MySQL InnoDB issue not using indexes correctly [Percona 5.6] I just installed Percona 5.6 on my new CentOS 6.4 server. It's a fast machine 32 core xenon, 72GB ram, 8x SAS RAID 10 setup. So far so good 

My old server is a bit less powerful, and was running MySQL 5.1 still. So this was quite an upgrade. But I'm having some issues with InnoDB, it is not using the indexes correctly on some tables it seems. Where on my old machine the same queries were running fine.

Both servers have the same database. I did a mysqldump on the old machine and imported it onto the new Percona 5.6 server. Indexes stayed the same. Both servers use the same my.cnf config settings.

Table items has indexes on: item_id, item_format, item_private and contains about 40 million rows. Table formats has index on: format_id and contains about 250 rows.

SELECT 
i.item_name, i.item_key, i.item_date, f.format_long
FROM
items i, formats f
WHERE 
i.item_format = f.format_id
AND
i.item_private = 0 
ORDER BY 
i.item_id DESC LIMIT 8


On my old server this query takes about 0.0003 seconds. On the new server it takes over 100 seconds.

Query with EXPLAIN on OLD server. 

+----+-------------+-------+--------+---------------+---------+---------+----------------------+------+-------------+
| id | select_type | table |  type  | possible_keys |   key   | key_len |         ref          | rows |    Extra    |
+----+-------------+-------+--------+---------------+---------+---------+----------------------+------+-------------+
|  1 | SIMPLE      | i     | index  | item_format   | PRIMARY |       4 | NULL                 |    8 | Using where |
|  1 | SIMPLE      | f     | eq_ref | PRIMARY       | PRIMARY |       4 | dbname.i.item_format |    1 |             |
+----+-------------+-------+--------+---------------+---------+---------+----------------------+------+-------------+


Query with EXPLAIN on NEW [problem] server.

+----+-------------+-------+------+---------------+-------------+---------+--------------------+------+---------------------------------+
| id | select_type | table | type | possible_keys |     key     | key_len |        ref         | rows |              Extra              |
+----+-------------+-------+------+---------------+-------------+---------+--------------------+------+---------------------------------+
|  1 | SIMPLE      | f     | ALL  | PRIMARY       | NULL        | NULL    | NULL               |  219 | Using temporary; Using filesort |
|  1 | SIMPLE      | i     | ref  | item_format   | item_format | 4       | dbname.f.format_id | 3026 | Using where                     |
+----+-------------+-------+------+---------------+-------------+---------+--------------------+------+---------------------------------+


You can see that it's using temporary and filesort. This seems to be the reason for the slowness.

Any idea how I could resolve this issue?
First of all: This is not because of Percona, the differences you are getting are because of the upgrade to 5.6. Percona Server rarely modifies the SQL optimiser from upstream. The changes come from the new optimiser in MySQL 5.6, which Percona Server 5.6 uses and that was heavily optimised between the two version (usually, for the best).

The reason why the execution is slower is because with an index on (item_format, item_private), it thinks that the query will be faster by getting the results using that index, but in reality, that would cause the join to be done in the "wrong" order. The best index here is (item_private) -assuming it is selective enough, if not it would be the primary key-, as it can use item_private for filtering and the hidden PRIMARY KEY inside the secondary key for ordering, while it uses the PRIMARY KEY of format for the join. Please note that (item_filtering) or (item_filtering, item_private) are not good indexes in this case.

By looking at the optimiser trace and the handler status, the problem seems to come by the predicted number of rows: the old method, in 5.6, seems to predict a full table scan, while the actual number of rows read is -more or less- the number of rows in the LIMIT clause. This seems to be a regression in the query optimiser, and it should be reported if you confirm that it is not due to any special personal configuration. It is specially bad, as it prefers the creation of a temporary table for the join (potentially on disk, so it may be very slow in some cases) over a very light scan.

You have been already told several ways of avoiding this problem for the time being: not creating an index containing item_filtering, using STRAIGHT_JOIN or forcing the usage of item_filtering (or PRIMARY).