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I think if you have more than one processor or core and the process is multithreaded then it can go over 100%.
Ie, if you have a quad-core machine and your process is consuming the entirity of two cores then it will show as using 200% of your CPU. If the process is using all of all the cores then it will show as 400%.
As to how to make it use less, it really depends on your app, what is it?
What is the java application in question? Is it something you have written or is it something someone else has written?
If it isn't time sensitive and it is interfering with your other applications then you could always set its nice level so that it runs at a lower priority.
That said, unless you actually need your CPUs for something else you might as well leave it. Its probably not the best outlook but I dont like to see my fast CPUs being unused, the nearer they are to full utilisation then I know i'm getting my monies worth
"If no arguments are given, `nice' prints the current scheduling
priority, which it inherited. Otherwise, `nice' runs the given COMMAND
with its scheduling priority adjusted. If no ADJUSTMENT is given, the
priority of the command is incremented by 10. You must have
appropriate privileges to specify a negative adjustment. The priority
can be adjusted by `nice' over the range of -20 (the highest priority)
to 19 (the lowest)."
An example would be:
$ nice -n 10 nice
This would lower the priority of the 'nice' command ;-).