Docker 1.12: Multiple replicas, single database

From the Flyway FAQ:

Can multiple nodes migrate in parallel? Yes! Flyway uses the locking technology of your database to coordinate multiple nodes. This ensures that even if even multiple instances of your application attempt to migrate the database at the same time, it still works. Cluster configurations are fully supported.

There is no easy way to coordinate this among containers. It basically requires a distributed lock solution. The first container that gets the lock could create db, while, other containers that not get the lock need to wait.

In AWS, you could leverage DynamoDB for it. DynamoDB supports conditional update. The container first tries to create the lock key in DynamoDB with "attribute_not_exists(yourKey)". The first creation will succeed and other creations will be rejected. The first container needs to create another key in DynamoDB to indicate the db is ready. Other containers simply waits till the ready key is created.

Or you could do it in your service deployment script. The script could create the service with 1 replica. Then keep checking if db is created. If yes, scale the service, such as docker service update yourservicce --replicas 5.