The steps for upgrading MySQl on a cPanel server.

go to WHM > Software > MySQL Upgrade for doing the upgrade process. we  will need to run EasyApache after the upgrade, Rebuild Apache and PHP automatically with last saved defaults. in Step 3 where it has the "Unattended upgrade." option. if we choose the interactive option, we will  be given an opportunity to rebuild Apache and PHP at that point. If we do not select to rebuild Apache and PHP after updating MySQL if the version is changed , then PHP will not have the correct libmysql built and PHP + MySQL will not functio properly