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Accelerating multiple sequence alignment with the cell BE processor

Hans Vandierendonck UGent, Sean Rul UGent and Koen De Bosschere UGent (2009) COMPUTER JOURNAL. 53(6). p.814-826
abstract
The Cell Broadband Engine (BE) Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, most notably the extensive support for vectorization, scratch pad memories and explicit programming of direct memory accesses (DMAs) and mailbox communication. While these features strongly increase programming complexity, it is generally claimed that significant speedups can be obtained by using Cell BE processors. This paper presents our experiences with using the Cell BE architecture to accelerate Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is in obtaining high performance. By making extensive use of vectorization and by parallelizing the application across all cores, we demonstrate a speedup of 24.4 times when using 16 synergistic processor units on a QS21 Cell Blade compared to single-thread execution on the power processing unit. As the Cell BE exploits a large number of slim cores, our highly optimized implementation is just 3.8 times faster than a 3-thread version running on an Intel Core2 Duo, as the latter processor exploits a small number of fat cores.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
cell broadband engine, bio-informatics, parallelization
journal title
COMPUTER JOURNAL
Comput. J.
volume
53
issue
6
pages
814 - 826
Web of Science type
Article
Web of Science id
000279185400014
JCR category
COMPUTER SCIENCE, HARDWARE & ARCHITECTURE
JCR impact factor
1.394 (2009)
JCR rank
17/48 (2009)
JCR quartile
2 (2009)
ISSN
0010-4620
1460-2067
DOI
10.1093/comjnl/bxp086
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
749808
handle
http://hdl.handle.net/1854/LU-749808
date created
2009-09-17 15:26:34
date last changed
2012-10-31 14:47:56
@article{749808,
  abstract     = {The Cell Broadband Engine (BE) Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, most notably the extensive support for vectorization, scratch pad memories and explicit programming of direct memory accesses (DMAs) and mailbox communication. While these features strongly increase programming complexity, it is generally claimed that significant speedups can be obtained by using Cell BE processors. This paper presents our experiences with using the Cell BE architecture to accelerate Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is in obtaining high performance. By making extensive use of vectorization and by parallelizing the application across all cores, we demonstrate a speedup of 24.4 times when using 16 synergistic processor units on a QS21 Cell Blade compared to single-thread execution on the power processing unit. As the Cell BE exploits a large number of slim cores, our highly optimized implementation is just 3.8 times faster than a 3-thread version running on an Intel Core2 Duo, as the latter processor exploits a small number of fat cores.},
  author       = {Vandierendonck, Hans and Rul, Sean and De Bosschere, Koen},
  issn         = {0010-4620},
  journal      = {COMPUTER JOURNAL},
  keyword      = {cell broadband engine,bio-informatics,parallelization},
  language     = {eng},
  number       = {6},
  pages        = {814--826},
  title        = {Accelerating multiple sequence alignment with the cell BE processor},
  url          = {http://dx.doi.org/10.1093/comjnl/bxp086},
  volume       = {53},
  year         = {2009},
}

Chicago
Vandierendonck, Hans, Sean Rul, and Koen De Bosschere. 2009. “Accelerating Multiple Sequence Alignment with the Cell BE Processor.” Computer Journal 53 (6): 814–826.
APA
Vandierendonck, H., Rul, S., & De Bosschere, K. (2009). Accelerating multiple sequence alignment with the cell BE processor. COMPUTER JOURNAL, 53(6), 814–826.
Vancouver
1.
Vandierendonck H, Rul S, De Bosschere K. Accelerating multiple sequence alignment with the cell BE processor. COMPUTER JOURNAL. 2009;53(6):814–26.
MLA
Vandierendonck, Hans, Sean Rul, and Koen De Bosschere. “Accelerating Multiple Sequence Alignment with the Cell BE Processor.” COMPUTER JOURNAL 53.6 (2009): 814–826. Print.