Not withstanding javafan's excellent questions, a couple of possibilities that I've used successfully in the past to speed up updates.
- Upload the data required to make the updates into a simple, unindexed scratch table using the bulk loader.
Apply the updates from the scratch table to their destination(s) using a stored procedure.
- Temporarily delete any indexes or foreign keys from the table to be updated, that aren't explicitly required for the update process, and re-create them afterwards.
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