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Without having to script an 'optimize table' query to do all the databases/tables, we would like to run mysqlcheck --optimize --all-database instead.

What are the drawbacks of doing this through mysqlcheck; both would defragment the tables, correct?

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mysqlcheck just runs a bunch of 'optimize table' SQL statements for you, so functionally they do the same thing.

Note that 'optimize table' for innodb just maps to an 'ALTER TABLE foo engine = innodb' statement. This rebuilds the entire table. Depending on the size of your table this may take a very long time, during which the table is locked and unavailable.

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