Performance evaluation of BLAST on SMP machines

  • Authors:

  • Hong-Soog Kim;Hae-Jin Kim;Dong-Soo Han

  • Affiliations:

  • School of Engineering, Information and Communications University, Daejeon, Korea;School of Engineering, Information and Communications University, Daejeon, Korea;School of Engineering, Information and Communications University, Daejeon, Korea

  • Venue:
  • ISPA'06 Proceedings of the 2006 international conference on Frontiers of High Performance Computing and Networking
  • Year:
  • 2006

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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.