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All my table in the db are created after I enabled the option "innodb_file_per_table", so I don't understand why ibdata1 is still growing from time to time, even with a very slow speed.

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When you use file_per_table, it doesn't mean that ibdata* isn't used at all. There will still be stored "meta-data" for all your InnoDB tables ... Only the data itself goes to the other files

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