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I have 5000 databases on one server.

Switching databases is taking a long time sometimes 2 seconds. (use databaseA)

IT is showing up in a my slow queries log. Is there any way to make this go faster.. some form indexing or some other configuration?

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Short of beefing up your server hardware, you could start splitting off databases to several servers, as 5000 databases on a single server is pretty huge.

Something that will cut your I/O wait, which is most likely an issue is an SSD, but a good one costs hundreds of $.

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5000 databases doesn't seem like alot to me considering the databases themselves are all pretty small bar a few of them. it doesn't make sense to me that it would take 2 seconds to traverse 5000 databases when it could traverse 5000 rows in a fraction of the time.. – Derek Organ Oct 28 '09 at 15:26
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