You can change the way that the slave sites are created easily.
Just change the JMS template rule that you are using to add a rule concerning the DB name.
The problem of the backup and the number of tables in a DB is not related to the stability.
The problem of backup that you probably encounter is related to the number of files that MySQL can lock simultanously. This is a configuration of MySQL that you can ajust.
For us, the limitation should better analyzed in terms of performance and also in terms of the number of files that are created for a specific DB.
The number of files can be computed as the number of MySQL tables * 3.
So if a website requires 100 tables and that you have 15 websites, this mean that the DB uses 4500 files in the same directory on the disk.
This means that MySQL needs to lock 4500 files to perform the backup.
So if you have problem with the Backup, you should have a look on the number of MySQL tables that can be locked simultanously and find a tradeoff between the number of files in a same DB and the performance.
Personnaly, I try avoid have more than 15,000 files into the same directory.
The operating system can become slower when you have a very large number of files in a same directory.
If you have problem of locking to backup a DB, you can also add a parameter in the MySQL Dump to ignore the locking.
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