Mysql is a free database; available with GPL or with a commercial license.
MySql homepage has all the details.
Mysql is very popular, as it offers respectable features and performance without the costs of Sybase, Oracle etc.
It runs on lots of platforms, linux being one of the more popular ones, and is quite robust.
One gotcha: are you using the older org.gjt.mysql classes or the "newer official" one? It's a good idea to search lots of files and ensure you're consistent.