메뉴 건너뛰기




Volumn 38, Issue 8, 2012, Pages 344-364

Investigation into scaling I/O bound streaming applications productively with an all-FPGA cluster

Author keywords

BLAST; FPGA; High performance computing; Network On Chip; Reconfigurable Computing; System On Chip

Indexed keywords

BLAST; HIGH PERFORMANCE COMPUTING; NETWORK ON CHIP; RECONFIGURABLE COMPUTING; SYSTEM ON CHIPS;

EID: 84862705598     PISSN: 01678191     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.parco.2011.12.002     Document Type: Article
Times cited : (2)

References (67)
  • 13
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino-acid sequence of two proteins
    • S.B. Needleman, and C.D. Wunsch A general method applicable to the search for similarities in the amino-acid sequence of two proteins J. Mol. Biol. 48 1972 443 453
    • (1972) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 14
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • T. Smith, and M.S. Waterman Identification of common molecular subsequences J. Mol. Biol. 147 1981 195 197
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.1    Waterman, M.S.2
  • 19
    • 32744475601 scopus 로고    scopus 로고
    • N.U. Services
    • N.U. Services, GenBank Overview, 2005, .
    • (2005) GenBank Overview
  • 23
    • 35748958091 scopus 로고    scopus 로고
    • Single pass streaming BLAST on FPGAs
    • DOI 10.1016/j.parco.2007.09.003, PII S0167819107001032, High-Performance Computing Using Accelerators
    • M.C. Herbordt, J. Model, B. Sukhwani, Y. Gu, and T. VanCourt Single pass streaming BLAST on FPGAs Parallel Comput. 33 10-11 2007 741 756 (Pubitemid 350051062)
    • (2007) Parallel Computing , vol.33 , Issue.10-11 , pp. 741-756
    • Herbordt, M.C.1    Model, J.2    Sukhwani, B.3    Gu, Y.4    VanCourt, T.5
  • 29
    • 13244298267 scopus 로고    scopus 로고
    • SS-Wrapper: A package of wrapper applications for similarity searches on linux clusters
    • C. Wang, and E. Lefkowitz SS-Wrapper: a package of wrapper applications for similarity searches on linux clusters Bioinformatics 2004 5
    • (2004) Bioinformatics , pp. 5
    • Wang, C.1    Lefkowitz, E.2
  • 30
    • 13244259261 scopus 로고    scopus 로고
    • DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
    • M. Schmollinger, K. Nieselt, M. Kaufmann, and B. Morgenstern DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors Bioinformatics 2004 5
    • (2004) Bioinformatics , pp. 5
    • Schmollinger, M.1    Nieselt, K.2    Kaufmann, M.3    Morgenstern, B.4
  • 31
    • 0036083631 scopus 로고    scopus 로고
    • BeoBLAST: Distributed BLAST and PSI-BLAST on a Beowulf cluster
    • J. Grant, R. Dunbrack, F. Manion, and M. Ochs BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster Bioinformatics 18 2002 765 766 (Pubitemid 34679125)
    • (2002) Bioinformatics , vol.18 , Issue.5 , pp. 765-766
    • Grant, J.D.1    Dunbrack, R.L.2    Manion, F.J.3    Ochs, M.F.4
  • 32
    • 0344838600 scopus 로고    scopus 로고
    • Wrapping up BLAST and other applications for use on Unix clusters
    • DOI 10.1093/bioinformatics/btg007
    • K. Hokamp, D. Shields, K. Wolfe, and D. Caffrey Wrapping up BLAST and other applications for use on UNIX clusters Bioinformatics 19 2003 441 442 (Pubitemid 36284952)
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 441-442
    • Hokamp, K.1    Shields, D.C.2    Wolfe, K.H.3    Caffrey, D.R.4
  • 33
    • 0141840819 scopus 로고    scopus 로고
    • Soap-HT-BLAST: High throughput BLAST based on Web services
    • DOI 10.1093/bioinformatics/btg244
    • J. Wang, and Q. Mu Soap-HT-BLAST: high throughput BLAST based on web services Bioinformatics 19 14 2003 1863 1864 (Pubitemid 37220485)
    • (2003) Bioinformatics , vol.19 , Issue.14 , pp. 1863-1864
    • Wang, J.1    Mu, Q.2
  • 36
    • 33746090715 scopus 로고    scopus 로고
    • Parallel blast: Chopping the database
    • M. Salisbury Parallel blast: chopping the database Genome Tech. 2005
    • (2005) Genome Tech.
    • Salisbury, M.1
  • 37
    • 0036462147 scopus 로고    scopus 로고
    • Database allocation strategies for parallel BLAST evaluation on clusters
    • R.L.D.C. Costa, and S. Lifschitz Database allocation strategies for parallel BLAST evaluation on clusters Distrib. Parallel Databases 13 1 2003 99 127
    • (2003) Distrib. Parallel Databases , vol.13 , Issue.1 , pp. 99-127
    • Costa, R.L.D.C.1    Lifschitz, S.2
  • 38
    • 0141506106 scopus 로고    scopus 로고
    • Parallel BLAST on split databases
    • DOI 10.1093/bioinformatics/btg250
    • D.R. Mathog Parallel BLAST on split databases Bioinformatics 19 2003 1865 1866 (Pubitemid 37220486)
    • (2003) Bioinformatics , vol.19 , Issue.14 , pp. 1865-1866
    • Mathog, D.R.1
  • 46
    • 35348928208 scopus 로고    scopus 로고
    • Parallel genomic sequence-search on a massively parallel system
    • DOI 10.1145/1242531.1242542, 2007 Computing Frontiers, Conference Proceedings
    • O. Thorsen, B. Smith, C.P. Sosa, K. Jiang, H. Lin, and A. Peters Parallel Genomic Sequence-Search on a Massively Parallel System CF '07: Proceedings of the 4th International Conference on Computing Frontiers 2007 ACM New York, NY, USA 59 68 (ISBN 978-1-59593-683-7) (Pubitemid 47582210)
    • (2007) 2007 Computing Frontiers, Conference Proceedings , pp. 59-68
    • Thorsen, O.1    Smith, B.2    Sosa, C.P.3    Jiang, K.4    Lin, H.5    Peters, A.6    Feng, W.-C.7
  • 48
    • 33746091677 scopus 로고    scopus 로고
    • ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis
    • C. Member-Oehmen, and J. Member-Nieplocha ScalaBLAST: a scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis IEEE Trans. Parallel Distrib. Syst. 17 8 2006
    • (2006) IEEE Trans. Parallel Distrib. Syst. , vol.17 , Issue.8
    • Member-Oehmen, C.1    Member-Nieplocha, J.2
  • 63
    • 84856853619 scopus 로고    scopus 로고
    • NSF Center for High Performance Reconfigurable Computing (CHREC)
    • NSF Center for High Performance Reconfigurable Computing (CHREC), NOVO-G: Adaptively Custom Research Supercomputer, 2005.
    • (2005) NOVO-G: Adaptively Custom Research Supercomputer
  • 64
    • 70349112707 scopus 로고    scopus 로고
    • Phoenix: A runtime environment for high performance computing on chip multiprocessors. Parallel, distributed and network-based processing
    • A. Pant, H. Jafri, V. Kindratenko, Phoenix: a runtime environment for high performance computing on chip multiprocessors. Parallel, distributed and network-based processing, in: 2009 17th Euromicro International Conference on 2009, pp. 119-126.
    • 2009 17th Euromicro International Conference on 2009 , pp. 119-126
    • Pant, A.1    Jafri, H.2    Kindratenko, V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.