Is it possible to have separate binary logs per database in mysql?

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I am looking at a replicated system that replicates four different databases to a bunch of slaves. I am having a problem that one application/database is running some big queries that are holding up replication in the other databases.

Obviously I am looking at other ways to deal with this problem, but one of my thoughts is to whether it's possible to have each database use separate binary logs, so that one log being stuck doesn't hold up updates to the other databases.

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MySQL 5.6 supports Multi-Threaded Slaves which would solve your problem without creating new instances.

Tungsten Replicator may also be an option if you aren't able to upgrade to 5.6.

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You might consider looking at the replicate-ignore-database settings for slaves. Of course that means this db won't be available on your slave, but it sounds like that's what you're asking for.

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Separate instances. At least for the one application.