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Kalan:
Would federating all of them instead be still terribly slow?
yes. MySQL federation is not useful for what people want to use it for (joins). for anything beyond simple single-row queries (like the toolserver database), it's far too slow.
a better alternative would be MySQL Cluster. i've looked at this in the past, but it had some restrictions that made it unsuitable for us. once these are resolved, it would be easier for both users (as all databases would appear to be on the same server) and for us (as it makes it much easier to add additional capacity to the cluster).
- river.