sudo cp /etc/php.ini /home/httpd/domain.com/
#edit /home/httpd/domain.com/php.ini as required
#then
sudo vi /home/apache/conf/domains/domain.com.conf
#and add this line in <ifmodule mod_php5.c="">
PHPINIDir /home/httpd/domain.com
#restart apache
/etc/init.d/httpd restart
This shall allow you to set allow passthru or system or exec call per domain.
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