Table 9:
Execution times (seconds) using different number of cores: sort command. Highlighted are fastest time and number of times faster than sequential BigSeqKit
| 1 | 2 | 4 | 8 | 16 | 32 | 64 (2 nodes) | 128 (4 nodes) | 256 (8 nodes) | |
|---|---|---|---|---|---|---|---|---|---|
| D1 | |||||||||
| samtools | 1,590.3 [0.10×] | – | – | – | – | – | – | – | – |
| seqkit | 169.0 [0.97×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 164.4 | 86.2 | 46.2 | 33.5 | 24.2 | 14.5 [11.3×] | 13.8 | 13.5 | 12.9 [12.7×] |
| D2 | |||||||||
| samtools | 1,672.5 [0.25×] | – | – | – | – | – | – | – | – |
| seqkit | 1,050.5 [0.40×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 422.8 | 221.6 | 117.6 | 81.7 | 62.1 | 34.9 [12.1×] | 21.5 | 15.8 | 13.2 [32.0×] |
| D3 | |||||||||
| samtools | 1,203.5 [0.44×] | – | – | – | – | – | – | – | – |
| seqkit | 497.5 [1.05×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 523.8 | 272.5 | 144.2 | 100.7 | 77.6 | 43.2 [12.1×] | 26.5 | 18.6 | 15.8 [33.1×] |
| D4 | |||||||||
| samtools | 3,835.1 [0.36×] | – | – | – | – | – | – | – | – |
| seqkit | 3,122.2 [0.44×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 1,377.3 | 708.5 | 372.5 | 243.7 | 171.5 | 94.6 [14.6×] | 57.6 | 46.0 | 36.0 [38.3×] |
| D5 | |||||||||
| samtools | 1,899.6 [0.85×] | – | – | – | – | – | – | – | – |
| seqkit | 3,350.4 [0.48×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 1,612.4 | 839.2 | 443.2 | 239.2 | 137.2 | 84.2 [19.1×] | 53.4 | 40.2 | 39.2 [41.1×] |
| D6 | |||||||||
| samtools | Out of Mem. | – | – | – | – | – | – | – | – |
| seqkit | Out of Mem. | – | – | – | – | – | – | – | – |
| BigSeqKit | 18,309.6 | 9,439.6 | 4,899.2 | 2,592.8 | 1,444.4 | 839.7 [21.8×] | 215.8 | 165.3 | 139.6 [131.1×] |