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When I vnc into the box as a regular user the ulimit is 1024
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I guess you mean the number of open files (nofile) that 1024 is the default value for any system. If there is a different nofile while you ssh into the box in question, then someone has change it maybe from inside the sshd startup script (/etc/init.d/sshd). Check if that's the case and if you insist to increase nofile for vnc do the same for vncserver startup script (/etc/init.d/vncserver). To increase nofile you should run:
