If you have a site on your cPanel VPS that needs a custom php.ini file, you can set that up by following these steps:
1,Copy /usr/local/lib/php.ini to the site's Web root folder (public_html).
>cp /usr/local/lib/php.ini /home/USERNAME/public_html
2,Make sure the file is owned by their cPanel user
>chown USERNAME:USERNAME php.ini
3,Add the following to the site's ".htaccess" file
SetEnv PHPRC /home/USERNAME/public_html/php.ini
or
suPHP_conf /home/user/someplace/php.ini
Custom Values should be added in .htaccess in a format as shown in example below
php_value memory_limit 128M
php_value max_execution_time 3600
php_value post_max_size 5M
php_value upload_max_filesize 5M
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