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From my experience, a rebooted server works better especially after having performance issues with a certain program.
Depending on the distro you're using a simple restart command should do it. Google says on solaris something like this:
svcadm restart java
or svcadm restart javad
or maybe svcadm restart tomcatd
whatever the name of your java daemon is - put that in the command. That should gracefully restart the java server.
Don't restart the whole server. That can go badly, particularly if something doesn't come back to life - you've now got an offline server. There's very little need to restart most nix servers.