What method are you using to install VuFind? I am not aware of any reason why you should be unable to run it on Ubuntu with mariadb; I know the software works with Ubuntu 16.04 and with mariadb, but I'm not sure if both of those things have been tested simultaneously
before. Perhaps the .deb package is causing a problem, though it appears to be designed generically to support any mysql compatible database. Perhaps installing manually could make a difference, though.
In any case, it should be possible to get this working one way or another. Please let me know if I can do anything more to help.