For whatever reason , some people still want to run the old version of MySQL4.1 in there new cPanel servers, which seems a little issue , as the default database version in new cPanel server installs is MySQL5.

Here are the simple steps to downgrade the database (this should only be done on a new server without any account on it yet)

nano /var/cpanel/cpanel.config

search for the mysql version 

Ctrl + w , mysql

Now log into WHM and make sure MySQL 4.1 is checked in

Main >> Server Configuration >> Tweak Settings

And now change the version from 5.0 to 4.1

 and now you need to run

 /scripts/mysqlup --force

to force the downgrade .

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