Get your system root password with this:

cat /var/clearos/system_database/root

When you run through the script, use the system Mysql socket (I think you did) /var/lib/system-mysql/mysql.sock and the user 'root' along twith that password obtained from the command above.

Worked for me.

B.

Thanks Ben but it does not seem to work for me.
I get the same error.
What version of the script do you run?

In case someone runs into the same issue:
change the script from
218 mysql="mysql"
219 mysqladmin="mysqladmin":
TO:
218 mysql="/usr/clearos/sandbox/usr/bin/mysql"
219 mysqladmin="/usr/clearos/sandbox/usr/bin/mysqladmin"

After this couple of changes the scripts will run.
218 is the line number in version 1.6 of the script.

You can migrate your system-mysql to faster spindles (RAID 10 or SSD) by using this guide.

Thanks Dave,
These are two different issues.
I am looking to optimize ( I already may be running db on the mirrored ssd )
You proposing faster hardware