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© Oxford University Press

Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison

Perry L. Miller , Prakash M. Nadkarni and William R. Pearson 1

Department of Anesthesiology, Yale University School of Medicine 333 Cedar Street, New Haven, CT 06510
1Department of Biochemistry, University of Virginia Charlottesville, VA 22908, USA

A platform program that performs biological sequence comparison provides a case study to compare the relative advantages of a machine–independent approach to parallel computation versus a machine-specific approach. The program consists of two routines: (i) PSCANLIB, which compares a single biological sequence against a database of sequences, and (ii) PCOMPLJB, which compares a database of sequences against another database of sequences, or against itself. The program was first parallelized to run on the Intel Hypercube parallel computer using native Hypercube commands to coordinate the parallel computation. The parallelization logic of the program was then translated into a machine–independent parallel programming language, Linda. Tliese two approaches to parallelization are contrasted in terms of: (i) the expressive power of the logic that coordinates the parallel computation, (ii) the portability of the machine–independent version to other parallel machines and (Hi) the relative efficiency of the two versions of the program. In the benchmark tests reported, the benefits of the machine–independent approach were achieved with only a modest sacrifice in efficiency.

Received on June 20, 1991; accepted on October 2, 1991

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