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I have a table (InnoDB) with data length around 36G and index length 23G.

It had a composite primary key across three columns.

As an initial attempt to reduce the size of this table, I dropped the primary key (wasn't actually needed anyway). Yet, the data length and index length are the same.

Is this to be expected?

UPDATE innodb_file_per_table is enabled on this database


mysql> show create table event;

CREATE TABLE `event` (
`owner_id` varchar(36) NOT NULL,
`key_id` varchar(255) NOT NULL,
`value` varchar(255) NOT NULL,
KEY `owner_id_idx` (`owner_id`)) ENGINE=InnoDB DEFAULT CHARSET=utf8 
share|improve this question
I can't really imagine a table where a compound PK is unnecessary. Could you tell how it can be? Does it have some historical reasons? – dezso Jun 14 '13 at 10:57
Do you have innodb_file_per_table enabled ??? – RolandoMySQLDBA Jun 14 '13 at 16:50
This was an excellent question because the PRIMARY KEY is tied into the Clustered Index (as I mentioned in my answer). +1 !!! – RolandoMySQLDBA Jun 15 '13 at 2:48
Can you show us the output of SHOW CREATE TABLE tablename;? – ypercubeᵀᴹ Jun 15 '13 at 10:30
up vote 3 down vote accepted


It is really the other way around : The size of the table contributes to the size of the primary key. Therefore, YES it was to be expected.


The Primary Key resides within gen_clust_index, a.k.a. the Clustered Index.

According to the MySQL Documentation on the Clustered Index

How the Clustered Index Speeds Up Queries

Accessing a row through the clustered index is fast because the row data is on the same page where the index search leads. If a table is large, the clustered index architecture often saves a disk I/O operation when compared to storage organizations that store row data using a different page from the index record. (For example, MyISAM uses one file for data rows and another for index records.)

From this description, the InnoDB Storage Engine has each row sits inside the Clustered Index.

In light of this, two questions need answering:

  1. Why does dropping the PRIMARY KEY not shrink the Clustered Index?
  2. Why does OPTIMIZE TABLE not shrink the Clustered Index?

The answer to both questions is but one. The MySQL Documentation on the Clustered Index says:

If the table has no PRIMARY KEY or suitable UNIQUE index, InnoDB internally generates a hidden clustered index on a synthetic column containing row ID values. The rows are ordered by the ID that InnoDB assigns to the rows in such a table. The row ID is a 6-byte field that increases monotonically as new rows are inserted. Thus, the rows ordered by the row ID are physically in insertion order.

Think about it : OPTIMIZE TABLE is rendered ineffective since you made no attempt to delete any rows. Since you did not delete any rows, all the space occupied by rows will still sit within the Clustered Index. You merely traded-in one key (your Primary Key) for another (the 6-byte row ID).

What are the ways to shrink the Clustered Index ?

I have one of three(3) techniques you may need to do

TECHNIQUE #1 : Reducing the Length of your Columns

  • shrink INTs to SMALLINTs or TINYINTs
  • shrink VARCHAR(255) to VARCHAR(128)

TECHNIQUE #2 : Delete Old Rows

  • Look for rows with really old timestamps, then either
    • Delete the Old Rows
    • Archive the Old Rows in another table

TECHNIQUE #3 : Dropping Columns From the Table

  • This is true in theory
  • Nobody wants to lose data in the Process
  • Archive the Table Before Dropping Columns


Before you apply one of these three(3) techniques, please backup your table.


Once you have applied one of these three(3) techniques, then you can do one of the following in order to shrink the Clustered Index (for let's say, mydb.mytable):

  • OPTIMIZE TABLE mydb.mytable;
  • ALTER TABLE mydb.mytable ENGINE=InnoDB;

Give it a Try !!!

UPDATE 2013-06-17 07:34 EDT

Here is your last comment

So if the original primary key was greater than 6-bytes wouldn't I expect to see a decrease in the clustered index size?

Even if PRIMARY KEY is now CHAR(255), each row sits inside the Clustered Index. Each page in InnoDB is 16K. The 6-byte row ID (which InnoDB still uses internally anyway) is still embedded within the same pages. Dropping the PRIMARY KEY is more of a logical dropping than a physical one. That's why I said earlier

You merely traded-in one key (your Primary Key) for another (the 6-byte row ID)

The physical act of dropping the PRIMARY KEY may entail running around to every row in tombstoning (flagging) each row not to use some internal column combination for the PRIMARY KEY but to revert back to the row ID. That would hardly change the usage of a 16K InnoDB Page, regardless of the Row Length Being Long (which may allow for a few rows within the Page) or Short (which may allow for many more rows within the Page).

Running OPTIMIZE TABLE to shrink it still won't make any noticeable change because the flagging mechanism still exists for the Clustered Index. The exact same number of rows, given the average length of your rows in the table, keeps the Clustered Index the same size.

Look over the three techniques I mentioned before and the MySQL Documentation on the Clustered Index. Given the number of rows in the table and your current table definition, if you cannot reduce column sizes, remove columns, delete rows and archive them elsewhere, then there is nothing you can do to shrink the table.

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So if the original primary key was greater than 6-bytes wouldn't I expect to see a decrease in the clustered index size? – agileDBA Jun 17 '13 at 8:03

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