I am still trying to figure out what is going on here. I have installed cpufrequtils and set both cpu0 and cpu1 to 'performance'. Not much seems to have improved.
I did notice now that every now and then the %wa goes up. Sometimes over 50%. Is this perhaps a disk io issue? Any ideas how I can track down what is causing the waiting? I still feel that either Ubuntu or Tomcat need to be told to use / allow more cpu usage for the processors / threads because the %us peaks at arounf 15%. As stated previously on another machine this runs through in a fraction of the time and %us on that machine runs between 80-90%.
Any clues would be greatly appreciated. Thanks.