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I have a large InnoDB table that I want to alter by adding a small column to. I'm prepared to wait a while, but I'm wondering how much disk space will the ALTER TABLE command consume while it's running? Will I need enough room on my disk for two full copies of the table?

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Yes. You will need enough space for two copies of the table. MySQL performs alterations of tables by creating a new table, copying data from the old, and then deleting the old table.

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