Parallel computing applied to breeding value estimation in dairy cattle

Journal of Dairy Science
I Strandén, M H Lidauer

Abstract

Continuous genetic evaluation of dairy cattle with test-day models is desired in Finland. However, the computing time for the genetic evaluation is 4 d and exceeds the minimum of a weekend. Three parallel implementations of the preconditioned conjugate gradient iterative solver were programmed and compared to identify the best strategy for solving mixed model equations using parallel computing. The programs were used to solve two random regression test-day models with approximately 7.28 and 49.9 million unknowns. The latter model will be used in the Finnish dairy cattle evaluation. Computing times for the smaller model with the four processors available were 52, 32, and 27% of the single processor program when the complexity of the parallel program was increased. In practice, the best program required the most programming because the other parallel programs could not solve the larger model because of excess memory requirements. Parallel computing with four processors reduced the time to obtain solutions of Finnish dairy cattle evaluations to under 2 d. Benefit from parallel computing will be increased if amount of computing memory is increased.

References

May 26, 1999·Journal of Dairy Science·I Misztal, T J Lawlor
Jan 12, 2000·Journal of Dairy Science·I Strandén, M Lidauer
Jan 12, 2000·Journal of Dairy Science·M LidauerA Kettunen

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Citations

Aug 3, 2006·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·E NegussieM Lidauer
May 16, 2008·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·M H LidauerE A Mäntysaari
Jun 12, 2010·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·I AguilarI Misztal
Aug 13, 2013·Journal of Dairy Science·D D MaulfairA J Heinrichs
Nov 5, 2003·Journal of Dairy Science·S S BlockY R Boisclair
Nov 5, 2003·Journal of Dairy Science·T J DeVriesK A Beauchemin
May 23, 2007·Journal of Dairy Science·M NealW J Fulkerson
May 23, 2007·Journal of Dairy Science·A N HristovJ W Ellsworth
May 23, 2007·Journal of Dairy Science·D H KleinschmitA R Hippen
May 23, 2007·Journal of Dairy Science·H LapierreG E Lobley
Aug 19, 2007·Journal of Dairy Science·B N JanicekM L Gibson
Aug 19, 2007·Journal of Dairy Science·K F KnowltonK F Wilson
Aug 19, 2007·Journal of Dairy Science·M Cerrato-SánchezA Ferret
Dec 24, 2011·Journal of Dairy Science·H LapierreG E Lobley

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