I’m currently publishing Multiple Back-Propagation software (http://dit.ipg.pt/MBP/) which has a CUDA implementation of Back-Propagation and Multiple Back-Propagation algorithms under GPL 3 license. However I received a mail message saying that I might have problems with NVIDIA license (with the v3 license). I wrote all the code including the CUDA code so I don’t see why this might be a problem. But since this is the first time I publish anything under open source, I would like to know if I might have any problem and if I can avoid it by publishing it under GPL 2.1.
It sounds like you need to talk to someone expert in copyright law in the jurisdiction where you are planning to establish primary copyright (Portugal and/or the European Union, I am guessing). I very much doubt you will find that here.
I don’t see why it would be a problem…you should be able to license it however you want, just like any other code. For a while, there were restrictions on re-distributing the CUDA runtime and cutil libraries (and there may still be, you’ll have to check), but that wouldn’t matter if you were just releasing the source.
EDIT: avidday is right…there may be something specific about your jurisdiction that interferes with the new license.