Aside from looking into root cause issues like file leaks, etc. in order to do a legitimate increase the "open files" limit and have that persist across reboots, consider editing
/etc/security/limits.conf
by adding something like this
jetty soft nofile 2048
jetty hard nofile 4096
where "jetty" is the username in this case. For more details on limits.conf, see http://linux.die.net/man/5/limits.conf
log off and then log in again and run
ulimit -n
to verify that the change has taken place. New processes by this user should now comply with this change. This link seems to describe how to apply the limit on already running processes but I have not tried it.
The default limit 1024 can be too low for large Java applications.