I have a program that does a bunch of initialization stuff before it starts into it's main event loop. This initialization usually takes about 1 second. I tried running this program in debug mode without any breakpoints or watches, just starting it up. What normally takes 1 second took over four hours to run. The main java process reports 253 minutes of CPU time. During this time top/vmstat/iostat all reported 100 user time, no IO and no virtual memory.
This is an a Fedora 1 intel box with a 2.8ghz pentium and 2gb of memory, etc, etc, etc.
Any ideas on why I would see such a huge difference in performance?