Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.
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.
Nadkarni
P M
PM
Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06510.
Miller
P L
PL
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D016208:Databases, Factual; D008838:Microcomputers; D012984:Software