3.1 Installation

WOMBAT is distributed as a pre-compiled executable file. A number of versions are available. The main target operating system is Linux. In addition, executable files for Windows environments are available.

3.1.1 Installation for LINUX operating systems



1. Download the version appropriate to your machine from
http://didgeridoo.une.edu.au/km/wombat.php
2. Uncompress and unpack the file (nn = 32  or 64  or win) using
   tar -zxvf wombatnn  .tar.gz
This will create the directory WOMBAT which contains the executable wombat.
3. Check that your system recognises wombat as an executable file, e.g. using
   ls -l WOMBAT/wombat
If necessary, use the chmod command to add executable permission or access permission for other users, e.g.
   chmod a+x WOMBAT/wombat.
4. Make sure that the operating system can find wombat, by doing one of the following :

HINT: PATH is set in your login file, e.g. .login_usr, or shell start-up file, e.g. .tcshrc; use printenv PATH to check your current PATH settings.
You make have to log out and log in again before changes in your PATH are recognised, and wombat is found by the system.


3.1.2 Installation under WINDOWS

Windows is not an operating system that is well suited to scientific computations. Two versions of WOMBAT are available that will run under Windows. However, these are slower than their Linux counterparts and restricted in the size of the analyses that they will accommodate (see 3.1.5).



1. Download
http://didgeridoo.une.edu.au/km/wombat.php

UNZIP wombatwin2.zip. This will give you the executable file wombat.exe.
2. Check that this is recognised as an executable file by clicking the file properties tab – change if required.
3. Move wombat.exe to a directory of your choice and, if necessary, add this directory to the PATH that the operating system searches when looking for executable files – see the documentation for your version of Windows for details.

HINT: You may be able to inspect the setting for PATH by opening a command window (type cmd.exe into the “Run” box in the start menu & hit return) and typing ECHO %PATH%.
Under XP, right-click on My Computer (from the start menu), choose Properties, then Advanced and the Environment Variables tab. This will open a dialog box which will list the existing variables and their settings. If PATH already exists, choose Edit and add the WOMBAT directory – remember to use the full path and to separate it from the existing variables by a semi-colon. Otherwise choose New and create it.


3.1.3 Running WOMBAT

WOMBAT is expected to be run from a command line interface, i.e. you need to open a ‘terminal’ window and type in the appropriate command, hitting return to start the program running.

The general form of the command (under Linux and its emulation) is
   wombat options parfile
with parfile the ‘parameter file’ specifying everything WOMBAT needs to know about the input files and models of analysis (see 4 for full details), and options any run time options you may wish to give (see 5). If you have not put the executable file somewhere the operating system can find it (or have not modified your PATH settings), you will need to replace wombat above by the full path, e.g. /home/agbu/WOMBAT/wombat if the program has been placed in /home/agbu/WOMBAT.

3.1.3.1 Running WOMBAT under Windows

If you have installed MinGW/MSYS, you should open such ‘terminal’ and run WOMBAT in it in the same way as under Linux. Otherwise, you should open a DOS type window and type the command in it. Remember to use backwards rather than forward slash(es) if you need to type a full path to the executable.

You can run wombat.exe by simply double-clicking on it. However, this is not recommended! WOMBAT creates screen output which lets you monitor how a run is progressing. More importantly, this screen output will provide some diagnostics when something has gone wrong, e.g. help you remedy errors in the parameter or other input files. Hence, if you really want to start WOMBAT by double-clicking on an icon, you should make sure that the window which is opened does not close automatically after the run finishes or aborts! A simple way to do this is to create a .bat file.

rem Simple .bat file to run WOMBAT in a DOS window 1
rem Assumptions: 2
rem  1) parameter file is wombat.par 3
rem  2) other run time options are given in wombat.par 4
rem  3) wombat.exe resides in  C:\Program_Files\WOMBAT 5
@echo off 6
color 70 7
echo "Ready to run WOMBAT" 8
pause 9
C:\Program_Files\WOMBAT\wombat -v 10
echo "WOMBAT has finished" 11
pause 12
exit 13

3.1.4 Examples and testing

A number of worked examples, complete with output files and captured screen output, are provided; see chapter 9 for further details. These can be downloaded and installed in analogous manner to the program. This description is appropriate for Linux and Cygwin; for Windows adjust as appropriate, e.g. by replacing forward with backward slashes, etc.

1.
Download examples.tar.gz from
http://didgeridoo.une.edu.au/km/wombat.php
2.
Uncompress and unpack the file using
   tar -zxvf examples.tar.gz
Do this in the same directory as above! This will create the directory Examples with subdirectories Example1, ...  , Examplen  .

Each subdirectory contains the input and output files for a run of WOMBAT, together with a records of the screen output in the file typescript. To test your installation,

1.
Choose an example and change into its directory.
2.
Make a new temporary subdirectory, e.g. try.

N.B.: This should be a ‘parallel’ directory to sub-directories A,B,...  , i.e. Examplen  /try not Examplen  /A/try. Otherwise, you need to adjust the paths to the data and pedigree files in the parameter file for WOMBAT to be able to find them !

3.
Copy all input files to the temporary directory.
4.
Change into the temporary directory and run WOMBAT, using the same command line options (if any) as shown in the beginning of typescript.
5.
Compare your output files with those supplied – apart from date and time they should be virtually identical; small discrepancies in higher decimals may occur though.
6.
Delete temporary subdirectory.

Repeat for at least one more example.

3.1.5 Compilation notes

3.1.5.1 Linux

64-bit versions of WOMBAT have been compiled under Ubuntu 14.04 or CentOS 6, using either the Lahey lf95 (version 8.00a) or the Intel ifort (version 13.01.1) compiler. For the latter, versions loading multi-threaded BLAS and LAPACK routines from the MKL library are available.

32-bit versions are no longer maintained.

3.1.5.2 Windows

The Windows versions of WOMBAT have been ‘cross-compiled’ under Linux using the gfortan compiler. Both 32- and 64-bit versions are available.

Previous versions compiled under Cygwin or MinGW are no longer maintained.

3.1.6 Updates

WOMBAT is set up to ‘expire’ after a certain date. Usually this is approximately 2–3 years after compilation (not download!) date. This feature aims at reducing the number of outdated copies being used, and any associated problems. WOMBAT will print out a warning message when used in the month preceding the expiry date. In addition, a run time option is available to query the program for this date.

If your copy of WOMBAT has expired – or you simply want to update to a newer version, please repeat the installation steps outlined above (section 3.1).