PHP-FPM you need to have the mcrypt php module installed.

1. what version of centmin mod and php ?
2. what version php upgrade from and to ?
3. what centos version ? 6 or 7 ?
4. how long ago did you install or update centmin mod ? looks like must be quite old as you're still using APC Cache which is buggy with PHP 5.5+ and higher, i'd switch to Zend Opcache via centmin.sh menu option 12 submenu options after you have updated centmin mod code as outlined below
5. I'd update centmin mode code first as in past there was as bug with older centmin mod code and missing mcrypt on centos 6. Though it seems you do have mcrypt. Try nginx & php-fpm service restart

Upgrading Centmin Mod Code to Latest Version

Upgrading Centmin Mod involves 2 parts.

1. Upgrading the actual Centmin Mod code outlined at Upgrade Centmin Mod - CentminMod.com LEMP Nginx web stack for CentOS This is heart of Centmin Mod where the code is the engine that runs centmin.sh shell based menu and all the automation you're accustomed to.
2. Upgrade software that Centmin Mod installed or manages. For this part following outline at Upgrade - How to upgrade Centmin Mod | Centmin Mod Community

So essentially, you can upgrade from .07 to .08 in place, but not everything is upgraded as some things like server initial environment setup isn't changed i.e. how swap, tmp setup and allocation are created etc. The main parts from part 2 above are what in place upgrades do i.e. Nginx and PHP-FPM compilation and config/settings parameters and MariaDB version from 5.5 to 10.0.x. If you want the full environment changed including tmp and swap setup to .08's configuration, then you would need a fresh OS install and fresh .08 initial install. You can think of it like upgrading Windows 7 to Windows 8. An in place upgrade will upgrade code but won't change your computer environment from when you installed Windows 7 i.e. disk configuration and partition sizes won't change from when you initially installed Windows 7. Only way to change that would be fresh Windows 8 install.

I'd take care of this first by updating centmin mod code as outlined above and then running centmin.sh menu option 15 to recompile imagick php extension

 

still need rest of the answers to the questions on your server environment too

To troubleshoot, you need to check the the php upgrade log at /root/centminlogs and instructions under Sharing logs and errors heading for using Pastebin.com or Gists to share a sanitised version of the contents of the initial install log. You can see full details at How to troubleshoot Centmin Mod initial install issues

Also post output for the following

Code (Text):

php -v
php --ini
php -m

 

this could also be a bug in your php app as it could be looking for a linux distro mcrypt package install like yum or apt based but Centmin Mod LEMP's PHP-FPM installs mcrypt via source compile so might be not what your php app is checking for ? so ask your php app's dev/author

 

any reason not using newer PHP ? try PHP 5.5.32 or 5.6.18 and with Zend Opcache much faster and more updated as PHP 5.4 EOL

 

try and see

also you can run this php script to confirm if mcrypt exists

PHP:

<?php
if (! function_exists ("mcrypt_encrypt")) {
  die ("mcrypt php module missing.");
} else {
  echo "mcrypt php module exists";
}
?>