Table 4 Illustration of the parallel efficiency of DAIRRy-BLUP for a data set with 100,000 individuals genotyped for 360,000 SNPs
SNPsDedicated CPU cores (P)Time per iterationTime for read-in + setup CTime for solving MMETotal memory usage, GB
30,00016 hr 44 min5 hr 3 min1 hr 41 min3.73
360,000a1151 days30 days121 days537
360,0007208 hr 50 min1 hr 49 min7 hr 0 min831
Speedup Embedded Image416399412
Efficiency Embedded Image57.3%55.4%57.7%
  • Speedup is calculated as the ratio between the computing time on a single CPU core and the computing time on P = 720 CPU cores. Parallel efficiency is defined as the ratio between the actual speedup and the maximum speedup, which is equal to the number of dedicated CPU cores.

  • a Results for a data set with 360,000 SNPs on a single CPU core are estimated based on results of the data set with 30,000 SNPs, cubic complexity of the solving algorithm, and square complexity of the setup of matrix C and memory usage.