When using FastCGI (FCGI) as the loader for PHP, traditional phpvalues in the .htaccess file as well as custom php.ini files in the publichtml 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.