This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
Ubuntu itself doesn't use any JRE. So I assume you're looking at a specific Java app that uses one of the JREs installed on your system. You can use the ps command (for instance something like "ps -ef" or "ps -efo") to find which processes are running, including the entire command line used to launch the app.
I don't think that you'll find a global default memory config for Java. It would infringe on the "write once, run anywhere" paradigm by making it uncertain whether a given system could properly run random apps without overrides of their own. And, truthfully, overriding the global memory defaults on account of a single application's needs is a little rude to all the other apps, anyway.
It would make more sense to run the affected command in a shell script with appropriate options set in the java command in the script, especially since the non-memory parts of that particular command line aren't exactly easy either.
An IDE is no substitute for an Intelligent Developer.