Percona-Server: slow TokuDB queries after upgrading from 5.6 to 5.7. ANALYZE TABLE doesn't resolve the problem After upgrading from Percona-TokuDB 5.6.29-76.2 to 5.7.19-17 we see some very slow queries on some tables without primary keys, but multiple non-unique indexes. The box we migrated to is pretty well equipped (768 GB RAM, PCIe SSDs). We used mysql_upgrade after migration.

After investigating Percona 5.7 tokudb poor query performance - wrong (non-clustered) index chosen we tried ANALYZE TABLE, even with RECOUNT_ROWS, REPAIR TABLE, ALTER TABLE *** FORCE without any effect. 

Typical table structure:

CREATE TABLE `letter_archiv_12375` (
 `user_id` int(12) unsigned NOT NULL DEFAULT '0',
 `letter_id` mediumint(6) unsigned NOT NULL DEFAULT '0',
 `crypt_id` bigint(12) unsigned NOT NULL DEFAULT '0',
 `mailerror` tinyint(1) unsigned NOT NULL DEFAULT '0',
 `unsubscribe` tinyint(1) unsigned NOT NULL DEFAULT '0',
 `send_date` date NOT NULL,
 `code` varchar(255) NOT NULL DEFAULT '',
 KEY `crypt_id` (`crypt_id`),
 KEY `letter_id` (`letter_id`),
 KEY `user_id` (`user_id`)
) ENGINE=TokuDB 


A simple query like that takes 4 seconds on a table with 200m rows.

UPDATE hoovie_1.letter_archiv_14167
                          SET unsubscribe = 1
                        WHERE letter_id = "784547"
                          AND user_id   = "2881564";


The cardinality values are correct. EXPLAIN will result in:

id  select_type table   partitions  type    possible_keys       key     key_len ref rows    filtered    Extra
1   UPDATE  letter_archiv_14167 NULL    range   letter_id,user_id   letter_id   3   const   1   100.00  Using where


The only solution is to remove and re-create at least one index. After dropping and re-creating the index letter_id the table will perform well (in 0.01 s).

The EXPLAIN will change to 

id  select_type table   partitions  type    possible_keys       key     key_len ref rows    filtered    Extra
1   UPDATE  letter_archiv_14167 NULL    range   user_id,letter_id   user_id     4   const   99  100.00  Using where


We have some thousands of TokuDB tables in production - a performance loss of factor 300-500 is a problem. 

So we are unsure to migrate to 5.7 - this behaviour could occur even after re-creating all indexes again.

Any ideas?
Add this composite index:

INDEX(letter_id, user_id)  -- in either order


Do you deliberately not have a PRIMARY KEY?