Performance analysis of IBM Cell Broadband Engine on sequence alignment

Yang Song, Gregory M. Striemer, Ali Akoglu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

The Smith-Waterman (SW) algorithm is the most accurate sequence alignment approach used by computational biologists for DNA matching. However it's computational complexity makes SW impractical to use in clinical environment compared to much faster but less accurate sequence alignment technique such as BLAST. High performance computing community is examining alternative multi core architectures such as IBM Cell Broadband Engine (BE) and Graphics Processing Units (GPUs) that address the limitations of modern cache-based designs. In this paper we investigate the performance of IBM Cell BE architecture in the context of SW. We present an analysis on architectural features of the Cell BE, study the architecture's fitness for accelerating sequence alignment based on its parallel processing power, interconnect structure and communication protocols among the processing cores. We then evaluate the performance of Cell BE against the state of art implementation of SW on NVIDIA's Tesla GPU. Results show that based on the memory architecture of the SW algorithm, Cell BE performs much better than Tesla GPU in terms of both cycle count and execution time metrics. Compared to purely serial implementation, in terms of cycle count, while state of the art GPU implementation delivers 15x speedup, our solution achieves 64x speedup.

Original languageEnglish (US)
Title of host publicationProceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009
Pages439-446
Number of pages8
DOIs
StatePublished - Dec 1 2009
Event2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009 - San Francisco, CA, United States
Duration: Jul 29 2009Aug 1 2009

Publication series

NameProceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009

Other

Other2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009
CountryUnited States
CitySan Francisco, CA
Period7/29/098/1/09

ASJC Scopus subject areas

  • Hardware and Architecture
  • Control and Systems Engineering

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    Song, Y., Striemer, G. M., & Akoglu, A. (2009). Performance analysis of IBM Cell Broadband Engine on sequence alignment. In Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009 (pp. 439-446). [5325421] (Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009). https://doi.org/10.1109/AHS.2009.16