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Specifications

  • CPU: Intel Core i7-9700K Processor (12M Cache, 5 GHz all cores)
  • RAM: 2x8 GB dual-channel DDR4 (4133 MHz, 17-17-17-37-400-2T with tight subtimings)
  • OS: Microsoft Windows 10 Pro 64 Bit (with MEM_LARGE_PAGES support enabled)
  • Compiler: Clang 11.0.0 '-Ofast -march=skylake -fopenmp -DNDEBUG'

The times are the minimum of five runs measuring single-threaded (ST) and multi-threaded (MT) performance of suffix array construction.

Silesia Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
dickens 10192446 0.204 sec ( 50.00 MB/s) 0.446 sec ( 22.87 MB/s) +118.64% 0.120 sec ( 84.98 MB/s) 0.296 sec ( 34.42 MB/s) +146.88%
mozilla 51220480 1.105 sec ( 46.34 MB/s) 1.819 sec ( 28.15 MB/s) +64.60% 0.712 sec ( 71.96 MB/s) 1.206 sec ( 42.47 MB/s) +69.44%
mr 9970564 0.187 sec ( 53.21 MB/s) 0.370 sec ( 26.92 MB/s) +97.66% 0.131 sec ( 76.03 MB/s) 0.261 sec ( 38.22 MB/s) +98.95%
nci 33553445 0.641 sec ( 52.38 MB/s) 1.151 sec ( 29.16 MB/s) +79.59% 0.364 sec ( 92.20 MB/s) 1.036 sec ( 32.39 MB/s) +184.65%
ooffice 6152192 0.116 sec ( 53.23 MB/s) 0.180 sec ( 34.26 MB/s) +55.38% 0.082 sec ( 75.06 MB/s) 0.108 sec ( 57.08 MB/s) +31.51%
osdb 10085684 0.224 sec ( 45.02 MB/s) 0.361 sec ( 27.94 MB/s) +61.12% 0.154 sec ( 65.61 MB/s) 0.272 sec ( 37.07 MB/s) +77.00%
reymont 6627202 0.125 sec ( 53.09 MB/s) 0.249 sec ( 26.61 MB/s) +99.49% 0.076 sec ( 87.44 MB/s) 0.183 sec ( 36.22 MB/s) +141.39%
samba 21606400 0.401 sec ( 53.82 MB/s) 0.661 sec ( 32.70 MB/s) +64.59% 0.274 sec ( 79.00 MB/s) 0.467 sec ( 46.27 MB/s) +70.74%
sao 7251944 0.181 sec ( 40.02 MB/s) 0.232 sec ( 31.24 MB/s) +28.10% 0.132 sec ( 55.02 MB/s) 0.143 sec ( 50.63 MB/s) +8.67%
webster 41458703 1.020 sec ( 40.64 MB/s) 2.190 sec ( 18.93 MB/s) +114.70% 0.595 sec ( 69.72 MB/s) 1.653 sec ( 25.08 MB/s) +177.98%
x-ray 8474240 0.215 sec ( 39.35 MB/s) 0.337 sec ( 25.13 MB/s) +56.58% 0.153 sec ( 55.40 MB/s) 0.184 sec ( 46.10 MB/s) +20.19%
xml 5345280 0.079 sec ( 67.54 MB/s) 0.138 sec ( 38.87 MB/s) +73.78% 0.050 sec ( 106.50 MB/s) 0.108 sec ( 49.52 MB/s) +115.06%

Large Canterbury Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
bible.txt 4047392 0.066 sec ( 61.40 MB/s) 0.140 sec ( 28.95 MB/s) +112.14% 0.038 sec ( 106.74 MB/s) 0.100 sec ( 40.58 MB/s) +163.00%
E.coli 4638690 0.079 sec ( 58.74 MB/s) 0.199 sec ( 23.35 MB/s) +151.59% 0.038 sec ( 121.18 MB/s) 0.154 sec ( 30.15 MB/s) +301.95%
world192.txt 2473400 0.037 sec ( 66.72 MB/s) 0.075 sec ( 32.92 MB/s) +102.65% 0.023 sec ( 108.02 MB/s) 0.050 sec ( 49.58 MB/s) +117.85%

Manzini Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
chr22.dna 34553758 0.778 sec ( 44.43 MB/s) 2.005 sec ( 17.23 MB/s) +157.85% 0.436 sec ( 79.27 MB/s) 1.676 sec ( 20.61 MB/s) +284.61%
etext99 105277340 3.174 sec ( 33.17 MB/s) 7.083 sec ( 14.86 MB/s) +123.15% 1.739 sec ( 60.53 MB/s) 5.345 sec ( 19.70 MB/s) +207.33%
gcc-3.0.tar 86630400 1.930 sec ( 44.89 MB/s) 3.458 sec ( 25.05 MB/s) +79.18% 1.188 sec ( 72.90 MB/s) 2.508 sec ( 34.54 MB/s) +111.04%
howto 39422105 0.912 sec ( 43.24 MB/s) 1.884 sec ( 20.93 MB/s) +106.60% 0.557 sec ( 70.80 MB/s) 1.279 sec ( 30.83 MB/s) +129.64%
jdk13c 69728899 1.630 sec ( 42.79 MB/s) 3.019 sec ( 23.10 MB/s) +85.25% 1.008 sec ( 69.20 MB/s) 2.490 sec ( 28.00 MB/s) +147.11%
linux-2.4.5.tar 116254720 2.688 sec ( 43.25 MB/s) 4.980 sec ( 23.34 MB/s) +85.27% 1.651 sec ( 70.40 MB/s) 3.540 sec ( 32.84 MB/s) +114.34%
rctail96 114711151 3.162 sec ( 36.27 MB/s) 6.370 sec ( 18.01 MB/s) +101.41% 1.813 sec ( 63.27 MB/s) 5.009 sec ( 22.90 MB/s) +176.26%
rfc 116421901 2.929 sec ( 39.75 MB/s) 5.689 sec ( 20.46 MB/s) +94.23% 1.681 sec ( 69.24 MB/s) 4.182 sec ( 27.84 MB/s) +148.70%
sprot34.dat 109617186 2.983 sec ( 36.75 MB/s) 6.324 sec ( 17.33 MB/s) +112.03% 1.712 sec ( 64.03 MB/s) 4.509 sec ( 24.31 MB/s) +163.38%
w3c2 104201579 2.450 sec ( 42.53 MB/s) 4.426 sec ( 23.54 MB/s) +80.67% 1.565 sec ( 66.57 MB/s) 3.570 sec ( 29.19 MB/s) +128.10%

Large Text Compression Benchmark Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
enwik8 100000000 2.841 sec ( 35.20 MB/s) 6.209 sec ( 16.11 MB/s) +118.58% 1.604 sec ( 62.36 MB/s) 4.446 sec ( 22.49 MB/s) +177.24%
enwik9 1000000000 40.718 sec ( 24.56 MB/s) 82.407 sec ( 12.13 MB/s) +102.39% 19.138 sec ( 52.25 MB/s) 63.373 sec ( 15.78 MB/s) +231.14%

The Gauntlet Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
abac 200000 0.003 sec ( 73.23 MB/s) 0.002 sec ( 130.08 MB/s) -43.71% 0.002 sec ( 94.65 MB/s) 0.002 sec ( 125.78 MB/s) -24.75%
abba 10500596 0.169 sec ( 62.02 MB/s) 0.431 sec ( 24.36 MB/s) +154.64% 0.090 sec ( 116.53 MB/s) 0.442 sec ( 23.76 MB/s) +390.38%
book1x20 15375420 0.328 sec ( 46.85 MB/s) 0.720 sec ( 21.36 MB/s) +119.34% 0.195 sec ( 79.02 MB/s) 0.505 sec ( 30.47 MB/s) +159.34%
fib_s14930352 14930352 0.341 sec ( 43.80 MB/s) 1.070 sec ( 13.95 MB/s) +213.96% 0.173 sec ( 86.06 MB/s) 1.059 sec ( 14.10 MB/s) +510.23%
fss10 12078908 0.239 sec ( 50.54 MB/s) 0.811 sec ( 14.89 MB/s) +239.49% 0.135 sec ( 89.17 MB/s) 0.793 sec ( 15.24 MB/s) +485.07%
fss9 2851443 0.041 sec ( 68.79 MB/s) 0.123 sec ( 23.12 MB/s) +197.52% 0.025 sec ( 116.35 MB/s) 0.121 sec ( 23.59 MB/s) +393.28%
houston 3839141 0.037 sec ( 103.92 MB/s) 0.024 sec ( 162.18 MB/s) -35.92% 0.018 sec ( 209.58 MB/s) 0.023 sec ( 164.72 MB/s) +27.24%
paper5x80 956322 0.014 sec ( 69.13 MB/s) 0.024 sec ( 40.00 MB/s) +72.82% 0.008 sec ( 112.87 MB/s) 0.020 sec ( 47.87 MB/s) +135.81%
test1 2097152 0.039 sec ( 53.45 MB/s) 0.084 sec ( 24.82 MB/s) +115.35% 0.020 sec ( 106.42 MB/s) 0.080 sec ( 26.25 MB/s) +305.39%
test2 2097152 0.039 sec ( 53.87 MB/s) 0.058 sec ( 36.02 MB/s) +49.56% 0.019 sec ( 109.39 MB/s) 0.052 sec ( 40.23 MB/s) +171.92%
test3 2097088 0.037 sec ( 56.56 MB/s) 0.046 sec ( 45.93 MB/s) +23.13% 0.031 sec ( 67.13 MB/s) 0.047 sec ( 44.81 MB/s) +49.79%

Pizza & Chilli Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
dblp.xml 296135874 8.428 sec ( 35.14 MB/s) 16.001 sec ( 18.51 MB/s) +89.85% 4.749 sec ( 62.36 MB/s) 12.932 sec ( 22.90 MB/s) +172.29%
dna 403927746 14.257 sec ( 28.33 MB/s) 36.002 sec ( 11.22 MB/s) +152.53% 6.462 sec ( 62.51 MB/s) 32.014 sec ( 12.62 MB/s) +395.42%
english.1024MB 1073741824 51.568 sec ( 20.82 MB/s) 104.407 sec ( 10.28 MB/s) +102.47% 22.777 sec ( 47.14 MB/s) 84.357 sec ( 12.73 MB/s) +270.37%
pitches 55832855 1.222 sec ( 45.70 MB/s) 2.380 sec ( 23.46 MB/s) +94.78% 0.820 sec ( 68.10 MB/s) 1.422 sec ( 39.26 MB/s) +73.45%
proteins 1184051855 60.105 sec ( 19.70 MB/s) 124.688 sec ( 9.50 MB/s) +107.45% 25.981 sec ( 45.57 MB/s) 79.149 sec ( 14.96 MB/s) +204.65%
sources 210866607 5.381 sec ( 39.19 MB/s) 10.210 sec ( 20.65 MB/s) +89.74% 3.223 sec ( 65.42 MB/s) 7.350 sec ( 28.69 MB/s) +128.03%

Pizza & Chilli Repetitive Corpus

file size libsais 2.1.0 (ST) divsufsort 2.0.2 (ST) speedup (ST) libsais 2.1.0 (MT) divsufsort 2.0.2 (MT) speedup (MT)
cere 461286644 16.184 sec ( 28.50 MB/s) 34.422 sec ( 13.40 MB/s) +112.69% 7.349 sec ( 62.77 MB/s) 30.502 sec ( 15.12 MB/s) +315.04%
coreutils 205281778 5.264 sec ( 39.00 MB/s) 10.506 sec ( 19.54 MB/s) +99.58% 3.090 sec ( 66.43 MB/s) 8.170 sec ( 25.13 MB/s) +164.39%
einstein.de.txt 92758441 2.449 sec ( 37.87 MB/s) 4.582 sec ( 20.25 MB/s) +87.06% 1.381 sec ( 67.19 MB/s) 3.744 sec ( 24.78 MB/s) +171.18%
einstein.en.txt 467626544 15.279 sec ( 30.61 MB/s) 31.504 sec ( 14.84 MB/s) +106.20% 7.902 sec ( 59.18 MB/s) 27.152 sec ( 17.22 MB/s) +243.60%
Escherichia_Coli 112689515 3.360 sec ( 33.54 MB/s) 7.495 sec ( 15.03 MB/s) +123.06% 1.683 sec ( 66.94 MB/s) 6.283 sec ( 17.94 MB/s) +273.25%
influenza 154808555 3.816 sec ( 40.57 MB/s) 8.982 sec ( 17.24 MB/s) +135.38% 2.209 sec ( 70.07 MB/s) 7.757 sec ( 19.96 MB/s) +251.11%
kernel 257961616 7.091 sec ( 36.38 MB/s) 13.511 sec ( 19.09 MB/s) +90.54% 3.866 sec ( 66.72 MB/s) 10.158 sec ( 25.40 MB/s) +162.74%
para 429265758 15.407 sec ( 27.86 MB/s) 32.821 sec ( 13.08 MB/s) +113.03% 6.905 sec ( 62.17 MB/s) 29.143 sec ( 14.73 MB/s) +322.06%
world_leaders 46968181 0.880 sec ( 53.35 MB/s) 1.301 sec ( 36.11 MB/s) +47.73% 0.460 sec ( 102.16 MB/s) 1.054 sec ( 44.58 MB/s) +129.18%
dblp.xml.00001.1 104857600 4.445 sec ( 23.59 MB/s) 5.913 sec ( 17.73 MB/s) +33.03% 1.976 sec ( 53.07 MB/s) 5.130 sec ( 20.44 MB/s) +159.62%
dblp.xml.00001.2 104857600 4.423 sec ( 23.71 MB/s) 6.050 sec ( 17.33 MB/s) +36.78% 1.967 sec ( 53.32 MB/s) 5.217 sec ( 20.10 MB/s) +165.27%
dblp.xml.0001.1 104857600 3.062 sec ( 34.24 MB/s) 5.534 sec ( 18.95 MB/s) +80.70% 1.427 sec ( 73.50 MB/s) 4.664 sec ( 22.48 MB/s) +226.91%
dblp.xml.0001.2 104857600 3.118 sec ( 33.63 MB/s) 5.592 sec ( 18.75 MB/s) +79.32% 1.664 sec ( 63.00 MB/s) 4.763 sec ( 22.01 MB/s) +186.21%
dna.001.1 104857600 3.090 sec ( 33.94 MB/s) 6.368 sec ( 16.47 MB/s) +106.10% 1.539 sec ( 68.13 MB/s) 5.338 sec ( 19.64 MB/s) +246.87%
english.001.2 104857600 3.445 sec ( 30.44 MB/s) 5.920 sec ( 17.71 MB/s) +71.87% 1.745 sec ( 60.08 MB/s) 4.268 sec ( 24.57 MB/s) +144.55%
proteins.001.1 104857600 3.406 sec ( 30.79 MB/s) 5.884 sec ( 17.82 MB/s) +72.76% 1.797 sec ( 58.36 MB/s) 3.667 sec ( 28.59 MB/s) +104.12%
sources.001.2 104857600 2.916 sec ( 35.96 MB/s) 4.828 sec ( 21.72 MB/s) +65.55% 1.599 sec ( 65.58 MB/s) 3.695 sec ( 28.38 MB/s) +131.08%
fib41 267914296 8.390 sec ( 31.93 MB/s) 37.397 sec ( 7.16 MB/s) +345.72% 3.794 sec ( 70.61 MB/s) 37.158 sec ( 7.21 MB/s) +879.30%
rs.13 216747218 6.425 sec ( 33.74 MB/s) 28.994 sec ( 7.48 MB/s) +351.30% 2.807 sec ( 77.21 MB/s) 31.609 sec ( 6.86 MB/s) +1025.97%
tm29 268435456 8.931 sec ( 30.06 MB/s) 31.267 sec ( 8.59 MB/s) +250.09% 3.729 sec ( 71.99 MB/s) 31.384 sec ( 8.55 MB/s) +741.69%

Large pages and multi-core systems support

Large-pages and OpenMP improves the libsais performance. Here is an example of such improvements on Manzini Corpus.

file size baseline LP LP w 2c LP w 3c LP w 4c LP w 5c LP w 6c LP w 7c LP w 8c
chr22.dna 34553758 43.50MB/s 50.18MB/s 61.20MB/s 73.66MB/s 78.91MB/s 81.20MB/s 81.49MB/s 81.52MB/s 80.42MB/s
etext99 105277340 32.96MB/s 40.73MB/s 50.19MB/s 59.34MB/s 62.97MB/s 64.06MB/s 62.83MB/s 63.08MB/s 62.49MB/s
gcc-3.0.tar 86630400 44.32MB/s 50.13MB/s 58.51MB/s 68.85MB/s 73.82MB/s 75.76MB/s 76.14MB/s 75.85MB/s 75.24MB/s
howto 39422105 42.78MB/s 48.10MB/s 57.38MB/s 67.75MB/s 71.91MB/s 73.67MB/s 73.61MB/s 73.17MB/s 72.38MB/s
jdk13c 69728899 42.70MB/s 47.77MB/s 54.50MB/s 64.85MB/s 69.63MB/s 71.66MB/s 72.15MB/s 71.96MB/s 71.24MB/s
linux-2.4.5.tar 116254720 42.46MB/s 48.85MB/s 57.60MB/s 67.92MB/s 72.29MB/s 73.88MB/s 74.11MB/s 73.59MB/s 73.27MB/s
rctail96 114711151 36.39MB/s 43.19MB/s 50.96MB/s 60.60MB/s 64.33MB/s 65.43MB/s 65.79MB/s 65.78MB/s 65.18MB/s
rfc 116421901 39.81MB/s 46.76MB/s 55.92MB/s 66.48MB/s 70.79MB/s 71.68MB/s 72.21MB/s 71.92MB/s 71.06MB/s
sprot34.dat 109617186 36.09MB/s 45.06MB/s 53.26MB/s 61.60MB/s 59.69MB/s 62.25MB/s 67.20MB/s 66.84MB/s 66.38MB/s
w3c2 104201579 42.97MB/s 47.09MB/s 54.01MB/s 63.79MB/s 67.67MB/s 69.84MB/s 69.94MB/s 69.65MB/s 68.86MB/s

Note, multi-core scalability is limited by RAM bandwidth and adding more RAM channels improves performance: enwik9 BWT throughput in MB/s on Azure DS14 v2 (Intel Xeon Platinum 8171M)

libsais64 for inputs larger than 2GB

Starting from version 2.2.0 libsais64 could process inputs larger than 2GB.

The times below are the minimum of five runs measuring multi-threaded (MT) performance of suffix array construction on Azure DS14 v2 (Intel Xeon Platinum 8171M).

file size libsais64 2.2.0 (MT) divsufsort64 2.0.2 (MT) speedup (MT)
english 2210395553 61.499 sec ( 34.28 MB/s) 435.199 sec ( 4.84 MB/s) +607.65%
GRCh38.p13.fa 3321586957 84.068 sec ( 37.68 MB/s) 782.938 sec ( 4.05 MB/s) +831.32%
enwik10 10000000000 303.542 sec ( 31.42 MB/s) 1927.351 sec ( 4.95 MB/s) +534.95%

Additional memory

The libsais reuses space allocated for suffix array during construction. Sometimes this free space is not sufficient for most optimal algorithm (this is uncommon) and libsais will need to fallback to less efficient one (libsais has 4 algorithms at different break-points point: 6k, 4k, 2k and 1k; where k is alphabet size). To improve performance for those cases you could allocating additional space at the end of suffix array.

file size libsais + O(n) (ST) libsais + O(1) (ST) speedup (ST) libsais + O(n) (MT) libsais + O(1) (ST) speedup (MT)
osdb 10085684 0.222 sec ( 45.52 MB/s) 0.228 sec ( 44.20 MB/s) +2.97% 0.150 sec ( 67.30 MB/s) 0.162 sec ( 62.25 MB/s) +8.11%
x-ray 8474240 0.190 sec ( 44.52 MB/s) 0.217 sec ( 39.11 MB/s) +13.82% 0.122 sec ( 69.46 MB/s) 0.156 sec ( 54.16 MB/s) +28.25%
sao 7251944 0.175 sec ( 41.48 MB/s) 0.182 sec ( 39.75 MB/s) +4.37% 0.127 sec ( 57.26 MB/s) 0.140 sec ( 51.87 MB/s) +10.39%
ooffice 6152192 0.113 sec ( 54.55 MB/s) 0.117 sec ( 52.45 MB/s) +4.01% 0.081 sec ( 76.38 MB/s) 0.088 sec ( 70.30 MB/s) +8.65%
abac 200000 0.002 sec ( 84.36 MB/s) 0.003 sec ( 73.63 MB/s) +14.56% 0.002 sec ( 105.08 MB/s) 0.002 sec ( 86.64 MB/s) +21.27%
test3 2097088 0.034 sec ( 61.54 MB/s) 0.037 sec ( 56.45 MB/s) +9.03% 0.028 sec ( 75.76 MB/s) 0.032 sec ( 64.93 MB/s) +16.68%
  • All other files from Benchmarks above do not suffer from this fallbacks.