Installation Notes

System Requirements

• Linux (kernel >= 2.4.20)
• g++ compiler, version 3.1.x or higher
• for further details refer to Stxxl homepage

Installation

• download the program and unzip it
  
• download the Stxxl library and unzip it
  
• 'stxxl' has to be a subdirectory of 'code' (e.g., create an appropriate symbolic link)
• configure the program (see configuration notes)
• execute 'make' in the directory 'code/tmess/'
• execute 'make dc3' in the directory 'code/skewalg/'
• execute 'make cksa' in the directory 'code/sacheck/'

Running the benchmark program

• cd code/tmess/
• 'start' prints usage information
• e.g., 'start 13 input_size  input_file' runs the DC3/Skew algorithm with the first 'input_size' MBytes of the file 'input_file'
  
• Type 'start' for further options ('start 12 ...' for 4-Discarding and 'start 11 ...' for 4-Tupling)
• the progress is reported to std::out
  
• the configuration, the input parameters, statistical data (as running time, I/O volume, ...) is reported to std::out

Running skew (DC3) algorithm

• cd code/skewalg/
• 'dc3' prints usage information
• run 'dc3' with specified INPUT_SIZE, INPUT_FILE, and OUTPUT_FILE

Running external memory suffix array checker

• cd code/sacheck/
• 'cksa' prints usage information
• run 'dc3' with specified SUFFIX_ARRAY and INPUT_STRING file names

Other Algorithms

• The 2-Tupling and the 2-Discarding algorithm can be found in the sub directory 'code/oldsa/'
• For installation run 'make' in '/code/oldsa/tmess/ and run it with 'start 11 ...' in 'code/oldsa/tmess/'
• For 2-Discarding do the same with 'start 12 ...'
• A non pipelines doubling algorithms can be found in 'code/nopipedoub/' and started with 'start input_size input_file'
• A suffix array checker can be found in 'code/sachecker/' (watch the 'main.cpp' file for how to use it)
• In 'code/tools/',  and 'code/lcp/' there are smaller programms for lcp array construction and more (mostly less than two pages of code per programm)