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If you are teying to upgrade MySQL on cPanel server check this link Upgrade MySQL on cPanel Server
Below are the steps how to upgrade your MySQL version for PCI compliance or some other uses.
First check what is your MySQL version using the below command
[root@centosBox ~]# rpm -qa | grep mysql mysql-5.1.69-1.el6_4.x86_64 mysql-devel-5.1.69-1.el6_4.x86_64 mysql-server-5.1.69-1.el6_4.x86_64 mysql-libs-5.1.69-1.el6_4.x86_64
Remove all the old mysql version using the command
rpm -e --nodeps mysql-5.1.69-1.el6_4.x86_64 mysql-devel-5.1.69-1.el6_4.x86_64 mysql-server-5.1.69-1.el6_4.x86_64 mysql-libs-5.1.69-1.el6_4.x86_64
Now download and install MySQL-5.6 using the below command.
wget http://dev.mysql.com/get/Downloads/MySQL-5.6/MySQL-5.6.16-1.el6.x86_64.rpm-bundle.tar mkdir MySQL cd MySQL tar -xvf MySQL-5.6.16-1.el6.x86_64.rpm-bundle.tar yum install MySQL*rpm
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