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Performance Evaluation of BLAST on SMP Machines

  • Conference paper
Frontiers of High Performance Computing and Networking – ISPA 2006 Workshops (ISPA 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4331))

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Abstract

BLAST is a tool for finding biologically similar sequences to given query sequences in annotated sequence database. Since the number of sequences in the database increases at exponential rate, and the number of users drastically increases, the performance of BLAST is a primary concern to service sites like NCBI. NCBI developed a parallel BLAST for the speedup of BLAST using threads on SMP machines. But the speedup is still limited due to the architectural limitations of SMP machines. Distributed memory multiprocessor can be an alternative choice for cost-effective search in very large scale sequence data. However for an optimized configuration of Cluster systems and SMP machines, the performance study of BLAST on SMP machines is essential. In this paper, we analyze BLAST and BLAST algorithms to enhance the performance of BLAST on parallel machines and report the performance of BLAST on SMP machines. Some important runtime characteristics of BLAST are identified through the performance evaluation. According to our performance test, PC clusters or clusters of low-way SMP machines outperform high-way SMP machines in terms of cost-effectiveness. Besides, BLAST on Linux operating system shows better performance than BLAST on Solaris operating system in the same configurations.

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Author information

Authors and Affiliations

  1. School of Engineering, Information and Communications University, 119 Munjiro, Yuseong-Gu, Daejeon, 305-600, Korea

    Hong-Soog Kim, Hae-Jin Kim & Dong-Soo Han

  2. Electronics and Telecommunications Research Institute, 161 Gajeong-dong, Yusong-Gu, Daejeon, 305-350, Korea

    Hong-Soog Kim

Authors
  1. Hong-Soog Kim
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  2. Hae-Jin Kim
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  3. Dong-Soo Han
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Editor information

Editors and Affiliations

  1. Department of Computing, School of Informatics, University of Bradford, BD7 1DP, Bradford, U.K.

    Geyong Min

  2. Dipartimento di Ingegneria dell’ Informazione - Second, University of Naples - Italy, Real Casa dell’Annunziata - via Roma, 29 81031, Aversa (CE), Italy

    Beniamino Di Martino

  3. Department of Computer Science, St. Francis Xavier University, Antigonish, Canada

    Laurence T. Yang

  4. Department of Computer Science and Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China

    Minyi Guo

  5. Department of Computer Science, Chemnitz University of Technology, Germany

    Gudula Rünger

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© 2006 Springer-Verlag Berlin Heidelberg

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Kim, HS., Kim, HJ., Han, DS. (2006). Performance Evaluation of BLAST on SMP Machines. In: Min, G., Di Martino, B., Yang, L.T., Guo, M., Rünger, G. (eds) Frontiers of High Performance Computing and Networking – ISPA 2006 Workshops. ISPA 2006. Lecture Notes in Computer Science, vol 4331. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11942634_69

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  • DOI: https://doi.org/10.1007/11942634_69

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-49860-5

  • Online ISBN: 978-3-540-49862-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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