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At the same time on a machine there must not be a second server that is using the same port number. So if you want to use the same port number for old NMDDB and new NMDDB you must temporarily switch the port of one of this services during data migration
To migrate metadata it's recommended to have two MySQL services running on the same machine. If there are no firewall restriction you can run services also on different machines.
service #1 - is the service where the new meta-database is installed - it has to run in federated mode. service #2 - is the service where the old meta-database is installed - it may also run in federated mode.