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If your MySQL data directory has many files such as:
log-bin=mysql-binis enabled in your /etc/my.cnf (or in the startup script).
There are two ways to fix this problem:
The first is to stop the MySQL server from creating these binary files. The only reason you would need the binary log files is if you are doing mysql replication from a master to a slave. In this case, these files are necessary, at least until the slave(s) has caught up with the master. To stop this from logging, comment out (using #) the line containing ‘log-bin’.
The second is to continue logging – this is necessary as stated above if you are performing SQL replication.
You can add a line to your /etc/my.cnf file which will only keep these files around as long as necessary. The line is:
expire_logs_days = X
Where X is the number of days you’d like to keep them around. I would recommend 10, but this depends on how busy your MySQL server is and how fast these log files grow. Just make sure it is longer than the slowest slave takes to replicate the data from your master.