Table 3 Genomic relationship matrix calculation times (sec)
From: Second-generation PLINK: rising to the challenge of larger and richer datasets
Dataset | Machine | GCTA | PLINK 1.90 | Ratio |
|---|---|---|---|---|
synth1p | Mac-2 | 222.2 | 7.2 | 31 |
Mac-12 | 184.7 | 5.0 | 37 | |
Linux32-8 | 248.4 | 10.9 | 22.8 | |
Linux64-512 | 4.4 | 9.6 | 0.46 | |
Win32-2 | 373.1 | 39.3 | 9.5 | |
Win64-2 | 367.2 | 6.6 | 56 | |
synth2p | Mac-2 | nomem | 805.8 | |
Mac-12 | 17.0 k | 138.3 | 123 | |
Linux32-8 | nomem | 1153.4 | ||
Linux64-512 | 65.1 | 318.9 | 0.20 | |
Win32-2 | nomem | 2007.2 | ||
Win64-2 | nomem | 450.1 | ||
chr1snp | Mac-2 | nomem | 87.1 | |
Mac-12 | 2260.9 | 50.9 | 44.4 | |
Linux32-8 | nomem | 94.3 | ||
Linux64-512 | 58.3 | 91.6 | 0.64 | |
Win32-2 | nomem | 317.5 | ||
Win64-2 | nomem | 65.7 |