Using the mysql upgrade option in cpanel will not work with cloud Linux. It’s also a little different than what the Cloudlinux site says.
How to install new package:
1) yum install governor-mysql –enablerepo=cloudlinux-updates-testing
2) /usr/share/lve/dbgovernor/mysqlgovernor.py –install
For upgrading to MySQL 5.5(for example), you should to do:
1) /usr/share/lve/dbgovernor/db-select-mysql –mysql-version=mysql55
2) /usr/share/lve/dbgovernor/db-select-mysql –install-now
3) for cPanel can be needed to rebuild php through easyapache