Table 8:
Execution times (seconds) using different number of cores: seq 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 | |||||||||
| pyfastx | 151.8 [0.56×] | – | – | – | – | – | – | – | – |
| seqkit | 234.4 [0.36×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 84.4 | 43.5 | 22.5 | 11.6 | 6.3 | 4.8 [17.6×] | 4.7 | 3.7 | 3.5 [24.1×] |
| D2 | |||||||||
| pyfastx | 209.4 [1.15×] | – | – | – | – | – | – | – | – |
| seqkit | 234.0 [1.03×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 240.9 | 128.5 | 65.0 | 34.6 | 19.5 | 10.7 [22.5×] | 6.1 | 4.3 | 4.0 [60.2×] |
| D3 | |||||||||
| pyfastx | 400.5 [0.90×] | – | – | – | – | – | – | – | – |
| seqkit | 541.2 [0.67×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 360.2 | 182.7 | 93.4 | 48.1 | 27.1 | 20.2 [17.8×] | 8.6 | 5.1 [65.5×] | 5.5 |
| D4 | |||||||||
| pyfastx | 901.2 [1.13×] | – | – | – | – | – | – | – | – |
| seqkit | 981.7 [1.03×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 1,014.7 | 508.8 | 257.1 | 129.1 | 66.3 | 36.6 [27.7×] | 22.5 | 15.2 | 10.6 [95.7×] |
| D5 | |||||||||
| pyfastx | 1,051.4 [0.94×] | – | – | – | – | – | – | – | – |
| seqkit | 1,165.5 [0.85×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 987.6 | 500.2 | 259.1 | 135.9 | 73.6 | 41.5 [23.8×] | 26.1 | 17.9 | 16.2 [60.9×] |
| D6 | |||||||||
| pyfastx | 7,657.6 [1.23×] | – | – | – | – | – | – | – | – |
| seqkit | 9,080.5 [1.04×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 9,420.3 | 4,712.1 | 2,400.3 | 1,323.4 | 755.5 | 430.3 [21.9×] | 110.3 | 70.2 | 55.5 [169.7×] |