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answers:

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MySQL introduced a server side utility that lets you manage multiple instances on a remote machine. I am looking for similar functionality for earlier versions of mysql.

[1]http://dev.mysql.com/doc/refman/5.0/en/instance-manager.html

+1  A: 

I am not familiar with the instance manager, but I have used phpMyAdmin on several systems (including a remotely hosted server) with great success. It supports MySQL 5.0 and 4.1.

Joe Skora
Thanks Joe,I think was a bit vague, in my question when I said "manage multiple instances". Actually what instance manager lets you do is to start/stop multiple mysql processes with different ports and options. All of these processes have independent lifecycle, permissions, data-directory and so on
Tahir Akhtar