Sunday, 13 November 2011

Performance Tuning Tools for MySQL on LINUX

How to Performance Tune MySQL for Wordpress

Since I have been working a lot with Wordpress, PHP and Apache I have had to get used to the limitations of MySQL and the applications that are available to connect to MySQL databases such as Navicat or PHPMyAdmin.

As well as all the missing DML such as CTE's I really miss the very useful Data Management Views (DMV's) that has as they make optimising a database very easy and I have built up a large collection of SQL Server Performance Reports and tools to help me debug database performance issues.

Since working with Wordpress I have seen a lot of Plugins that use very poor SQL techniques and it seems most plugin authors that create their own tables in the Wordpress database don't even think about indexes that could increase performance of some very badly written SQL.

Having to sift through the slow query log and then run an EXPLAIN on each query is a time consuming job whereas setting up a scheduled job to monitor missing indexes and then list all suggestions is very easy to do in MSSQL with their Data Management Views (DMV's) that hold information about missing indexes, high cost queries, cached query plan re-use and much more.

My SQL Optimisation for Wordpress and LINUX

There are a number of tools available for performance tuning MySQL and I have listed a few below.

MySQLTuner is a Perl script that analyzes your MySQL performance and, based on the statistics it gathers, returns recommendations based on the ShowVariables SQL that you can adjust to increase performance.

One of the good things about having root access to your own LINUX server (VPS or dedicated) is the ability to SSH in and then load and install programs remotely with a few lines of code from the command prompt.

To load and run on your server do the following:

Change the directory to your program folder e.g:

cd /usr/bin

Load the tool in remotely with a WGET command e.g:


Change the permissions to make it executable e.g:

chmod +x

Run the tool e.g

myhost:/usr/bin# /usr/bin/

>>  MySQLTuner 1.2.0 - Major Hayden 
>>  Bug reports, feature requests, and downloads at
>>  Run with '--help' for additional options and output filtering
Please enter your MySQL administrative login: root
Please enter your MySQL administrative password:

-------- General Statistics --------------------------------------------------
[--] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.0.51a-24+lenny5-log
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: +Archive -BDB +Federated -InnoDB -ISAM -NDBCluster
[--] Data in MyISAM tables: 419M (Tables: 98)
[!!] Total fragmented tables: 9

-------- Security Recommendations  -------------------------------------------
[OK] All database users have passwords assigned

-------- Performance Metrics -------------------------------------------------
[--] Up for: 3d 3h 0m 33s (5M q [22.010 qps], 58K conn, TX: 102B, RX: 1B)
[--] Reads / Writes: 87% / 13%
[--] Total buffers: 314.0M global + 2.6M per thread (100 max threads)
[OK] Maximum possible memory usage: 576.5M (55% of installed RAM)
[OK] Slow queries: 1% (70K/5M)
[OK] Highest usage of available connections: 16% (16/100)
[OK] Key buffer size / total MyISAM indexes: 64.0M/196.8M
[OK] Key buffer hit rate: 100.0% (18B cached / 5M reads)
[OK] Query cache efficiency: 83.1% (4M cached / 5M selects)
[!!] Query cache prunes per day: 61605
[OK] Sorts requiring temporary tables: 0% (207 temp sorts / 356K sorts)
[!!] Joins performed without indexes: 35147
[!!] Temporary tables created on disk: 44% (309K on disk / 690K total)
[OK] Thread cache hit rate: 99% (329 created / 58K connections)
[!!] Table cache hit rate: 13% (191 open / 1K opened)
[OK] Open file limit used: 22% (231/1K)
[OK] Table locks acquired immediately: 99% (1M immediate / 1M locks)

-------- Recommendations -----------------------------------------------------
General recommendations:
    Run OPTIMIZE TABLE to defragment tables for better performance
    Adjust your join queries to always utilize indexes
    When making adjustments, make tmp_table_size/max_heap_table_size equal
    Reduce your SELECT DISTINCT queries without LIMIT clauses
    Increase table_cache gradually to avoid file descriptor limits
Variables to adjust:
    query_cache_size (> 40M)
    join_buffer_size (> 128.0K, or always use indexes with joins)
    tmp_table_size (> 200M)
    max_heap_table_size (> 200M)
    table_cache (> 200)

You should carefully read the output, especially the recommendations at the end.

It shows exactly which variables you could adjust in the [mysqld] section of your my.cnf (on Debian and Ubuntu the full path is /etc/mysql/my.cnf). but be careful as this is only advice and you should find out as much as you can before changing core configuration settings.

Whenever you change your my.cnf file, make sure that you restart MySQL with this command (or use your GUI)

/etc/init.d/mysql restart

You can then run MySQLTuner again to see if it has further recommendations to improve the MySQL performance.

Another tool of a similar nature is the MySQLReport tool which can be found at

Information can be found here about how to read and analyse the report that is produces from this link

You can load it up remotely and build it on your server in a similar way making use of an HTTP tool like CURL or WGET etc:


--2011-11-13 02:58:47--
Connecting to||:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 38873 (38K) [application/x-perl]
Saving to: `mysqlreport'

100%[======================================>] 38,873      --.-K/s   in 0.1s

2011-11-13 02:58:47 (254 KB/s) - `mysqlreport' saved [38873/38873] 

Once loaded give the newly installed file execute permission with the following command

chmod +x

You then call it by passing through the details of the system you want to analyse e.g:

mysqlreport --user root --host localhost --password mypsw100

MySQL 5.0.51a-24+lenny5  uptime 3 3:21:16       Sun Nov 13 03:04:11 2011

__ Key _________________________________________________________________
Buffer used    52.33M of  64.00M  %Used:  81.76
  Current      61.15M            %Usage:  95.55
Write hit      99.96%
Read hit       99.97%

__ Questions ___________________________________________________________
Total           5.96M    22.0/s
  QC Hits       4.60M    17.0/s  %Total:  77.25
  DMS           1.07M     3.9/s           17.97
  Com_        226.52k     0.8/s            3.80
  COM_QUIT     58.22k     0.2/s            0.98
  +Unknown        408     0.0/s            0.01
Slow (2)       70.43k     0.3/s            1.18  %DMS:   6.58  Log:  ON
DMS             1.07M     3.9/s           17.97
  SELECT      935.60k     3.4/s           15.70         87.35
  UPDATE      127.41k     0.5/s            2.14         11.90
  INSERT        7.63k     0.0/s            0.13          0.71
  DELETE          450     0.0/s            0.01          0.04
  REPLACE           0       0/s            0.00          0.00
Com_          226.52k     0.8/s            3.80
  set_option  169.55k     0.6/s            2.84
  change_db    56.71k     0.2/s            0.95
  optimize         91     0.0/s            0.00

__ SELECT and Sort _____________________________________________________
Scan           68.94k     0.3/s %SELECT:   7.37
Range          42.09k     0.2/s            4.50
Full join      35.21k     0.1/s            3.76
Range check         0       0/s            0.00
Full rng join       0       0/s            0.00
Sort scan     300.33k     1.1/s
Sort range     56.97k     0.2/s
Sort mrg pass     207     0.0/s

__ Query Cache _________________________________________________________
Memory usage   36.03M of  40.00M  %Used:  90.07
Block Fragmnt  10.04%
Hits            4.60M    17.0/s
Inserts       842.73k     3.1/s
Insrt:Prune    4.33:1     2.4/s
Hit:Insert     5.46:1

__ Table Locks _________________________________________________________
Waited          1.44k     0.0/s  %Total:   0.08
Immediate       1.77M     6.5/s

__ Tables ______________________________________________________________
Open              200 of  200    %Cache: 100.00
Opened          1.54k     0.0/s

__ Connections _________________________________________________________
Max used           16 of  100      %Max:  16.00
Total          58.52k     0.2/s

__ Created Temp ________________________________________________________
Disk table    310.39k     1.1/s
Table         381.99k     1.4/s    Size: 200.0M
File              431     0.0/s

__ Threads _____________________________________________________________
Running             1 of    1
Cached              7 of    8      %Hit:  99.44
Created           329     0.0/s
Slow                3     0.0/s

__ Aborted _____________________________________________________________
Clients           588     0.0/s
Connects           17     0.0/s

__ Bytes _______________________________________________________________
Sent          102.63G  378.3k/s
Received        1.95G    7.2k/s

__ InnoDB Buffer Pool __________________________________________________
Usage               0 of       0  %Used:   0.00
Read hit        0.00%
  Free              0            %Total:   0.00
  Data              0                      0.00 %Drty:   0.00
  Misc              0                      0.00
  Latched           0                      0.00
Reads               0       0/s
  From file         0       0/s            0.00
  Ahead Rnd         0       0/s
  Ahead Sql         0       0/s
Writes              0       0/s
Flushes             0       0/s
Wait Free           0       0/s

__ InnoDB Lock _________________________________________________________
Waits               0       0/s
Current             0
Time acquiring
  Total             0 ms
  Average           0 ms
  Max               0 ms

__ InnoDB Data, Pages, Rows ____________________________________________
  Reads             0       0/s
  Writes            0       0/s
  fsync             0       0/s
    Reads           0
    Writes          0
    fsync           0

  Created           0       0/s
  Read              0       0/s
  Written           0       0/s

  Deleted           0       0/s
  Inserted          0       0/s
  Read              0       0/s
  Updated           0       0/s

In a similar way you will need to know how to analyse each section to make the neccessary changes and you can find out what each calculation result means here:

Another good tool to use to find out what is going on in your database is MyTop. This is an application like Top that shows the current processes running on a server but for a MySQL database rather than the whole server. It does this by analysing the same data that SHOW PROCESSLIST would output.

You can obtain the code from

Once loaded you call it from your command prompt like the other commands passing in the host, database and password as well as a refresh rate if you require it. I think it defaults to 5 seconds but I like to use 1 second which you can change by supplying a parameter for --s parameter e.g:

mytop --user root --password mypsw --db myDB --s 1

The results look like this with a header that shows how many queries have run per second as well as slow queries from the slow quert log.

MySQL on localhost (5.0.51a-24+lenny5-log)                                 up 3+03:48:10 [03:31:05]
 Queries: 5.7M   qps:   22 Slow:     0.0         Se/In/Up/De(%):    77/00/00/00
             qps now:    2 Slow qps: 0.0  Threads:    3 (   3/   5) 00/00/00/00
 Key Efficiency: 100.0%  Bps in/out:   0.0/  0.6   Now in/out:  41.2/10.0k

      Id      User         Host/IP         DB      Time    Cmd Query or State
      --      ----         -------         --      ----    --- ----------
   58766      root       localhost strictly         0  Query show full processlist
   58772 darkpolit       localhost strictly         1  Query select CONCAT('http://www.strictly         
   58771 strictly        localhost strictly         4  Query select CONCAT('http://www.strictly         

Another method for those who don't have direct access into their LINUX server but only a control panel like CPANEL and use Wordpress for their website is my own Wordpress Plugin - the Strictly System Checker Plugin.

The Strictly System Checker is a Wordpress plugin that is designed to allow webmasters to monitor their site at regular intervals throughout the day and to be notified if the site goes down or experiences database problems or high server loads.

This plugin was not designed to be a replacement for professional server monitoring tools however it is a nice easy to use system that can aid webmasters in monitoring their Wordpress site as well as notifying the right person whenever the site is down or running into performance problems.

How it works

  • A CRON / WebCron job initiates an HTTP request to check whether the site can be accessed.
  • The system will check for the Error establishing a database connection error message as well as searching for an optional piece of text which can help indicate whether the page has loaded correctly.
  • If the error is found or the text cannot be found then a connection to the database is attempted.
  • If successful a CHECK and REPAIR is carried out on any tables that maybe corrupted.
  • An option exists to also check for fragmented tables and an OPTIMIZE command is carried out to fix any found.
  • An SQL report is carried out to report on some key performance indicators such as the number of connections, queries, reads, writes and more.
  • A report is carried out on the webserver to look at the current server load average and if it's above a specified threshold a report to the site administrator can be triggered.
  • A similar check is carried out on the database to ensure that there are no slow running queries or the connection limit hasn't been reached.
  • If problems are found an email is then sent to the site administrator with details of the report.
An example of a report that can be emailed to system administrators or viewed from the admin part of the website is below.

System Report: 2011-11-13 04:07:07

Initiating System Report...
Initiating an HTTP request to
The HTTP request to took 0 second(s) to respond and returned a status code of 200
The specified search text [read more] was found within the HTTP response
The server load is currently 0.48
The server load is okay
MySQL has been running for: 26 days 4 hours 18 mins 48 secs
Total Connections: 467253 - Aborted: 0 - Connections Per Hour 743
Total Queries: 21592142 - Queries / Per Hour 34365
Joins without indexes: 0 - Joins without indexes Per Hour 0
Total Reads: 4819507 (88%) - Total Writes 630029 (12%)
The system is currently configured to accept a maximum of 100 database connections
At the time of reporting the database was running 3 query
The current database load is 3%
The database load is okay
Initiating a check for fragmented tables and indexes
Optimized table: wp_options
Optimized table: wp_postmeta
Completed check for fragmented tables and indexes
The system report has completed all its tests successfully.

Report Completed At 2011-11-13 04:07:07

Strictly Software Plugins for Wordpress

So whilst I feel the tools available for MySQL performance monitoring are lacking when compared with those available with SQL 2008 there are some that will enable you to get the job done. Hopefully this article has been helpful and if you have any tools of your own please add them to t the comment section.

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