Update index values extremely slow on MySQL - mysql

Question

I have three tables, one is in database db1 and two are in database db2, all on the same MySQL server:
CREATE TABLE `db1`.`user` (
`id` bigint(20) UNSIGNED NOT NULL AUTO_INCREMENT,
`user_name` varchar(20) NOT NULL,
`password_hash` varchar(71) DEFAULT NULL,
`email_address` varchar(100) NOT NULL,
`registration_time` datetime NOT NULL DEFAULT CURRENT_TIMESTAMP,
`registration_hash` char(16) DEFAULT NULL,
`active` bit(1) NOT NULL DEFAULT b'0',
`public` bit(1) NOT NULL DEFAULT b'0',
`show_name` bit(1) NOT NULL DEFAULT b'0',
PRIMARY KEY (`id`),
UNIQUE KEY `user_name` (`user_name`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
CREATE TABLE `db2`.`ref` (
`id` bigint(20) UNSIGNED NOT NULL AUTO_INCREMENT,
`name` varchar(100) NOT NULL,
PRIMARY KEY (`id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
CREATE TABLE `db2`.`combination` (
`ref_id` bigint(20) UNSIGNED NOT NULL,
`user_id` bigint(20) UNSIGNED NOT NULL,
`arbitrary_number` tinyint(3) UNSIGNED NOT NULL DEFAULT '0',
PRIMARY KEY (`figurine_id`,`user_id`),
KEY `combination_user` (`user_id`),
KEY `combination_number` (`user_id`,`arbitrary_number`),
CONSTRAINT `combination_ref` FOREIGN KEY (`ref_id`) REFERENCES `ref` (`id`) ON UPDATE CASCADE,
CONSTRAINT `combination_user` FOREIGN KEY (`user_id`) REFERENCES `db1`.`user` (`id`) ON UPDATE CASCADE
) ENGINE=InnoDB DEFAULT CHARSET=utf8;
The table db1.user has around 600 records, the table db2.ref has around 800 records and the table db2.combination has around 300K records.
Now using Perl and DBD::mysql I perform the following query:
UPDATE `db1`.`user` SET `id` = (`id` + 1000)
ORDER BY `id` DESC
However, this query always stops mentioning the connection to the MySQL server was lost. Also executing this same query via PhpMyAdmin results in a timeout. Somehow the query just takes a very long time to execute. I guess it comes because all the foreign key values need to be updated.
Setting FOREIGN_KEY_CHECKS variable to OFF will not update the user_id column in the db.combination table, which do need to be updated.
I have also tried to manipulate the different timeouts (as suggested all over the internet), like this:
SET SESSION net_read_timeout=3000;
SET SESSION net_write_timeout=3000;
SET SESSION wait_timeout=6000;
I have verified that the new values are actually set, by retrieving the values again. However, even with these long timeouts, the query still fails to execute and after about 30 seconds the connection to the MySQL server is again lost (while amidst executing the UPDATE query)
Any suggestions on how to speed up this query are more than welcome.
BTW: The PK columns have a very large integer type. I will also make this type smaller (change to INT). Could this type change also improve the speed significantly?
UPDATE
I also performed an EXPLAIN for the query and it mentions in the Extra column that the query is doing a filesort. I would have expected that due to the indexes on the table (added them, as they were not there in the first place), no filesort would take place.

Answer 1

The 300K CASCADEs is probably the really slow part of the task. So, let's avoid it. (However, there may be a check the verify the resulting links; this should be not-too-slow.)
Disable FOREIGN KEY processing
Create new tables without FOREIGN KEYs. new_user, new_combination. (I don't know if new_ref is needed.)
Do this to populate the tables:
INSERT INTO new_xx (user_id, ...)
SELECT user_id + 1000, ...;
ALTER TABLE new_xx ADD FOREIGN KEY ...; (for each xx)
`RENAME TABLE xx TO old_xx, new_xx TO xx;
`DROP TABLE old_xx;
Enable FOREIGN KEY processing