Table 7:
Execution times (seconds) using different number of cores: sample 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 | 308.2 [0.67×] | – | – | – | – | – | – | – | – |
| seqkit | 196.1 [1.05×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 205.7 | 108.2 | 57.8 | 36.4 | 27.1 | 17.3 [11.9×] | 15.1 | 15.4 | 14.1 [14.6×] |
| D2 | |||||||||
| pyfastx | 458.7 [1.12×] | – | – | – | – | – | – | – | – |
| seqkit | 492.4 [1.04×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 514.5 | 271.7 | 143.8 | 98.1 | 76.1 | 42.2 [12.2×] | 36.1 | 30.1 | 26.4 [19.5×] |
| D3 | |||||||||
| pyfastx | 450.2 [0.88×] | – | – | – | – | – | – | – | – |
| seqkit | 491.7 [0.80×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 394.3 | 207.8 | 105.2 | 70.5 | 52.7 | 26.1 [15.1×] | 22.1 | 19.2 | 14.3 [27.6×] |
| D4 | |||||||||
| pyfastx | 1,929.1 [0.99×] | – | – | – | – | – | – | – | – |
| seqkit | 1,996.7 [0.96×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 1,912.8 | 1,000.5 | 529.3 | 365.8 | 283.4 | 156.3 [12.2×] | 90.4 | 56.2 | 36.5 [52.4×] |
| D5 | |||||||||
| pyfastx | 1,567.7 [0.71×] | – | – | – | – | – | – | – | – |
| seqkit | 1,057 [1.06×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 1,121.5 | 572.3 | 299.4 | 164.2 | 91.3 | 52.4 [21.4×] | 33.6 | 25.1 | 22.5 [49.8×] |
| D6 | |||||||||
| pyfastx | 9,507.7 [1.16×] | – | – | – | – | – | – | – | – |
| seqkit | 9,550 [1.16×] | – | – | – | – | – | – | – | – |
| BigSeqKit | 11,070.2 | 5,539.5 | 2,812.3 | 1,543.6 | 876.2 | 515.9 [21.5×] | 202 | 143.2 | 109.5 [101.1×] |