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fSAIS - External memory suffix array construction using inducing

Description

fSAIS is an implementation of the external-memory suffix array construction algorithm. The algorithm was described in the paper

@inproceedings{kkpz17alenex,
  author =    {Juha K{\"{a}}rkk{\"{a}}inen and Dominik Kempa
               and Simon J. Puglisi and Bella Zhukova},
  title =     {Engineering External Memory Induced Suffix Sorting},
  booktitle = {19th Meeting on Algorithm Engineering and Experimentation
               (ALENEX 2017)},
  pages     = {98--108},
  year      = {2017},
  doi       = {10.1137/1.9781611974768.8},
}

The latest version of fSAIS is available from https://github.com/dominikkempa/fsais.

Requirements

fSAIS has no external dependencies (libraries, cmake, etc). It only requires:

  • g++ compiler supporting the -std=c++0x flag (all modern versions)
  • A 64-bit operating system. The current version has been tested on Linux/PC.

Compilation and usage

The package contains a single Makefile in the main directory. Type make to build the executable. For usage instructions, run the program without any arguments.

Example

The simplest usage of fSAIS is as follows. Suppose the text is located in /data/input.txt. Then, to compute the suffix array of input.txt type:

$ ./construct_sa /data/input.txt

This will write the output suffix array to /data/input.txt.sa5. Each element of the suffix array is encoded using 40-bit integers, i.e., the output suffix array will take up 5n bytes of disk space. By default, the algorithm uses 3.5GiB of RAM for computation and it assumes that the input text is over byte alphabet (see below for explanation on how to adjust this). A more advanced usage is demonstrated below.

$ ./construct_sa ./input.txt -m 8gi -o ../input.txt.sa

Explanation:

  • The -m flag allows specifying the amount of RAM used during the computation (in bytes). In this example, the RAM limit is set to 8gi = 8 * 2^30 bytes (see below).
  • The -o flag allows specifying the location and filename of the output suffix array. The default location and filename is the same as input text, with the appended ".saX" suffix, where X is the used integer size (by default: 5 byte).

Notes:

  • The argument of the -m flag (RAM used during the computation) can be specified either explicitly or using common suffixes such as K, M, G, T, Ki, Mi, Gi, Ti, which respectively correspond to multipliers: 10^3, 10^6, 10^9, 10^12, 2^10, 2^20, 2^30, 2^40. Suffix names are not case-sensitive, e.g., Ti = ti, k = K.
  • The flags specifying RAM usage, output filename, etc. can be given in any order.
  • Filenames passed as command-line arguments can be given as relative paths, e.g., ../input.txt and ~/data/input.txt are valid paths, see also example above.
  • To enable additional statistics about the computation (alternative counter of I/O volume and tracing of the disk usage), uncomment line with AUX_DISK_FLAGS in the Makefile. When this flag is enabled, the computation could slow down thus this flag is disabled by default.
  • To change the type used to encode characters of the input text or the integer type used to encode positions in the text, adjust types "char_type" and "text_offset_type" as well as the value of the variable "text_alphabet_size" in the source file ./src/main.cpp.

Troubleshooting

  1. I am getting an error about the exceeded number of opened files.

Solution: The error is caused by the operating system imposing a limit on the maximum number of files opened by a program. The limit can be increased with the ulimit -n newlimit command. However, in Linux the limit cannot be increased beyond the so-called "hard limit", which is usually only few times larger. Furthermore, this is a temporary solution that needs to repeated every time a new session is started. To increase the limits permanently, edit (as a root) the file /etc/security/limits.conf and add the following lines at the end (including the asterisks):

* soft nofile 128000
* hard nofile 128000

This increases the limit to 128000 (use larger values if necessary). The new limits apply (check with ulimit -n) after starting new session.

Limitations

  • At present the only limitation in the usage of the algorithm is the need to ensure that the limit for the number of opened files in the system is sufficiently large to prevent the above error. This technical shortcoming will be eliminated in the future versions of fSAIS.

Terms of use

fSAIS is released under the MIT/X11 license. See the file LICENCE for more details. If you use this code, please cite the paper mentioned above.

Authors

fSAIS was implemented by: