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.
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.
As a courtesy, a 64-bit version of WOMBAT, womba_W64.zip, is available that will run under Windows. This has been cross-compiled under Linux and appears to run in MSYS and CYGWIN environments or a DOS window.
This can be downloaded from
For MSYS or CYGWIN adapt the Linux instructions for installation. Otherwise unzip wombat_W64.zip. This will give you the executable ﬁle wombat.exe.
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.
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 chapter 4 for full details), and options any run time options you may wish to give (see chapter 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.
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
A number of worked examples, complete with output ﬁles and captured screen output, are provided; see chapter 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.
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,
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 !
Repeat for at least one more example.
64-bit versions of WOMBAT have been compiled under Ubuntu 14.04 the Intel™ ifort (version 220.127.116.11) compiler together with the MKL library to provide highly optimised BLAS and LAPACK routines. Parallel execution is achieved by loading the multi-threaded version of this library together with OpenMP instructions.
32-bit versions are no longer maintained.
The Windows versions of WOMBAT have been ‘cross-compiled’ under Linux using the gfortan compiler (version 7.3) together with the OpenBLAS library. Only a 64-bit versions is supplied.
Previous versions compiled under Cygwin or MinGW are no longer maintained.
WOMBAT is set up to ‘expire’ after a certain date. Usually this is approximately 5–6 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).
WOMBAT caters for novice users by supplying defaults for most aspects of estimation. Essential sections of the manual to ‘get started’ are :
The most ‘diﬃcult’ part of using WOMBAT is to correctly set up the parameter ﬁle. The detailed rules given in chapter 4 are best understood following some example(s). The suite of examples provided templates for various types of analyses performed by WOMBAT, and a range of diﬀerent models.
HINT: A suitable strategy might be
- Choose the type of analysis you are interested in, and decide on the model of analysis. Start with a relatively simple scenario.
- Try to ﬁnd an example which matches the type of analysis and ﬁts a not too dissimilar model.
- Inspect the example parameter and input ﬁles.
- Read the description of individual entries in the parameter ﬁle (Chapter 4). Compare each section to the relevant section in the example parameter ﬁle.
- Try to modify the example ﬁle for your data (& pedigree) ﬁle and model.
WOMBAT has undergone fairly rigorous testing, more so for some models than for others. However, there are bound to be errors and inconsistencies – especially early in its development.
Errors in the input ﬁles are the most likely source of problems which are not a program bug. Some of these are trapped, leading to a programmed error stop (with a screen message of “exit WOMBAT” or “Programmed (error) stop for WOMBAT encountered”). Almost certainly, this is due to erroneous input, in particular a mistake in the parameter ﬁle ! You should be able to ﬁgure out what is wrong from the accompanying brief error message and ﬁx it. Others might simply cause the program to abort.
If – after thoroughly checking your parameter ﬁle and other input ﬁles – you think you have encountered a genuine error in the program, please submit a ‘bug report’, as speciﬁed below1 .
To submit an informative ‘bug report’, please carry out the following steps:
and extract the executable wombat_chk as described above.
This may sound like a lot of work, but is necessary to for me to even begin to try understanding what is going on !
As time progressed, additional specialised capabilities have been added to WOMBAT which are not (yet) fully covered in the manual. Some notes are distributed together with the examples illustrating these features, e.g.
The “Wicked WOMBAT Wiki” can be found at
It provides a selection of notes related to WOMBAT and general issues of REML estimation. In particular, there are frequently asked question sections covering