When using FastCGI (FCGI) as the loader for PHP, traditional php_values in the .htaccess file as well as custom php.ini files in the public_html directory no longer work. Instead we must create a wrapper for the main FCGI binary that causes the php.ini to be loaded from it's current working directory instead of the server-wide one.
First open .htaccess for the account in question and add the following lines to the bottom of the file:
AddHandler php5-fastcgi .php Action php5-fastcgi /cgi-bin/php5.fcgi
Next, you'll need to source your main server php.ini which is located in /usr/local/lib/. Also note that it needs to have the correct ownership so we'll take care of that too:
cd /home/user/public_html/cgi-bin/ cp -a /usr/local/lib/php.ini . chown user:user php.ini
Next we need to create the wrapper script. Create a file in your current directory (cgi-bin) called
php5.fcgi as defined above and add the following:
#!/bin/sh export PHP_FCGI_CHILDREN=1 export PHP_FCGI_MAX_REQUESTS=10 exec /usr/local/cpanel/cgi-sys/php5
Finally, make sure the ownership and permissions are correct on this file:
chown user:user php5.fcgi && chmod 0755 php5.fcgi
You can now edit the php.ini inside cgi-bin/ and change the desired values. You can verify they are set properly by inserting the phpinfo() function inside a PHP script on that user account.