How to shrink/purge ibdata1 file in MySQL

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. According to Bill Karwin's comment this is enabled by default as of version 5.6.6 of MySQL.

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

https://dev.mysql.com/doc/refman/5.6/en/innodb-file-per-table-tablespaces.html

As you want to reclaim the space from ibdata1 you actually have to delete the file:

1. Do a mysqldump of all databases, procedures, triggers etc except the mysql and performance_schema databases
2. Drop all databases except the above 2 databases
3. Stop mysql
4. Delete ibdata1 and ib_log files
5. Start mysql
6. Restore from dump

When you start MySQL in step 5 the ibdata1 and ib_log files will be recreated.

Now you're fit to go. When you create a new database for analysis, the tables will be located in separate ibd* files, not in ibdata1. As you usually drop the database soon after, the ibd* files will be deleted.

http://dev.mysql.com/doc/refman/5.1/en/drop-database.html

You have probably seen this:
http://bugs.mysql.com/bug.php?id=1341

By using the command ALTER TABLE <tablename> ENGINE=innodb or OPTIMIZE TABLE <tablename> one can extract data and index pages from ibdata1 to separate files. However, ibdata1 will not shrink unless you do the steps above.

Regarding the information_schema, that is not necessary nor possible to drop. It is in fact just a bunch of read-only views, not tables. And there are no files associated with the them, not even a database directory. The informations_schema is using the memory db-engine and is dropped and regenerated upon stop/restart of mysqld. See https://dev.mysql.com/doc/refman/5.7/en/information-schema.html.

Adding to John P's answer,

For a linux system, steps 1-6 can be accomplished with these commands:

1. mysqldump -u [username] -p[root_password] [database_name] > dumpfilename.sql
2. mysqladmin -u [username] -p[root_password] drop [database_name]
3. sudo /etc/init.d/mysqld stop
4. sudo rm /var/lib/mysql/ibdata1
sudo rm /var/lib/mysql/ib_logfile*
5. sudo /etc/init.d/mysqld start
6. mysqladmin -u [username] -p[root_password] create [database_name]
7. mysql -u [username] -p[root_password] [database_name] < dumpfilename.sql

Warning: these instructions will cause you to lose other databases if you have other databases on this mysql instance. Make sure that steps 1,2 and 6,7 are modified to cover all databases you wish to keep.

When you delete innodb tables, MySQL does not free the space inside the ibdata file, that's why it keeps growing. These files hardly ever shrink.

How to shrink an existing ibdata file:

https://dev.mysql.com/doc/refman/5.6/en/innodb-system-tablespace.html#innodb-resize-system-tablespace

You can script this and schedule the script to run after a fixed period of time, but for the setup described above it seems that multiple tablespaces are an easier solution.

If you use the configuration option innodb_file_per_table, you create multiple tablespaces. That is, MySQL creates separate files for each table instead of one shared file. These separate files a stored in the directory of the database, and they are deleted when you delete this database. This should remove the need to shrink/purge ibdata files in your case.

More information about multiple tablespaces:

https://dev.mysql.com/doc/refman/5.6/en/innodb-file-per-table-tablespaces.html