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Journal of Animal Science Abstract - Animal Genetics

Technical note: Acceleration of sparse operations for average-information REML analyses with supernodal methods and sparse-storage refinements12


This article in JAS

  1. Vol. 93 No. 10, p. 4670-4674
    Received: June 08, 2015
    Accepted: Aug 07, 2015
    Published: September 25, 2015

    3 Corresponding author(s): yutaka@uga.edu

  1. Y. Masuda 3*†,
  2. I. Aguilar,
  3. S. Tsuruta* and
  4. I. Misztal*
  1. * Department of Animal and Dairy Science, University of Georgia, Athens 30602
     Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 0808555, Japan
     Instituto Nacional de Investigación Agropecuaria, Canelones 90200, Uruguay


The objective of this study was to remove bottlenecks generally found in a computer program for average-information REML. The refinements included improvements to setting-up mixed-model equations on a hash table with a faster hash function as sparse matrix storage, changing sparse structures in calculation of traces, and replacing a sparse matrix package using traditional methods (FSPAK) with a new package using supernodal methods (YAMS); the latter package quickly processed sparse matrices containing large, dense blocks. Comparisons included 23 models with data sets from broiler, swine, beef, and dairy cattle. Models included single-trait, multiple-trait, maternal, and random regression models with phenotypic data; selected models used genomic information in a single-step approach. Setting-up mixed model equations was completed without abnormal termination in all analyses. Calculations in traces were accelerated with a hash format, especially for models with a genomic relationship matrix, and the maximum speed was 67 times faster. Computations with YAMS were, on average, more than 10 times faster than with FSPAK and had greater advantages for large data and more complicated models including multiple traits, random regressions, and genomic effects. These refinements can be applied to general average-information REML programs.

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