The code I'm talking about was incomprehensible on many levels -- most of the cryptically-named variables were global, and might have a comment explaining their meaning somewhere in the 200,000+ lines of code spread across 200 or so files, but it was often a struggle to find it. Other times, there would be no explanation at all. Even once you'd found out what it meant it was a struggle to keep it in your head and not confuse it with any of another bunch of similarly named variables (woe bedtide anyone who gets confused between nks, nqs and nkqs!)
This is all pretty typical of large scientific codes, though. Scientists are, as a class, the worst programmers on Earth.