Login to WHM as root user and go to Server Configuration >> Tweak Settings, select the version you need to upgrade in "MySQL" section, and click "Save". Open root level ssh session to your VPS and run the "/scripts/mysqlup" command, wait until installation will be completed; Login to WHM as root and go to Main >> Software >> Apache Update Click on the "Load Previous Config" button (if exists). Select PHP version and options you require. Also uncheck the "Skip Apache Build if up to date" option. Once done press "Start build" button and wait for some time.