Mysql – “copy to tmp table” for 24 hours, then timeout; when ALTERing to add PK & AI

MySQLperformancequery-performance

I downloaded the Wiktionary XML dump, and ran mwdumper.jar to insert the data into MySQL.

Following the advice in the manual, I commented out the PRIMARY KEY AUTO_INCREMENT part of the CREATE TABLE statements, for page, revision and text (which have millions of rows in each, and very large BLOB's); in order to aid in a much faster import time.

After the data had been inserted, I ran the CREATE INDEX statements, and these executed fine (in ~30 seconds each).

My problem is, I'm now trying to add the PK's in, and just on the first line, it ran for 86,400 seconds (24 hours), then timed out!

SHOW FULL PROCESSLIST shows State: copy to tmp table.

Here are the queries I'm trying to run – it's stuck on the first one:

ALTER TABLE revision MODIFY COLUMN rev_id int unsigned NOT NULL PRIMARY KEY AUTO_INCREMENT;
ALTER TABLE text MODIFY COLUMN old_id int unsigned NOT NULL PRIMARY KEY AUTO_INCREMENT;
ALTER TABLE page MODIFY COLUMN page_id int unsigned NOT NULL PRIMARY KEY AUTO_INCREMENT;

When I ran SHOW GLOBAL STATUS while the query was running, the Handler_read_rnd_next variable was increasing, and there were no other connected users or applications running on the db, to otherwise influence that var.

How can I speed this query up? It's running on a quad-core 3.5GHz development machine with 16GB of RAM, but it's barely using any of this power.

The only options that have been changed from the default install are:

max_allowed_packet = 1G
innodb_log_file_size = 100M
innodb_log_buffer_size = 100M

And in MySQL Workbench:

Any advice is appreciated!

Best Answer

Well, there's nothing to be done at this stage. You can't terminate the process (rather, you shouldn't) while running. You cannot modify major memory settings without restarting MySQL.

I, for one, am not enthusiast about loading all table data then loading indexes. However, doing this for the PRIMARY KEY is plain wrong. The advice you read related to secondary indexes. With adding a PRIMARY KEY InnoDB will rebuild your entire table all over again; so I'm afraid your entire first load step was redundant.

Nevertheless 7 hours for PK compared to 30 seconds for secondary index does not make sense. What is your innodb_buffer_pool_size? Which disks? RAID? Which file system?

Related Solutions

Mysql – Drop auto increment hack w/o alter table

I tried something similar just now

Here is MySQL for My PC

mysql> select * from information_schema.global_variables where variable_name='datadir' or variable_name like 'versio%';
+-------------------------+------------------------------+
| VARIABLE_NAME           | VARIABLE_VALUE               |
+-------------------------+------------------------------+
| VERSION_COMMENT         | MySQL Community Server (GPL) |
| VERSION                 | 5.5.12-log                   |
| VERSION_COMPILE_MACHINE | x86                          |
| DATADIR                 | C:\MySQL_5.5.12\data\        |
| VERSION_COMPILE_OS      | Win64                        |
+-------------------------+------------------------------+
5 rows in set (0.00 sec)

I will run this using MyISAM

Step 01) create a table called 'rolando'
Step 02) insert 'dominique' and 'diamond'
Step 03) copy the table structure to 'pamela'
Step 04) alter 'pamela' to not have auto_increment
Step 05) In DOS, copy rolando.MYD to pamela.MYD
Step 06) run REPAIR TABLE pamela; (Rebuild pamela.MYI)
Step 07) run SELECT COUNT(1) FROM pamela;
Step 08) run SHOW CREATE TABLE pamela\G
Step 09) run SELECT * FROM pamela;
Step 10) insert 'carlik' into pamela
Step 11) run SELECT * FROM pamela;

Let's see if these steps are kosher.

Here are Steps 1-4

mysql> drop table if exists rolando;
Query OK, 0 rows affected (0.02 sec)

mysql> drop table if exists pamela;
Query OK, 0 rows affected (0.00 sec)

mysql> create table rolando
    -> (
    ->     name varchar(20),
    ->     id int not null auto_increment,
    ->     primary key (id)
    -> ) ENGINE=MyISAM;
Query OK, 0 rows affected (0.05 sec)

mysql> insert into rolando (name) values ('dominique'),('diamond');
Query OK, 2 rows affected (0.00 sec)
Records: 2  Duplicates: 0  Warnings: 0

mysql> select * from rolando;
+-----------+----+
| name      | id |
+-----------+----+
| dominique |  1 |
| diamond   |  2 |
+-----------+----+
2 rows in set (0.00 sec)

mysql> create table pamela like rolando;
Query OK, 0 rows affected (0.05 sec)

mysql> show create table rolando\G
*************************** 1. row ***************************
       Table: rolando
Create Table: CREATE TABLE `rolando` (
  `name` varchar(20) DEFAULT NULL,
  `id` int(11) NOT NULL AUTO_INCREMENT,
  PRIMARY KEY (`id`)
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1
1 row in set (0.00 sec)

mysql> show create table pamela\G
*************************** 1. row ***************************
       Table: pamela
Create Table: CREATE TABLE `pamela` (
  `name` varchar(20) DEFAULT NULL,
  `id` int(11) NOT NULL AUTO_INCREMENT,
  PRIMARY KEY (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1
1 row in set (0.02 sec)

mysql> alter table pamela modify id int(11) unsigned not null;
Query OK, 0 rows affected (0.11 sec)
Records: 0  Duplicates: 0  Warnings: 0

mysql> show create table pamela\G
*************************** 1. row ***************************
       Table: pamela
Create Table: CREATE TABLE `pamela` (
  `name` varchar(20) DEFAULT NULL,
  `id` int(11) unsigned NOT NULL,
  PRIMARY KEY (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1
1 row in set (0.00 sec)

mysql> select count(1) from pamela;
+----------+
| count(1) |
+----------+
|        0 |
+----------+
1 row in set (0.01 sec)

mysql>

Here is Step 6

C:\>copy C:\MySQL_5.5.12\data\test\rolando.MYD C:\MySQL_5.5.12\data\test\pamela.MYD
        1 file(s) copied.

C:\>

Here are the rest of the Steps starting at Step 7

mysql> repair table pamela;
+-------------+--------+----------+------------------------------------+
| Table       | Op     | Msg_type | Msg_text                           |
+-------------+--------+----------+------------------------------------+
| test.pamela | repair | warning  | Number of rows changed from 0 to 2 |
| test.pamela | repair | status   | OK                                 |
+-------------+--------+----------+------------------------------------+
2 rows in set (0.03 sec)

mysql> select count(1) from pamela;
+----------+
| count(1) |
+----------+
|        2 |
+----------+
1 row in set (0.00 sec)

mysql> insert into pamela (name,id) values ('carlik',3);
Query OK, 1 row affected (0.00 sec)

mysql> select * from pamela;
+-----------+----+
| name      | id |
+-----------+----+
| dominique |  1 |
| diamond   |  2 |
| carlik    |  3 |
+-----------+----+
3 rows in set (0.00 sec)

mysql>

Dangerous game, isn't it ???

Guess what? Stuff like this is actually published in "High Performance MySQL : Optimization, Backups, Replication, and more", Pages 146-148 under the Subheading Speeding Up ALTER TABLE. Page 147 Paragraph 1 says:

The technique we are about to demonstrate is unsupported, undocumented, and may not work. Use it at your risk. We advise you to back up you data first!

I also had an earlier post when someone ask a similar question : Can I rename the values in a MySQL ENUM column in one query?

You got guts, @atxdba !!!

Mysql – Finding rows for a specified date range

Another way to get the result is this. It finds first all groups that the teacher has surely taught (or is going to) by checking that she has started within the month and then in another subquery it finds - for every group - the last teacher that started at the first day of the month or earlier.

With the unique index you have on the table, the second subquery should be quite efficient. The first subquery would benefit from an index on (teacherid, startdate, groupid):

SELECT groupid
FROM pupilgroupteacher
WHERE teacherid = @teacher 
  AND startdate >= @month + INTERVAL 1 DAY
  AND startdate < @month + INTERVAL 1 MONTH

UNION DISTINCT

SELECT gg.groupid
FROM 
    ( SELECT DISTINCT groupid
      FROM pupilgroupteacher
    ) AS gd
  JOIN pupilgroupteacher AS gg
    ON  gg.groupid = gd.groupid
    AND gg.startdate =
        ( SELECT MAX(gi.startdate)
          FROM pupilgroupteacher AS gi 
          WHERE gi.groupid = gd.groupid
            AND gi.startdate < @month + INTERVAL 1 DAY
        )
WHERE gg.teacherid = @teacher ;

Best Answer

Related Solutions

Mysql – Drop auto increment hack w/o alter table

Mysql – Finding rows for a specified date range

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