Enable innodb_file_per_table

 Note: You may wish to convert MyISAM tables to InnoDB tables before you proceed.

innodb_file_per_table is by default ON Mysql 5.6.6 and onwards. There is plenty of stuff on Google about pros & cons ofinnodb_file_per_table.

This post details how to enable innodb_file_per_table on an existing database. Because innodb_file_per_table affects new tables only, created after innodb_file_per_table is enabled, we need to recreate old databases to force innodb_file_per_table on old tables and reclaim some disk space.

Backup First

Create a dir to take backups:

cd ~
mkdir backup
cd backup

Copy mysql data files (raw)

If all goes well, we will not need this.

For better results, shut down PHP and other apps/scripts which update mysql. You can keep Nginx running and server non-logged in visitors cached content.

service mysql stop && cp -ra /var/lib/mysql mysqldata && service mysql start

Take mysqldump

As soon as above line completes, take a mysqldump of all databases

mysqldump --routines --events --flush-privileges --all-databases > all-db.sql

Drop Databases

Create a sql file to drop all databases EXCEPT mysql database

mysql -e "SELECT DISTINCT CONCAT ('DROP DATABASE ',TABLE_SCHEMA,' ;') FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_SCHEMA <> 'mysql' AND TABLE_SCHEMA <> 'information_schema';" | tail -n+2 > drop.sql

Verify if drop.sql has correct database names and then execute drop.sql queries.

mysql < drop.sql

Verify all InnoDB tables gone

SELECT table_name, table_schema, engine FROM information_schema.tables WHERE engine = 'InnoDB';

Remove InnoDB files

Stop mysql server first

service mysql stop

Then

rm /var/lib/mysql/ibdata1 && rm /var/lib/mysql/ib_logfile0 && rm /var/lib/mysql/ib_logfile1

At this point most likely you will have only /var/lib/mysql/mysql directory only.

Enable innodb_file_per_table

Open my.cnf file

vim /etc/mysql/my.cnf

Add following lines

innodb_file_per_table = 1
innodb_file_format = barracuda

Time to import from mysqldump

Start mysql server now

service mysql start

Run mysql import

mysql < all-db.sql

Force mysql_upgrade (to generate performance_schema)

mysql_upgrade --force

Good Luck!