@InfraBlue,
It is hard to speak in the abstract without knowing detail about the specific problems and the hardware involved.
Maybe these supercomputers weren't designed with this class of problem in mind (but obviously I without the specifics all we can do is speculate).
I am just guessing based on things I have worked on before... I am guessing that the GPU does parallel processing (where many computations can happen at the same time) much better than the supercomputer.