I recently ran into an issue where I would update the Cpanel instance using the:

/scripts/upcp –force

To update Cpanel, as I normally do. However I noticed that when I did it this time, It did not update MySQL. Thinking that’s fine, I’ll just check the MySQL 5.0 button in Main >> Server Configuration >> Tweak Settings. However the option to update to version 5.0 was not there…. This was puzzling indeed.

I then ran /scripts/mysqlup –force . That didn’t help either, version 4 was still there and no sign of version 5. I then tried to see what rpm’s where in place;

rpm -qa | grep My

Nothing but MySQL 4……. Still at a complete loss.

Then I finally looked at the config file for cpanel;

/var/cpanel/cpanel.config

Look at that:

maxemailsperhour=0
maxmem=128
myname=cpaneld
mysql-version=5.1
mysqldebug=0
nativessl=1
nobodyspam=0
nouserbackupwarn=0

MySQL 5.1????????? Changing this to 5.0 and then running the /scripts/mysqlup --force
command fixed this issue. I now can select MySQL 5.0 by going to  Main >> Server Configuration >>
Tweak Settings.

Looks like the new update of Cpanel has borked the MySQL install.