The /var/lib/mysql/ibdata1 file can grow gigantic, here is the procedure to reduce the size of it :
1) Dump all databases as one file
mysqldump -u root -p --all-databases --routines --verbose --skip-lock-tables --result-file=alldb.sql
2) drop all databases
3) Stop MySQL, delete the ibdata1 file, restart MySQL
/etc/init.d/mysqld stop cd /var/lib/mysql rm ibdata1 file /etc/init.d/mysqld start
5) Reimport all databases
mysql -u root -p < alldb.sql