They had at least one Cray on site in the novel, a few SGI workstations seems very plausible.

While it is true that Silicon Graphics eventually acquired Cray Computer, they did it after the novel, and the film's release, but I would suppose that even before the 1996 acquisition that SGI and Cray machines were very good partners, like peas in a pod.

It is important to remember that nobody who operated a Cray did it in isolation. The supercomputers always require some extra workstations arrayed around it in order to get stuff done. Of course, there were remote connections too, but often there would be at least one sort of "dedicated user console" that was closely coupled to the supercomputer itself. I believe that some supercomputers of that era were poorly equipped to actually handle interactive user sessions, and that's why.