Question

I’m using InnoDB database with a single file configuration (in /var), so no innodb_file_per_table.

In the MySql workbench, when I query for the databases used space, with this query

SELECT table_schema "Database", sum( data_length + index_length ) / 1024 / 1024 "Data     Base Size in MB" 
FROM information_schema.TABLES GROUP BY table_schema;

It says that I have 47 GB of data.
However the size of ibdata1 is 99 GB…

I know that ibdata1 contains a bunch of other things other that table data, like Table Indexes, MVCC (Multiversioning Concurrency Control) Data and Table Metadata

So my question is: Is it normal that supposedly 52 GB of ibdata1 is medatada and a bunch of other things? Usually, how much data beside table data should the ibdata1 file contains?

Answer 1

No, it is not normal that you would have that much metadata. It is normal though that the ibdata file can grow to a ridiculous size if you aren’t using innodb_file_per_table.

Your ibdata file will grow when your database grows, but it will never actually shrink.

So, for example, if you had 130 GB of data at one point and deleted a bunch of it, the ibdata file would still be 130 GB after the data was purged. It will just have a bunch of “free space” that it will then use for subsequent inserts.

As for shrinking the file, there’s not much you can really do aside from wiping out your database and restoring it. This answer has some good instructions on how to do that.

Howto: Clean a mysql InnoDB storage engine?

You also might want to consider using innodb_file_per_table as deleting data from a table and later optimizing that table will actually shrink the size of the individual table files