idbdata problem with MySQL

How to shrink/purge ibdata1 file in MySQL – Stack Overflow

That ibdata1 isn’t shrinking is a particularly annoying feature of MySQL. The ibdata1 file can´t actually be shrunk unless you delete all databases, remove the files and reload a dump. But you can configure MySQL so that each table, including its indexes, is stored as a separate file. In that way ibdata1 will not grow as large. It was a while ago I did this. However, to setup your server to use separate files for each table you need to change my.cnf in order to enable this: [mysqld] innodb_file_per_table=1