I set /etc/security/limits.conf so that root has a high ulimit. However, after restarting the system some of the processes running as root still have a limit of 1024. Does the limits.conf not apply to all applications?

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The limits set through /etc/security/limits.conf only apply to processes that pass through the PAM stack and have the pam_limits module applied.

It's likely these processes do not go through PAM.

I think you'd have to find out where they are started from and manually set the ulimit there using the ulimit command.

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In Redhat there is initscript that can set ulimits for things started via init.

man initscript for details

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Good to know about. I wasn't aware of this feature, but it certainly looks like it would solve the problem of processes that do not go through PAM. Also, it doesn't appear to be Redhat specific, as I have the same thing on my SuSE and Gentoo systems. – Kamil Kisiel Jul 22 '09 at 23:52
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