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I'm trying to install phpMyAdmin (via scripts) as a subdomain on Virtualmin and be able access a database from the top domain.
I have try to create a sub server but it creates separate DB as well so PAM is not able to reach a DB from the top domain.
phpMyAdmin is just an interface for accessing the database. It will provide you access to what ever database you use the login details for.
So you can have:
Main - foo.com DB - fooDB DB User - fooDBUsr Sub - bar.foo.com DB - barDB DB User - barDBUsr
phpMyAdmin installed to bar.foo.com would allow access to either database as long as the correct login is used. If you use the barDBUsr login you will only see the barDB database, if you use the fooDBUsr login you will see the fooDB database.
If you used the root database login you would see all the databases.