Mysql Server Login and Permission Deny Error
First of all before performing an upgrade you should have taken a backup of all important databases (or simply all databases) using the mysqldump command. 

Anyhow, to fix this please run:

shell&gt; mysql_upgrade 


To understand more what mysql_upgrade does see here.

If you get permissions errors:

mysql_upgrade -u root -p (give the root password here)


If still it fails, rename /etc/my.cnf to /etc/my.cnfbku and then rerun the command.

This will fix all the issues regarding the upgrade.