My dad worked with a few Crays when he was in University. They were having problems with it, and he was explaining to me how they debugged it. I'm sure I have it wrong, but the way I understood it is that they first had to drain all the liquid out of the tower into a special container, then directly hooked up some probes to the machine at certain parts. Without the liquid cooling, it could only be run for a fraction of a second or it'd overheat. It had a special mode where it'd step the machine in very short bursts, allowing the guy debugging it to peak at the data. If it wasn't messing up at one part, he take the probes out and stick them somewhere else, then step the machine and analyze.
