MySQL database optimization with indices

Why MySQL indices are so important? Here at Vevida, we like to help our customers as much as possible. Even with optimizing a MySQL database when they don’t ask for it, or when a customer doesn’t know performance can be improved. For example by adding an index because we spotted a slow query in our slow-query log.

MySQL fix. Image via Flickr by Luis M. Gallardo D
MySQL fix. Image via Flickr by Luis M. Gallardo D

Fix MySQL indices and slow queries

An index is used by MySQL to help find rows quickly. We want to make it as easy as possible for MySQL to find the relevant rows, the more precise or specific we are the less the number of rows MySQL has to fetch.

The other day I spotted the following in MySQL slow-query log, in which MySQL needed roughly 3 seconds to examine 8035 and send 872 rows. That looks like a good optimization candidate…

# Time: 140605 16:41:34
# User@Host: database[database] @ server-01.example.com [1.1.11.111]
# Thread_id: 4660034  Schema: database  QC_hit: No
# Query_time: 3.010892  Lock_time: 0.000062  Rows_sent: 872  Rows_examined: 8035
use database;
SET timestamp=1401979294;
SELECT * FROM sContent WHERE sYear = '2014' AND sPublish = 1 and ('2014-06-05 16:41:30' Between sVisible_from And sVisible_untill or sVisible_unlimited

So I started with examining the query:

Examining a query with MySQL EXPLAIN SELECT

The MySQL EXPLAIN statement is used to obtain a query execution plan. That is, an explanation of how MySQL would execute a query. This means I can use EXPLAIN SELECT to examine the query.

MariaDB [database]> explain SELECT * FROM sContent WHERE sYear = '2014' AND sPublish = 1 and ('2014-06-05 16:41:30' Between sVisible_from And sVisible_untill or sVisible_unlimited = 1) ORDER BY sDate_insert DESC;
+------+-------------+-------------+------+----------------------------------------+----------------+---------+-------+------+-----------------------------+
| id   | select_type | table       | type | possible_keys                          | key            | key_len | ref   | rows | Extra                       |
+------+-------------+-------------+------+----------------------------------------+----------------+---------+-------+------+-----------------------------+
|    1 | SIMPLE      | sContent | ref     | sPublish,sVisible_unlimited            | sPublish       | 2       | const | 7091 | Using where; Using filesort |
+------+-------------+-------------+------+----------------------------------------+----------------+---------+-------+------+-----------------------------+
1 row in set (0.03 sec)

Here I see indices exist: sPublish, sVisible_unlimited, and only sPublish is used.

In the WHERE clause there is sYear = '2014', but sYear isn’t indexed. I use the statement DESCRIBE (or DESC) to describe the table definitions. This is an synonym of EXPLAIN, but mostly used for describing table definitions.

MariaDB [database]> desc sContent;
+--------------------------+--------------+------+-----+---------------------+-----------------------------+
| Field                    | Type         | Null | Key | Default             | Extra                       |
+--------------------------+--------------+------+-----+---------------------+-----------------------------+
| cnt_id                   | int(11)      | NO   | PRI | NULL                | auto_increment              |
[...]
| sYear                    | varchar(4)   | YES  |     | NULL                |                             |
+--------------------------+--------------+------+-----+---------------------+-----------------------------+

I added an index on sYear:

ALTER TABLE `sContent` ADD INDEX (`sYear`);

and this gives a better result examining the query again with EXPLAIN:

MariaDB [database]> explain SELECT * FROM sContent WHERE sYear = '2014' AND sPublish = 1 and ('2014-06-05 16:41:30' Between sVisible_from And sVisible_untill or sVisible_unlimited = 1) ORDER BY sDate_insert DESC;
+------+-------------+-------------+------+-------------------------------------------------+----------+---------+-------+------+----------------------------------------------------+
| id   | select_type | table       | type | possible_keys                                   | key      | key_len | ref   | rows | Extra                                              |
+------+-------------+-------------+------+-------------------------------------------------+----------+---------+-------+------+----------------------------------------------------+
|    1 | SIMPLE      | sContent | ref     | sPublish,sVisible_unlimited,sYear               | sYear    | 7       | const | 1503 | Using index condition; Using where; Using filesort |
+------+-------------+-------------+------+-------------------------------------------------+----------+---------+-------+------+----------------------------------------------------+
1 row in set (0.00 sec)

By adding an index on this one column sYear, MySQL doesn’t have to search through 7091 rows, but only 1503. This saves considerable, which will improve database and website performance.

MySQL index optimization

Update: 2-4-2015, Why is a MySQL index so important? Today, I noticed the following query in the MySQL slow-log of a server (EXPLAIN added for investigation):

MariaDB [db_name]> EXPLAIN  SELECT * FROM tblproducts WHERE CampaignId=379 AND CampaignProductId='AB1005257';
+------+-------------+------------------+------+---------------+---------+---------+-------+--------+-------------+
| id   | select_type | table            | type | possible_keys | key     | key_len | ref   | rows   | Extra       |
+------+-------------+------------------+------+---------------+---------+---------+-------+--------+-------------+
|    1 | SIMPLE      | tblproducts | ref  | Index_5       | Index_5 | 5       | const | 146104 | Using where |
+------+-------------+------------------+------+---------------+---------+---------+-------+--------+-------------+
1 row in set (0.00 sec)

As you can see, there is an index present on the tblproducts table, called Index_5. But still MySQL has to plow through 146104 rows. Given the CampaignId field contains what appears to be an identifier, that makes a great option for an extra index!

I added the index: ALTER TABLE `tblproducts` ADD INDEX (`CampaignId`);

The added index optimized the query to only one result:

MariaDB [db_name]> EXPLAIN  SELECT * FROM tblproducts WHERE CampaignId=379 AND CampaignProductId='AB1005257';
+------+-------------+------------------+------+--------------------+------------+---------+-------------+------+-----------------------+
| id   | select_type | table            | type | possible_keys      | key        | key_len | ref         | rows | Extra                 |
+------+-------------+------------------+------+--------------------+------------+---------+-------------+------+-----------------------+
|    1 | SIMPLE      | tblproducts | ref  | Index_5,CampaignId | CampaignId | 308     | const,const |    1 | Using index condition |
+------+-------------+------------------+------+--------------------+------------+---------+-------------+------+-----------------------+
1 row in set (0.00 sec)

This is why MySQL index optimization is so important, even on the WordPress wp_options table.

1 thought on “MySQL database optimization with indices”

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    Are you running into MySQL load problems? Learn how to tune MySQL servers for a heavy InnoDB workload, by configuring innodb_buffer_pool_instances. Dividing the InnoDB buffer pool into multiple instances improves Disk I/O. By doing so, you run your database and website more efficiently and faster. Here is a little help for you.

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    Tune MySQL InnoDB buffer pool instances & size for heavy workloads

    All for more InnoDB Disk I/O performance on MySQL 5.5+.

    Tuning MySQL servers is an ever ongoing process. Every new MySQL version brings new configuration settings you can use to improve its performance. As a MySQL DBA you want your database server and databases to perform better than well, don’t you?

    MariaDB/MySQL 5.5.4 introduces new configuration settings for the InnoDB storage engine. This can greatly improve MySQL’s InnoDB performance, both in read and write operations.

    One of those settings is innodb_buffer_pool_instances. The innodb_buffer_pool_instances divides the InnoDB buffer pool into separate instances. Dividing your buffer pool into separate instances can improve concurrency, by reducing contention as different threads read and write to cached pages. Multiple buffer pool instances are configured using the innodb_buffer_pool_instances configuration option.

    You might also want to adjust the innodb_buffer_pool_size value:

    The larger the InnoDB buffer pool, the more InnoDB acts like an in-memory database. It reads data from disk once and then accesses the data from memory during subsequent reads. Buffer pool size is configured using the innodb_buffer_pool_size configuration option.

    Back to increasing innodb_buffer_pool_instances.

    The innodb_buffer_pool_instances divides the InnoDB buffer pool in a number of regions.

    The number of regions that the InnoDB buffer pool is divided into. For systems with buffer pools in the multi-gigabyte range, dividing the buffer pool into separate instances can improve concurrency, by reducing contention as different threads read and write to cached pages. Each page that is stored in or read from the buffer pool is assigned to one of the buffer pool instances randomly, using a hashing function. Each buffer pool manages its own free lists, flush lists, LRUs, and all other data structures connected to a buffer pool, and is protected by its own buffer pool mutex.This option takes effect only when you set the innodb_buffer_pool_size to a size of 1 gigabyte or more. The total size you specify is divided among all the buffer pools. For best efficiency, specify a combination of innodb_buffer_pool_instances and innodb_buffer_pool_size so that each buffer pool instance is at least 1 gigabyte.

    In MySQL versions prior to 5.5.4 this was not configurable and thus set to just one instance. Now you can increase innodb_buffer_pool_size, and you can divide the InnoDB buffer pool into multiple regions by setting innodb_buffer_pool_instances to 2, 3, 4 or 8. As long as innodb_buffer_pool_size is set high enough, and you have enough memory available in your MySQL database server. This increases InnoDB read/write threads.

    To enable multiple buffer pool instances, set the innodb_buffer_pool_instances configuration option to a value greater than 1 (the default) up to 64 (the maximum).

    How to restore single MySQL table from a full mysqldump backup file?

    For example, you can set innodb_buffer_pool_size to 6 GB and innodb_buffer_pool_instances to 4 in your my.cnf MySQL configuration file:

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    ; InnoDB buffer pool size in bytes. The primary value to adjust on a database server,
    ; can be set up to 80% of the total memory in these environments
    innodb_buffer_pool_size = 6000M

    ; If innodb_buffer_pool_size is set to more than 1GB, innodb_buffer_pool_instances

    ; divides the InnoDB buffer pool into this many instances.
    innodb_buffer_pool_instances = 4
    Code language: TOML, also INI (ini)

    In this example, I’ve used an innodb_buffer_pool_size of 6000M (6 GB), so there is 1500M available per innodb_buffer_pool_instance, which is more than the minimum 1 GB. As a rule of thumb, set your innodb_buffer_pool_size to approximately 70 – 80% of the RAM available.

    Innodb_buffer_pool_instances defaults

    Various MySQL versions have different innodb_buffer_pool_instances default values, here is an overview – listing – for you:

    MySQL version# InnoDB buffer pool instancesNotesMySQL 5.5 (<= 5.5.4)1not configurableMySQL 5.51–MySQL 5.6 (<= 5.6.5)1–MySQL 5.6 (>= 5.6.6)8or 1 if innodb_buffer_pool_size < 1GBMySQL 5.78or 1 if innodb_buffer_pool_size < 1GBMariaDB 10 (<= MariaDB 10.0.3)1–MariaDB 10 (>= MariaDB 10.0.4)8–

    InnoDB read and write I/O threads in MySQL

    Besides innodb_buffer_pool_instances, you can also increase the number of InnoDB read I/O threads and write I/O threads. These are configured with innodb_write_io_threads and innodb_read_io_threads.

    Both settings default to 4 threads. We can increase these to, for example, 8:

    ; Number of I/O threads for writes
    innodb_write_io_threads = 8
    ; Number of I/O threads for reads
    innodb_read_io_threads = 8
    Code language: TOML, also INI (ini)

    innodb_read_io_threads

    The number of I/O threads for read operations in InnoDB. The default value is 4.

    innodb_write_io_threads

    The number of I/O threads for write operations in InnoDB. The default value is 4.

    When should you increase the number of innodb_read_io_threads? When you see more than 64 × innodb_read_io_threads pending read requests in SHOW ENGINE INNODB STATUS, you might gain by increasing the value of innodb_read_io_threads.

    Optimizing InnoDB Disk I/O

    If you follow the best practices for database design and the tuning techniques for SQL operations, but your database is still slowed by heavy disk I/O activity, explore these low-level techniques related to disk I/O. If the Unix top tool or the Windows Task Manager shows that the CPU usage percentage with your workload is less than 70%, your workload is probably disk-bound, Optimizing InnoDB Disk I/O.

    Starting from MariaDB 10.0, the default number of innodb_buffer_pool_instances is 8. This means you have to configure your innodb_buffer_pool_size to at least 8 GB, see the defaults above.

    Protip, don’t over optimize: never make too many configuration changes at once. After changing one or two settings, let the server run for a few days so you can learn the effects of the changes. Then, if necessary, make additional changes to the configuration.

    Convert MyISAM to InnoDB tables for WordPress using a pluginFor WordPress, I created a plugin to convert MyISAM tables to InnoDB, that now is incorporated into the Vevida Optimizer WordPress plugin. The Vevida Optimizer plugin extends the automatic update feature already present in WordPress. WordPress core updates can be switched on or off, themes and translations can be automatically updated, and the plugin updates can be configured on a per-plugin basis.

    Innodb_buffer_pool_instances deprecated in MariaDB 10.5.1+

    Please note that in MariaDB 10.5.1 and up, innodb_buffer_pool_instances is deprecated and ignored (MDEV-15058). Oracle MySQL 8.0 still seem to support it though.

    Extra tips for MySQL performance tuning

    Besides optimizing InnoDB for a high-performance workload, there is more you can do to tune MySQL server and database performance. Here are some extra MySQL configuration tips for you. Some information might be outdated and obsolete but may hold valuable information for tuning your MySQL servers. Some settings may be ignored if you’re only using InnoDB as storage engine (tip: drop MyISAM, only use InnoDB!)

    Note: this is a translation and rewrite of my older Dutch post “MySQL performance en optimalisatie tips“, which is now deleted and links to here. Just in case you were wondering why you arrived here instead of the Dutch post after clicking a link :-)

    1: No two MySQL servers are the same

    When optimizing MySQL database servers, keep in mind that no server is equal to another. Settings that work well on one server, may degrade performance on a second. If you manage multiple servers with its configuration under version control (e.g almost -or exactly- the same MySQL configuration for all servers), choose what works best on all servers.

    To determine what you can improve, you first need to know how the server performs now. You can use some MySQL commands for this on your MySQL cli (data comes from my very old post).

    mysql> SHOW STATUS LIKE '%key_read%';
    +-------------------+-------------+
    | Variable_name | Value |
    +-------------------+-------------+
    | Key_read_requests | 11810240259 |
    | Key_reads | 9260357 |
    +-------------------+-------------+
    Code language: SQL (Structured Query Language) (sql)

    These two variables and values relate to the configured key_buffer_size

    In this old example, the database server has 4 GB of RAM and a configured key_buffer_size of 512 MB. The ratio (Key_read_requests / Key_reads) is approximately 1/1275, which is good but the key_buffer_size value may be increased to 768 MB. Even though this is not yet necessary.

    mysql> SHOW STATUS LIKE 'thread%';
    +-------------------+---------+
    | Variable_name | Value |
    +-------------------+---------+
    | Threads_cached | 0 |
    | Threads_connected | 76 |
    | Threads_created | 6234040 |
    | Threads_running | 2 |
    +-------------------+---------+
    Code language: SQL (Structured Query Language) (sql)

    These Threads_* variable values show you there are currently 76 connected threads, of which only 2 are really running a thread (executing a statement). This means 74 connections are idle.

    Here you can also see that there is no “thread cache” set up for MySQL: Threads_cached | 0

    You can use the MySQL Server System variable thread_cache_size to configure how many threads must be cached by MySQL. This is one of those configuration settings that, probably, provides the least performance gain, but still…

    Don’t set this one too high, somewhere between 20 and 40 is often good enough:

    thread_cache_size = 20Code language: TOML, also INI (ini)

    When you execute the previous statement again, the values will be:

    mysql> SHOW STATUS LIKE 'thread%';
    +-------------------+-------+
    | Variable_name | Value |
    +-------------------+-------+
    | Threads_cached | 14 |
    | Threads_connected | 98 |
    | Threads_created | 2896 |
    | Threads_running | 1 |
    +-------------------+-------+
    Code language: SQL (Structured Query Language) (sql)

    You now have 14 threads cached :)

    2: Miscellaneous MySQL configuration settings

    A few words on some miscellaneous configuration settings.

    2.1: tmp_table_size and max_heap_table_sizeThe default tmp_table_size and max_heap_table_size values are 16M. These two have to be equal in size! It sets the maximum size for internal in-memory tables, resulting in less creation of temporarily MyISAM tables on the file system. That in return, results in less disk I/O.

    https://dev.mysql.com/doc/refman/8.0/en/server-system-variables.html#sysvar_tmp_table_sizehttps://dev.mysql.com/doc/refman/8.0/en/server-system-variables.html#sysvar_max_heap_table_size

    2.2: join_buffer_sizeThe join_buffer_size sets a maximum buffer size for plain index scans, range index scans and joins without indices (and therefore perform full table scans). Keep this one low, 1M for example.

    MySQL database optimization with indices

    3. Use Diagnostics for improvements

    It is important to frequently run diagnostics and/or look up diagnostic data (for example in your information_scheme table). Percona has a lot of information about some key metrics:

    https://www.percona.com/doc/percona-server/8.0/index.html#diagnostics-improvements

    MySQL tuning, the conclusion

    Tuning MySQL and the InnoDB storage engine is an important step in further optimizing your hosting environment. Every new MySQL version brings new settings to improve your MySQL configuration, so be sure to read those changelogs.

    In this article we went over InnoDB Buffer Pool Size and InnoDB Buffer Pool Instances. Setting these properly greatly improves your MySQL server’s performance!

    But never (ever, ever) over-optimize! Please don’t make too many configuration changes at once. Make one or two and restart mysqld. After monitoring your system for a few days, running with the new configuration, you have data available to further optimize other MySQL settings.

    With InnoDB being the default storage engine, you also have to make sure you make use of this storage engine in MySQL. Therefore it is important to convert old MyISAM tables to InnoDB.
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