Parallelization of general-linkage analysis problems
Dwarkadas S, Schaffer AA, Cottingham RW Jr, Cox AL, Keleher P,
Zwaenepoel W
Human Heredity 1994 May-Jun;44(3):127-41
Abstract
We describe a parallel implementation of a genetic-linkage analysis
program that achieves good speed improvement, even for analyses on a
single pedigree and with a single starting recombination fraction
vector. Our parallel implementation has been run on three different
platforms: an Ethernet network of workstations, a higher-bandwidth
asynchronous transfer mode (ATM) network of workstations, and a
shared-memory multiprocessor. The same program, written in a
shared-memory programming style, is used on all platforms. On the
workstation networks, the hardware does not provide shared memory,
so the program executes on a distributed shared memory system that
implements shared memory in software. These three platforms
represent different points on the price/performance scale. Ethernet
networks are cheap and omnipresent, ATM networks are an emerging
technology that offers higher bandwidth, and shared-memory
multiprocessors offer the best performance because communication is
implemented entirely by hardware. On 8 processors and for the longer
runs, we achieve speedups between 3.5 and 5 on the Ethernet network
and between 4.8 and 6 on the ATM network. On the shared-memory
multiprocessor, we achieve speedups in the 5.5-6.5 range for all runs.
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