[warn] module php5_module is already loaded, skipping

You have two of the lines in your httpd.conf: LoadModule php5_module /usr/lib/apache/libphp5.so

Look into /etc/httpd/conf/httpd.conf and remove one off these lines

LoadModule php5_module /usr/lib/apache/libphp5.so
 
The php5_module is loaded directly in:

/etc/httpd/conf/httpd.conf

but also in the by that file included:

/etc/httpd/conf/extra/httpd-phpmodules.conf

which one should I delete when I'm using the custombuild system?
 
The php5_module is loaded directly in:

/etc/httpd/conf/httpd.conf

but also in the by that file included:

/etc/httpd/conf/extra/httpd-phpmodules.conf

which one should I delete when I'm using the custombuild system?

It doesn't really matter in my opinion but the most suitable place to load the module is within httpd-phpmodules.conf. You'll want to keep httpd.conf as clean as possible.
 
And of course you can find and edit the httpd script (in CentOS usually at /etc/rc.d/init.d/httpd to print the OK if you want; it's an ordinary (though fairly complex) bash script.

Jeff
 
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