This is really strange and I have no idea why no one seems to mention it, but if you are getting frustrated trying to install the ioncube loader on php-fpm, just ignore the instructions to create the 20-ioncube.ini file, and plug the line directly into the end of your php ini.
Steps to install ioncube loader with php5-fpm
sudo wget http://downloads2.ioncube.com/loader_downloads/ioncube_loaders_lin_x86-64.tar.gz
sudo tar xzf ioncube_loaders_lin_x86-64.tar.gz
mv /usr/local/ioncube/* /usr/lib/php5/20121212/
This is the same.
Now, instead of creating a file called 20-ioncube.ini or ioncube.ini directly add it to your php.ini file (On Ubuntu with a repository installed php5-fpm package, php.ini will be found at /etc/php5/fpm/php.ini)
At the very end add:
zend_extension = /usr/lib/php5/20121212/ioncube_loader_lin_5.5.so
Then restart php-fpm
service php5-fpm restart
If it still doesn’t work, try doing the same thing as root.
If you can’t find your php.ini, create a php file on your website with some random name. Open it in an editor and add the line:
Access the file on your site with a browser. It will have all kinds of info about php, including the configuration files (php.ini and others) locations.