Stallmann, Brglez, Ghosh: Execution Scripts

Directories corresponding to the bigraph classes are assumed to be in the directory ../data (wrt the current directory), but may be changed by setting the environment variable DATA_DIRECTORY.

The binaries for various bigraph generating programs are assumed to be on the current path or in the directory specified by the environment variable PROGRAM_DIRECTORY.

All of these scripts have at least one argument specifying the bigraph classes on which the treatments are to be executed (and all will print a usage message if no arguments are supplied). This argument is either the name of the subdirectory for a single class -- e.g. GB_1_rnd2_08 if the treatments are to be run on the random bigraph class R(1,3830,2) (see description of naming conventions in the top-level README.formats) -- or a quoted expression for multiple classes using Unix "wild cards" -- e.g. 'GB_1_rnd*_0[1-8]' for all random tree classes (the quotes are required to prevent premature shell expansion).

• sbg_run_all run_all - script to run all simple treatments on a specified class Usage: run_all where is a string specifying a set of subdirectories of the data directory (enclosed in single or double quotes to prevent globbing)

• sbg_run_dot run_dot - script to run the dot heuristic on a specified class Usage: run_dot where is a string specifying a set of subdirectories of the data directory (enclosed in single or double quotes to prevent globbing)

• sbg_run_mla run_mla - script to run the minimum linear arrangement algorithm on a class.

  Usage: run_mla class_name [number_of_subjects]

  class_name is a string specifying a set of subdirectories of the data directory (enclosed in single or double quotes to prevent globbing)

• sbg_run_tr run_tr - script to run a single treatment on a specified class Usage: run_tr [<# of subjects>] is the two-digit treatment number, e.g. 04 or 19 is a string specifying a set of subdirectories of the data directory (enclosed in single or double quotes to prevent globbing) is the maximum number of iterations

• sbg_run_tr23 run_tr23 - run tr23 on a given bigraph type (assumes that the script tr23 is in the same directory as where we're running this script). Matt Stallmann, 21 Oct 1999

• sbg_run_tr23_verbose run_tr23 - run tr23 on a given bigraph type (assumes that the script tr23 is in the same directory as where we're running this script). Note: this is the verbose version; it uses tr23_verbose instead of tr23 Features of the verbose version - the final .ord files are saved (since it takes a long time to recreate them) and a .itr file shows the progress of tr23. Matt Stallmann, 21 Oct 1999

• sbg_time_all time_all - script to do timing of all simple treatments on a specified class Usage: time_all where is a string specifying a set of subdirectories of the data directory (enclosed in single or double quotes to prevent globbing)

• sbg_time_dot time_dot - get timing stats for dot on a given bigraph type

• sbg_time_tr23 time_tr23 - get timing stats for tr23 on a given bigraph type (assumes that the script tr23_for_timing is in the same directory as where we're running this script). Matt Stallmann, 18 Mar 2001

• sbg_tr23 tr23 - a new treatment that alternates between barycenter and adaptive insertion Usage: tr23 dotfile initial_ord_file Matt Stallmann, 21 Oct 1999

• sbg_tr23_for_timing tr23_for_timing - outputs number of iterations for tr23 Usage: tr23 dotfile initial_ord_file Matt Stallmann, 18 Mar 2001

• sbg_tr23_verbose tr23 - a new treatment that alternates between barycenter and adaptive insertion (verbose version) Usage: tr23 dotfile initial_ord_file Matt Stallmann, 21 Oct 1999