Error: SecurityException in Application.cpp:188: Do not have root privileges. Executable not set-uid root?

Posted on July 17, 2013 Updated on July 17, 2013

After recovering my Cpanel server it was getting the Internal server error for every domain hosted and throwing  some messages in error log

[Wed Jul 17 09:46:14 2013] [error] [client 111.222.333.444] Premature end of script headers: index.php, referer: http://domain.com/
[Wed Jul 17 09:46:14 2013] [error] [client 111.222.333.444] SecurityException in Application.cpp:188: Do not have root privileges. Executable not set-uid root?

My server is configured for running suphp in CGI mode with Mod-security, So it will check the sticky bit of the suphp binary.The error was because the suphp binary was missing its suid permissions and assigning it fixed the issue.

chmod +s /opt/suphp/sbin/suphp

This should fix the issue instantly.