Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

P M Nadkarni; P L Miller

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PubMed · 1807632

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

P M Nadkarni·P L Miller

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Abstract

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

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Algorithms Amino Acid Sequence Base Sequence Databases, Factual Microcomputers Software Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

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BibTeX RIS

P M Nadkarni, P L Miller. 1991. Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.. https://pubmed.ncbi.nlm.nih.gov/1807632/

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