GMAT is written primarily in C++.
gmat.jar is an api wrapper to allow java code to access the core functionality as explained at http://gmat.sourceforge.net/docs/R2020a/api/userguide/GettingStarted.html
In other words,
gmat.jar would be used if you wanted to write your own java program that interacted with gmat functionality.
Running the gmat application is explained at https://sourceforge.net/projects/gmat/files/GMAT/GMAT-R2016a/
On Linux, open a terminal window and change directories to the GMAT bin
folder. The GMAT command line program is executed by running the GmatConsole
application in that folder:
The Beta GUI can be run using the same terminal window by running Gmat_Beta:
Linux users can create a launcher for either the command line application or
the GUI application by following the instructions for that process for their
The links from the NASA page to the sourceforge link can be a bit confusing. To make sure you are getting the instructions for the version you are downloading, navigate through https://sourceforge.net/projects/gmat/files/GMAT/ to the version you want to use.
UBUNTU 18.04 Note: Ubuntu 18.04 does not ship with libpng12.so, used by
the wxWidgets libraries bundled with the Ubuntu installation. You can
download the needed library from the Ubuntu packages site
Download the package and install it using the Ubuntu package manager.
The same page contains run instructions for other platforms as well.