron tomography (ET)
  • iterative methods
  • multi-GPUs
  • three-dimensional (3D) reconstruction

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