Publication
Title
Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)
Author
Abstract
Iterative reconstruction algorithms are becoming increasingly important in electron tomography of biological samples. These algorithms, however, impose major computational demands. Parallelization must be employed to maintain acceptable running times. Graphics Processing Units (GPUs) have been demonstrated to be highly cost-effective for carrying out these computations with a high degree of parallelism. In a recent paper by Xu et al. (2010), a GPU implementation strategy was presented that obtains a speedup of an order of magnitude over a previously proposed GPU-based electron tomography implementation. In this technical note, we demonstrate that by making alternative design decisions in the GPU implementation, an additional speedup can be obtained, again of an order of magnitude. By carefully considering memory access locality when dividing the workload among blocks of threads, the GPUs cache is used more efficiently, making more effective use of the available memory bandwidth.
Language
English
Source (journal)
Journal of structural biology. - New York
Publication
New York : 2011
ISSN
1047-8477
Volume/pages
176:2(2011), p. 250-253
ISI
000295904200013
Full text (Publishers DOI)
Full text (publishers version - intranet only)
UAntwerpen
Faculty/Department
Research group
Publication type
Subject
Affiliation
Publications with a UAntwerp address
External links
Web of Science
Record
Identification
Creation 23.08.2011
Last edited 13.04.2017
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