Hello,
just reading some git messages and old docs/notes that I wrote for the application, I dealt with this problem rebuilding the jogl package in my Ubuntu and all works fine.
The instructions that I followed for rebuild the package were detailed here:
https://web.archive.org/web/20140330235145/http://jogamp.org/jogl/doc/HowToBuild.html (Surely the page change since that time).
And checking the repository of the application, the version compiled of JOGL was 2.1.4, so I'm not sure if your problem was the same that mine in that moment (GLJPanel doesn't showed the animation for the training of my network).
I hope this help you.
Grettings.