Lauren HydeDirector and Lead Geneticist

September 16, 2015

REPORT

Current IGS Database12 breed associations16,000,000 animals340,000 new animals per year

Current SoftwareInitially developed in 1980s using Fortran 77Implemented multi-breed international cattle evaluation (MB-ICE) in 1997Last major modification in 2012 with multi-breed calving ease EPDsContinually being updated using Fortran 95Very limited

Current NeedsDirect incorporation of genomics into EPDsImproved accuracy computationAbility to handle quickly growing large databaseEfficiency and speed

Biometry Open Language Tools

The next generation in genomic evaluation

Leverage technology built for computer gaming

BOLT Major FeaturesFine grid to “embarrassingly” parallel capability

Multi-GPU (CUDA)Multi-coreMulti-threaded asynchronous execution

Shared memory for performance

BOLT Major FeaturesNovel algorithmsWritten in CIntegrated with Unix user utilitiesExtremely flexible

Complete set of extensible tools/commandsSimple user API

Biometry Open Language Toolkitcorr fblockinv mmultongpu mtmgpu csolvefsolve insbmtx mnvar absorbx csolvesfsolves invert mprin mmultgpu tsolveabsorbxm csub genomult invnrm pcgmgpuastarsetup csubm gpustat pedrecode sthmgibbscadd cudacheck grpcnt lambayes permsubcgen_z cudarnd grpmn libbolt rankchcat cvcat grps libboltcuda sdatecholesky cvcatcsr grps2 load2csc shmgrcln diag ident minmax sp2mmcmult include impute stack_ped ssgibbscnewr fbcsrmv imputegpu mmult transMcnewr2 fblockinv

Emphasizes sampler-based strategies to:--Incorporate genomics--Maximize accuracy

Mixed Model Equations

Animals →

Markers →

Genomic Information

Example of Performance Computing

6,625,000,000,000,000(6.6 quadrillion) flopCompute Time: 48m

(2.29 Tflops)

BOLT ImplementationScheduled for early 2016

Data issues (international IDs, breed compositions)Spring bull sales

Development and testingGrowth traits—framework built, testing well underwayCarcass traits—initial framework built, start testingThreshold traits—start after growth complete