Mysqltuner showing fragmented table on new Innodb table

I just installed MySQL 5.6 and created a database and a table.  I ran the mysqltuner script against it and it says that there is 1 fragmented table.

How is this possible with an empty table?  I have not specified innodb_file_per_table and it's storing the table and database in ibdata1 (or whatever the default store is called).

Is the mysqltuner reporting false data or did I miss something?

Thanks!
jelinekAsked:
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nemws1Connect With a Mentor Database AdministratorCommented:
It's throwing this because MySQL allocates a minimum size for INNODB tables, if I remember right, around 4Mb.  The tuner is throwing an error because the difference between the data amount (zero) and the allocated size (4mb) is 4mb!  It thinks you have 4mb of fragmented space, even though it is just unallocated.

In my own performance scripts, I won't throw out a fragementation error unless the *data* size (in your case, zero) is at least 25mb for this exact issue.
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jelinekAuthor Commented:
Very thorough explanation.  Thanks for the lesson on lesson on minimum table size and mysqltuner!
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nemws1Database AdministratorCommented:
Just a little more info.  You can see this in play if you run the following query to find fragmentation in tables:

SELECT
    table_schema
    , table_name
    , CONCAT(ROUND(data_length / ( 1024 * 1024 ), 2), 'MB') AS Data
    , CONCAT(ROUND(data_free  / ( 1024 * 1024 ), 2), 'MB') AS Free
    , (data_free / data_length) * 100 AS pfrag
    , data_length
FROM information_schema.TABLES
WHERE TABLE_SCHEMA NOT IN ('information_schema','mysql')
    AND (data_free / data_length) * 100 > 0
;

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If you look at the 'Free' column - you should see a *bunch* of '4.00MB' tables.  Of course, it's impossible for so many table to have the exact free space, so it must be a pre-allocation (you'll see some 3.00MB and 5.00MB or whatever in there as well - but they're all an even number).

Here's my usual 'find fragmentation tables' script, which tries to be a bit smarter about all this:

--
-- Table Fragmentation
--   run with '-r' to get correctly formatted output
--

-- minimum table size in megabytes
--   DO NOT set below 10!!
SET @min_data_size = 20;

-- minimum fragmentation percentage - industry standard minimum in 25
SET @min_frag_perc = 5;

--
-- Main query
SELECT
    CONCAT("-- "
           , "Table "
           , table_schema
           , "."
           , table_name
           , " fragementation is: "
           , ((data_free / data_length) * 100)
           , "\n"
           , "OPTIMIZE TABLE `"
           , table_schema
           , "`.`"
           , table_name
           , "`;") AS "--\n-- Fix MySQL Table Fragmentation\n--"
/*
    , table_schema
    , table_name
    , CONCAT(ROUND(data_length / ( 1024 * 1024 ), 2), 'MB') AS Data
    , CONCAT(ROUND(data_free  / ( 1024 * 1024 ), 2), 'MB') AS Free
    , (data_free / data_length) * 100 AS pfrag
    , data_length
*/
FROM information_schema.TABLES
WHERE TABLE_SCHEMA NOT IN ('information_schema','mysql')
    AND data_free > 0
    AND data_length > (@min_data_size * 1024 * 1024)
    AND ((data_free / data_length) * 100) > @min_frag_perc
;

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FishMongerCommented:
I have not specified innodb_file_per_table and it's storing the table and database in ibdata1

You should enable  innodb_file_per_table.  It will make it easier/faster when it comes time to optimize the tables, especially if you have a fair number of indexes and when your tables grow in size (over 1 million rows) to the point where you need to partition the tables.
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