A similar request came to us two years back when we had to upgrade MySQL version 4.0 to MySQL 5.0. We are listing here the same approach for the current needs of upgrading MySQL 5.0 to 5.1
File responsible for the MySQL version is /var/cpanel/cpanel.config
Open it, find the variable mysql-version and edit the value to read mysql-version=5.1
And finally run
/scripts/mysqlup
This should upgrade your MySQL version to MySQL 5.1. For better understanding of the process behind, /scripts/mysqlup, go through the code and browse the URL http://httpupdate.cpanel.net/mysqlinstall/
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Internal Server Error
Premature end of script headers: php: Please check / usr / local / cpanel / logs / error_log for the exact error.
Still trying to figure out what goes wrong to cause this.
Did you check that log file ? You can do a /scripts/makecpphp and see whether it fixes that error. Or if you are on a VPS, make sure that you have enough memory