With a large data set and a real time system, halting that applications using RDS for a mysqldump from a 5.5 instance and loading that data with the mysql command is impractical.
In the Amazon blog http://aws.typepad.com/aws/amazon-rds/page/2/ on July 1, 2013 Jeff Barr posts "Upgrading an existing database instance from MySQL 5.5 to MySQL 5.6 is not currently supported. However, we intend to provide this functionality in the near future."
7 months later, I don't see any answer from them. I'm looking for options to have a no outage or few minute outage to have an upgrade of MySQL 5.5 to MySQL 5.6 in the RDS environment.
Normally for an upgrade like this I make a MySQL 5.6 replica from a MySQL 5.5 master and then shutdown the applications, change the application MySQL connect to the 5.6 server, and restart the applications. Replicating an RDS MySQL 5.5 instance to a different version RDS replica or to an external replica is not an option in RDS.
What options have worked for people?