If you are not comparing Linux and Windows XP on the same machine, it is very difficult to tell what the difference is. It is possible that when the processor is faster, the GFX board and disk subsystem are slower.
Java transfers all of these I / O and GFX functions to the underlying OS, and the only thing you can do differently is to do less work or work more efficiently. This is likely to make both systems faster, since there are no special features for one OS that you can configure.
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