Table 2.
Comparison of run times on datasets from [12] on a 64-bit Intel CORE i3 machine with 4GB of RAM, Ubuntu 11.10 Operating System, Sun Java 1.6.0 26 and gcc 4.6.1. Run times are in seconds, averaged over 10 runs. Bold font indicates the best time. ML means out of memory, TL means more than 1 hour.
| Dataset | Run time | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Name | Length | |Σ| | RadixSA | BPR2 | BPR.9 | DivSuf Sort | QSuf Sort | SAIS | skew | Deep Shallow |
| Fibonacci | 20000000 | 2 | 7.88 | 12.48 | 14.05 | 6.81 | 26.44 | 5.50 | 14.53 | 369.48 |
| period 1000 | 20000000 | 26 | 2.12 | 3.52 | 5.71 | 3.15 | 20.42 | 6.59 | 23.27 | TL |
| period 20 | 20000000 | 17 | 1.44 | 1.95 | 43.39 | 1.83 | 11.05 | 2.83 | 7.15 | TL |
| period 500000 | 20000000 | 26 | 2.78 | 4.60 | 6.31 | 4.74 | 23.32 | 8.56 | 25.68 | 2844.37 |
| random | 20000000 | 26 | 2.25 | 3.34 | 4.87 | 6.35 | 5.02 | 11.75 | 22.05 | 5.69 |
| 3Ecoli.dna | 14776363 | 5 | 2.23 | 2.67 | 3.43 | 4.00 | 13.85 | 6.14 | 19.62 | 433.54 |
| 4Chlamydophila.dna | 4856123 | 6 | 0.61 | 0.67 | 0.90 | 1.71 | 3.24 | 1.93 | 5.24 | 4.80 |
| 6Streptococci.dna | 11635882 | 5 | 1.63 | 1.79 | 2.38 | 2.88 | 7.08 | 4.98 | 14.88 | 4.26 |
| A thaliana Chr4.dna | 12061490 | 7 | 1.27 | 1.74 | 2.40 | 3.02 | 5.13 | 5.37 | 15.71 | 3.52 |
| C elegans Chr1.dna | 14188020 | 5 | 1.61 | 1.95 | 2.65 | 3.21 | 6.91 | 5.69 | 17.18 | 6.92 |
| E coli.dna | 4638690 | 4 | 0.41 | 0.51 | 0.58 | 1.36 | 1.72 | 1.96 | 5.04 | 1.37 |
| H sapiens Chr22.dna | 34553758 | 5 | 4.40 | 5.66 | 8.21 | 7.76 | 15.31 | 15.59 | 49.70 | 10.98 |
| bible | 4047391 | 63 | 0.51 | 0.48 | 0.80 | 1.24 | 1.38 | 1.56 | 4.64 | 1.08 |
| etext | 105277339 | 146 | 19.40 | 23.09 | 43.46 | 26.56 | 62.63 | 54.70 | ML | 119.96 |
| etext 50M | 50000000 | 120 | 8.13 | 9.74 | 17.26 | 11.94 | 26.40 | 24.46 | 88.57 | 79.07 |
| gcc | 86630400 | 150 | 13.84 | 15.58 | 24.50 | 15.84 | 46.20 | 33.62 | 135.12 | 80.78 |
| gcc 50M | 50000000 | 121 | 7.21 | 9.56 | 13.26 | 8.31 | 28.43 | 17.73 | 68.65 | 264.90 |
| howto | 39422104 | 197 | 5.96 | 6.35 | 10.26 | 8.41 | 17.64 | 16.67 | 64.73 | 16.33 |
| jdk | 69728898 | 113 | 12.07 | 12.54 | 26.86 | 12.74 | 39.92 | 24.66 | 102.76 | 58.22 |
| jdk 50M | 50000000 | 110 | 8.32 | 8.30 | 17.05 | 8.91 | 26.30 | 17.58 | 71.31 | 36.98 |
| linux | 116254720 | 256 | 19.27 | 19.34 | 29.67 | 21.17 | 61.99 | 44.47 | ML | 58.71 |
| linux 50M | 50000000 | 256 | 7.62 | 7.60 | 10.50 | 8.84 | 27.54 | 18.18 | 76.10 | 31.92 |
| reuters | 114711150 | 93 | 19.76 | 25.08 | 60.72 | 25.07 | 74.78 | 49.17 | ML | 87.57 |
| reuters 50M | 50000000 | 91 | 7.84 | 9.53 | 20.41 | 10.24 | 26.94 | 20.29 | 77.25 | 33.68 |
| rfc | 116421900 | 120 | 21.18 | 22.08 | 42.75 | 22.55 | 66.28 | 47.99 | ML | 42.14 |
| rfc 50M | 50000000 | 110 | 8.23 | 8.39 | 14.85 | 9.24 | 24.80 | 19.61 | 76.64 | 16.63 |
| sprot | 109617186 | 66 | 18.48 | 22.79 | 47.07 | 25.52 | 69.58 | 50.40 | ML | 48.69 |
| sprot 50M | 50000000 | 66 | 7.57 | 9.10 | 16.81 | 10.88 | 28.07 | 21.69 | 78.47 | 20.03 |
| w3c | 104201578 | 256 | 18.82 | 18.78 | 35.94 | 20.01 | 74.09 | 38.29 | ML | 1964.80 |
| w3c 50M | 50000000 | 255 | 7.93 | 8.33 | 17.67 | 8.73 | 25.95 | 17.26 | 71.42 | 36.59 |
| world | 2473399 | 94 | 0.30 | 0.27 | 0.42 | 0.91 | 0.86 | 0.91 | 2.35 | 0.78 |