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answers:

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The size of MySQL ibdata is 4GB, but I don't think the data I have should take that much disk space. I am using MySQL InnoDB storage engine. Am I doing something wrong with configuration? How do I reclaim the disk space because deleting rows didn't help at all?

Thanks

A: 

When you delete stuff, the records are only marked as unused/free and will be reused when you insert more data. You cannot reclaim disc space without doing a full dump/reload of the database though(unless you have used the innodb_per_table option)

See more info here http://dev.mysql.com/doc/refman/5.1/en/adding-and-removing.html

nos
Thanks for the link.
Mark K