I took a look at GSAT. My initial guess would always be the code was just written poorly and inefficiently, but the code seems to have been written by someone who probably knew what they were doing. Could it have been done more efficiently? Certainly so, since any substantial piece of code has room for improvement. But I'd not quibble there.
Anyway, option 2 is just more likely. People solve small problems, and find they work quickly. So the answer is to throw a much larger problem at the code, and not realize the complexity grows rapidly with problem size.
I would just suggest you accept that big problems require big, FAST computers, or a large cup of coffee and a willingness to sit down with a large book to read while you wait for a result. The complete works of Shakespeare might be a good start. Don't forget to read all the footnotes. And read it a second time, because you probably missed something the first time through.
