Step 01) MySQLDump all databases into a SQL text file (call it SQLData.sql)
Step 02) Drop all databases (except mysql, performance_schema, and information_schema)
Step 03) Shutdown mysql
Step 04) Add the following lines to /etc/my.cnf
[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G
Whatever your set for innodb_buffer_pool_size, make sure innodb_log_file_size is 25% of innodb_buffer_pool_size.
Step 05) Delete ibdata1, ib_logfile0 and ib_logfile1
At this point, there should only be the mysql schema in /var/lib/mysql
Step 06) Restart mysql
This will recreate ibdata1 at 10MB, ib_logfile0 and ib_logfile1 at 1G each
Step 07) Reload SQLData.sql into mysql
ibdata1 will grow but only contain table metadata
Each InnoDB table will exist outside of ibdata1
