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Linux: Increasing the number of open file descriptors

We found an interesting issue on the same server (VM) when connection to terminal window in VNC and through ssh...
When trying to list the limit for the number of open files, the terminal window in VNC showed the limit to be 1024. Very low indeed. Increasing the limit using ulimit failed. The same server but now through ssh (putty), showed the same parameter to be 131029. This confused us a bit until we realized that the VNC session was initialized by the VNC daemon and disconnecting from it, merely closed the session but didn't restart the main process. When we restarted VNC, a terminal showed a much better value for nolimit of 65536. However, that was still different from the value we got when using an ssh session. The difference was explained in this document: Increasing the number of open file descriptors. You must align a few more config files...
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