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

• Published in: Journal of animal science 2015-10, Vol.93 (10), p.4670-4674
• Main Authors: Masuda, Y, Aguilar, I, Tsuruta, S, Misztal, I
• Format: Article
• Language: English
• Subjects: Algorithms; Animals; Breeding; Genome; Genomics - methods; Livestock - genetics; Models, Genetic; Software
• ISSN: 1525-3163
• DOI: 10.2527/jas.2015-9395

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.