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libsais

The libsais is a library for fast (see Benchmarks below) linear time suffix array, longest common prefix array and Burrows-Wheeler transform construction based on induced sorting algorithm described in the following papers:

  • Ge Nong, Sen Zhang, Wai Hong Chan Two Efficient Algorithms for Linear Suffix Array Construction, 2008
  • Juha Karkkainen, Giovanni Manzini, Simon J. Puglisi Permuted Longest-Common-Prefix Array, 2009
  • Nataliya Timoshevskaya, Wu-chun Feng SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction, 2014
  • Jing Yi Xie, Ge Nong, Bin Lao, Wentao Xu Scalable Suffix Sorting on a Multicore Machine, 2020

Copyright (c) 2021-2022 Ilya Grebnov ilya.grebnov@gmail.com

The libsais is inspired by libdivsufsort, sais libraries by Yuta Mori and msufsort by Michael Maniscalco.

Introduction

The libsais provides simple C99 API to construct suffix array and Burrows-Wheeler transformed string from a given string over constant-size alphabet. The algorithm runs in a linear time using typically only ~16KB of extra memory (with 2n bytes as absolute worst-case; where n is the length of the string). OpenMP acceleration uses 200KB of addition memory per thread.

  • The libsais works with compilers from GNU, Microsoft and Intel, but I recommend Clang for best performance.
  • The libsais is sensitive to fast memory and software prefetching and might not be suitable for some workloads. Please benchmark yourself.

License

The libsais is released under the Apache License Version 2.0

Changes

  • April 18, 2023 (2.7.2)
    • Fixed out-of-bound memory access issue for large inputs (libsais64).
  • June 19, 2022 (2.7.1)
    • Improved cache coherence for ARMv8 architecture.
  • April 12, 2022 (2.7.0)
    • Support for longest common prefix array (LCP) construction.
  • January 1, 2022 (2.6.5)
    • Exposed functions to construct suffix array of a given integer array.
    • Improved detection of various compiler intrinsics.
    • Capped free space parameter to avoid crashing due to 32-bit integer overflow.
  • October 21, 2021 (2.6.0)
    • libsais16 for 16-bit inputs.
  • October 15, 2021 (2.5.0)
    • Support for optional symbol frequency tables.
  • July 14, 2021 (2.4.0)
    • Reverse Burrows-Wheeler transform.
  • June 23, 2021 (2.3.0)
    • Burrows-Wheeler transform with auxiliary indexes.
  • April 27, 2021 (2.2.0)
    • libsais64 for inputs larger than 2GB.
  • April 19, 2021 (2.1.0)
    • Additional OpenMP acceleration.
  • April 4, 2021 (2.0.0)
    • OpenMP acceleration.
  • February 23, 2021 (1.0.0)
    • Initial release.

Versions of the libsais library

  • libsais.c (and corresponding libsais.h) is for suffix array, PLCP, LCP, forward BWT and reverse BWT construction over 8-bit inputs smaller than 2GB (2147483648 bytes).
    • This version of the library could also be used to construct suffix array of an integer array (with a caveat that input array must be mutable).
  • libsais64.c (and corresponding libsais64.h) is optional extension of the library for inputs larger or equlas to 2GB (2147483648 bytes).
  • libsais16.c (and corresponding libsais16.h) is independent version of the library for 16-bit inputs.

Examples of APIs (see libsais.h, libsais16.h and libsais64.h for complete APIs list)

    /**
    * Constructs the suffix array of a given string.
    * @param T [0..n-1] The input string.
    * @param SA [0..n-1+fs] The output array of suffixes.
    * @param n The length of the given string.
    * @param fs Extra space available at the end of SA array (0 should be enough for most cases).
    * @param freq [0..255] The output symbol frequency table (can be NULL).
    * @return 0 if no error occurred, -1 or -2 otherwise.
    */
    int32_t libsais(const uint8_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);

    /**
    * Constructs the suffix array of a given integer array.
    * Note, during construction input array will be modified, but restored at the end if no errors occurred.
    * @param T [0..n-1] The input integer array.
    * @param SA [0..n-1+fs] The output array of suffixes.
    * @param n The length of the integer array.
    * @param k The alphabet size of the input integer array.
    * @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
    * @return 0 if no error occurred, -1 or -2 otherwise.
    */
    int32_t libsais_int(int32_t * T, int32_t * SA, int32_t n, int32_t k, int32_t fs);

    /**
    * Constructs the burrows-wheeler transformed string of a given string.
    * @param T [0..n-1] The input string.
    * @param U [0..n-1] The output string (can be T).
    * @param A [0..n-1+fs] The temporary array.
    * @param n The length of the given string.
    * @param fs Extra space available at the end of A array (0 should be enough for most cases).
    * @param freq [0..255] The output symbol frequency table (can be NULL).
    * @return The primary index if no error occurred, -1 or -2 otherwise.
    */
    int32_t libsais_bwt(const uint8_t * T, uint8_t * U, int32_t * A, int32_t n, int32_t fs, int32_t * freq);

    /**
    * Constructs the original string from a given burrows-wheeler transformed string with primary index.
    * @param T [0..n-1] The input string.
    * @param U [0..n-1] The output string (can be T).
    * @param A [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
    * @param n The length of the given string.
    * @param freq [0..255] The input symbol frequency table (can be NULL).                	
    * @param i The primary index.
    * @return 0 if no error occurred, -1 or -2 otherwise.
    */
    int32_t libsais_unbwt(const uint8_t * T, uint8_t * U, int32_t * A, int32_t n, const int32_t * freq, int32_t i);

Benchmarks

Full list of benchmarks are moved to own Benchmarks.md file.

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.