MySQL: reducing ibdata file size for MyISAM tables

Question

My Question is actually very similar to this one and also includes a good answer for a case with InnoDB Engine tables:

https://dba.stackexchange.com/questions/8982/i

Answer 1

As mentioned MyISAM shouldn't be using ibdata. What are your innodb settings in your my.cnf, or in the MySQL shell type:

    SHOW VARIABLES LIKE "%innodb%";

Are these variables set?

    innodb_data_home_dir
    innodb_data_file_path

If you are not using INNODB at all you should be able to safely remove the ibdata and ib_logfile(s) and restart MySQL. Normally though removing these without dropping the tables first will cause issues. See How to shrink/purge ibdata1 file in MySQL

If you do have a MyISAM table over 5Gigs, it's recommended that you use INNODB anyway. (Anything over 4 Gigs). To troubleshoot you could try and add

    skip-innodb 

in the my.cnf if you are not using INNODB at all.