Table 6:
Execution times (seconds) using different number of cores: rmdup 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 | |||||||||
| seqkit | 178.9 [1.01×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 180.5 | 94.3 | 50.2 | 35.1 | 27.1 | 15.8 [11.4×] | 14.8 | 14.4 | 13.8 [13.1×] |
| D2 | |||||||||
| seqkit | 320.6 [1.04×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 333.3 | 174.7 | 93.5 | 65.9 | 49.9 | 26.5 [12.6×] | 15.9 | 14.1 [23.6×] | 15.0 |
| D3 | |||||||||
| seqkit | 515.5 [0.91×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 469.5 | 246.7 | 182.7 | 127.5 | 96.1 | 51.4 [9.1×] | 27.4 | 20.9 | 20.6 [22.8×] |
| D4 | |||||||||
| seqkit | 729.9 [0.99×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 720.5 | 378.5 | 197.5 | 139.7 | 102.9 | 54.0 [13.3×] | 30.5 | 16.4 | 14.1 [51.1×] |
| D5 | |||||||||
| seqkit | 2,173.6 [0.97×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 2,100.2 | 1,110.4 | 612.3 | 341.2 | 195.1 | 115.2 [18.2×] | 70.5 | 43.2 | 28.1 [74.7×] |
| D6 | |||||||||
| seqkit | 9,937.1 [1.11×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 11,022.3 | 5,578.5 | 3,006.7 | 1,709.6 | 1,004.1 | 600.1 [18.4×] | 275.2 | 241.6 | 228.8 [48.2×] |