Exploring I/O strategies for parallel sequence-search tools with S3aSim

Avery Chingt, Wu Chun Feng, Heshan Lin, Xiaosong Ma, Alok Choudhary

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

10 Citations (Scopus)

Abstract

Parallel sequence-search tools are rising in popularity among computational biologists. With the rapid growth of sequence databases, database segmentation is the trend of the future for such search tools. While I/O currently is not a significant bottleneck for parallel sequence-search tools, future technologies including faster processors, customized computational hardware such as FPGAs, improved search algorithms, and exponentially growing databases will emphasize an increasing need for efficient parallel I/O in future parallel sequence-search tools. Our paper focuses on examining different I/O strategies for these future tools in a modern parallel file system (PVFS2). Because implementing and comparing various I/O algorithms in every search tool is labor-intensive and time-consuming, we introduce S3aSim, a general simulation framework for sequence-search which allows us to quickly implement, test, and profile various I/O strategies. We examine a variety of I/O strategies (e.g., master-writing and various worker-writing strategies using individual and collective I/O methods) for storing result data in sequence-search tools such as mpiBLAST, pioBLAST, and parallel HMMer. Our experiments fully detail the interaction of computing and I/O within a full application simulation as opposed to typical I/O-only benchmarks.

Original languageEnglish
Title of host publicationProceedings of the IEEE International Symposium on High Performance Distributed Computing
Pages229-240
Number of pages12
Volume2006
Publication statusPublished - 1 Dec 2006
Externally publishedYes
Event15th IEEE International Symposium on High Performance Distributed Computing, HPDC-15 - Paris, France
Duration: 19 Jun 200623 Jun 2006

Other

Other15th IEEE International Symposium on High Performance Distributed Computing, HPDC-15
CountryFrance
CityParis
Period19/6/0623/6/06

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ASJC Scopus subject areas

  • Engineering(all)

Cite this

Chingt, A., Feng, W. C., Lin, H., Ma, X., & Choudhary, A. (2006). Exploring I/O strategies for parallel sequence-search tools with S3aSim. In Proceedings of the IEEE International Symposium on High Performance Distributed Computing (Vol. 2006, pp. 229-240). [1652154]