Abstract
In this work we discuss possible strategies for mapping sequential sequence comparison algorithms onto LAN-based message passing computer architectures. The software-integration tool used is the public-domain PVM 3.1 system. We present two possible mapping strategies, one centered around a file server using Guided Self Scheduling and the other based on socket to socket communications. We will show how communication latency and overall data-passing load is significantly reduced, as well as dynamic load balancing and fault tolerant capabilities are achieved. The mapping methodology used in this study can scale well from simple workstation clusters to far more complex general message-passing architectures.
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References
Barton, G. (1991), Scanning protein sequence data banks using a distributed processing network, CABIOS, 7(1), 85–88.
Coulson, A., Collins, J. and Lyall, A. (1987), Protein and nucleic-acid sequence database searching:a suitable case for parallel processing, The Comp.Journal,30(5),420–424.
Deshpande, A.S., Richards, D.S. and Pearson, W.R. (1991),A platform for biological sequence comparison on parallel computers, CABIOS, 7(2), 237–247.
Jones, R. (1992), Sequence pattern matching on a massively parallel computer, CABIOS, 8(4), 377–383.
Pearson, W.R. and Lipman, D.J.(1988), Improved tools for biological sequence comparison, Proc. Nat. Acad. Sci. USA, 85, 2444–2448.
Miller, P.L., Nadkarni, P.M. and Pearson, W. (1992a), Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison, CABIOS, 8(2), 167–175.
Miller, P.L., Nadkarni, P.M. and Bercovitz, P.A. (1992b), Harnessing networked workstations as a powerful parallel computer,CABIOS, 8(2), 141–147.
Polychonospoulos, C.D. (1989), Static and dynamic loop scheduling, in Parallel programming and compilers, Kluwer Academic Publishers.
Sunderam, V.S. (1990), PVM: A framework for parallel distributed computing, Concurrence, Practice and Experience, 2(4), 315–339.
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© 1994 Springer-Verlag Berlin Heidelberg
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Trelles-Salazar, O., Zapata, E.L., Carazo, JM. (1994). Mapping strategies for sequential sequence comparison algorithms on LAN-based message passing architectures. In: Gentzsch, W., Harms, U. (eds) High-Performance Computing and Networking. HPCN-Europe 1994. Lecture Notes in Computer Science, vol 796. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0020372
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DOI: https://doi.org/10.1007/BFb0020372
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