Checking MySQL: mysqltuner (and setting up your .my.cnf)

There are many ways to monitor your MySQL server; I’m going to start posting a few small articles monitoring your MySQL server.
Today we’ll start with the least intrusive and simplest method and also setup .my.cnf to ensure your scripts can login to MySQL.
Setting this up and following the first advice from this script will take 5 minutes of your time and provide you with a bit of insight.

DISCLAIMER: I’m not the author of this tool and you should exercise sound judgement in implementing any advice from mysqltuner.

For the script to run correctly you must have MySQL root access or at least an account with sufficient privileges. The script itself can be run as a non privileged user.
Let’s create one for this article:

useradd mysqlmonitor
sudo -i -u mysqlmonitor

create the .my.cnf file in your favorite editor with the following contents


Make sure this file can only be read by this user (and root)
chmod 600 .my.cnf

You can retrieve the script very easily:


Be sure to set the permissions on the resulting file:

chmod 700

After inspecting the file you should be able to run it by executing: ./ and get a report much like this:

>> MySQLTuner 1.2.0 – Major Hayden
>> Bug reports, feature requests, and downloads at
>> Run with ‘–help’ for additional options and output filtering

——– General Statistics ————————————————–
[–] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.5.28-29.1-log
[OK] Operating on 64-bit architecture

——– Storage Engine Statistics ——————————————-
[–] Status: +Archive -BDB -Federated +InnoDB -ISAM -NDBCluster
[–] Data in MyISAM tables: 51M (Tables: 715)
[–] Data in InnoDB tables: 39M (Tables: 336)
[–] Data in PERFORMANCE_SCHEMA tables: 0B (Tables: 17)
[–] Data in MEMORY tables: 0B (Tables: 2)
[!!] Total fragmented tables: 44

——– Security Recommendations ——————————————-
[!!] User ‘@localhost’ has no password set.

——– Performance Metrics ————————————————-
[–] Up for: 33d 11h 10m 37s (12M q [4.324 qps], 627K conn, TX: 51B, RX: 1B)
[–] Reads / Writes: 94% / 6%
[–] Total buffers: 2.1G global + 2.8M per thread (500 max threads)
[OK] Maximum possible memory usage: 3.5G (5% of installed RAM)
[OK] Slow queries: 0% (0/12M)
[OK] Highest usage of available connections: 9% (46/500)
[OK] Key buffer size / total MyISAM indexes: 1.0G/6.9M
[OK] Key buffer hit rate: 100.0% (35M cached / 2K reads)
[!!] Query cache is disabled
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 677K sorts)
[!!] Joins performed without indexes: 29977
[!!] Temporary tables created on disk: 43% (411K on disk / 950K total)
[OK] Thread cache hit rate: 99% (46 created / 627K connections)
[!!] Table cache hit rate: 13% (1K open / 9K opened)
[OK] Open file limit used: 2% (1K/65K)
[OK] Table locks acquired immediately: 99% (10M immediate / 10M locks)
[OK] InnoDB data size / buffer pool: 40.0M/1.0G

——– 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 (>= 8M)
join_buffer_size (> 128.0K, or always use indexes with joins)
tmp_table_size (> 128M)
max_heap_table_size (> 128M)
table_cache (> 10240)

To have this run every week is just a matter of setting up the cron properly:

crontab -e

[email protected]
@weekly $HOME/

Soon I will post how to setup a MySQL my.cnf that will work well for use in webhosting along with a few tips to safely try these configurations and revert back if needed.

Varnish for the impatient (RHEL / CentOS 6)


You may have heard of Varnish before and may want to see what the fuss is about and more importantly, get started yourself.
The format of this post is pretty simple, the command should be copy-paste-able and due to the magic of Yum and RPM should work for you.
The instructions do not include any control panel integration (I use Virtualmin, you probably use cPanel, Plesk or Directadmin. I have no experience with these)

However, before we get started:

Disclaimer: These instructions should *NOT* be executed on a live environment. You will have to test them first. I’m not responsible if you break your cPanel / Plesk environment. If you’re unsure, a very safe solution is to setup a new virtual server and make Varnish “backend” point to your old server.

With that out of the way, let’s get started..


Varnish has very little in hard requirements but as you would most likely store the content in memory, sufficient memory is a plus. If you’re running CentOS/RHEL 5/6 (64 bit preferred) you should be set.


You can get the current version and install instructions from the Varnish Site

For your convenience, you can use the following:

rpm --nosignature -i

yum -y install varnish

You can verify a succesful install by querying rpm:

rpm -q varnish

Which should yield something along the lines of: varnish-3.0.2-1.el5

This installs Varnish Cache and it’s dependencies (you’ll note that Varnish includes the use of a compiler such as GCC. This is required for compiling the configuration files from VCL)

You will then need to customize a few entries before you can start using Varnish. We’re going to assume you want to experiment with Varnish and thus run it from port 8080 instead of replacing Apache on port 80. I’ll detail the switch from port 8080 to 80 in a later post.


Varnish uses VCL files to route requests and determine how to cache and how long. VCL is a subset of the C programming language and is actually compiled into computer language when loaded. In essence your VCLs drive Varnish as if you programmed it, making the routing very efficient. For your convenience I’ve included a simple VCL for WordPress which does the following for you:

  • Setup a single backend (your backend is basically Apache on the same machine, but advanced setups can include loadbalancing)
  • Allow purge requests from localhost (for your WordPress plugins)
  • Strip cookies from all requests except login, wp-admin, comments
  • Disable caching of the admin interface

I’ve also included links to more advanced VCL setups which include more functionality. Keep in mind that this VCL is tailored to WordPress and static sites, but does not include provisions for other setups. I’ve taken this from the Varnish documentation and tweaked it slightly

You can download it here:

default.vcl (please don’t forget to modify the default backend to point to apache)


This file setups your Varnish preferences allowing you to customize your settings through a few different “Alternatives”. I tend to stick with the default enabled one: Alternative 3.

The included configuration sets the following for you:

  • Varnish uses port 8080
  • Admin IP is and port 2000
  • Varnish min threads 64 (spin up some threads to do work)
  • Varnish storage size to 1G
  • Varnish storage mode malloc (meaning in memory instead of to file)

A simple non scientific performance test

By now you must be wondering what we’re doing all this for. Let’s have some fun and benchmark a simple WordPress site (site contains text). is a local alias for a simple benchmark site. Both tests were run locally against the server using Apache Benchmark

The server is a Xen based virtual machine running on 3 E5440  @ 2.83GHz cores. The machine has 2 GB memory available and runs Centos 5.

Performance using a tweaked Apache setup (Apache worker, fcgid, W3 Total cache with page caching). When page caching is disabled the server crashes the PHP processes and only shows blank pages.

Without using Apache 2.4 and the event worker, this is as good as it will probably get…

Server Software:        Apache/2
Server Hostname:
Server Port:            80

Document Path:          /
Document Length:        10935 bytes

Concurrency Level:      250
Time taken for tests:   84.20278 seconds
Complete requests:      100000
Failed requests:        0
Write errors:           0
Total transferred:      1135200000 bytes
HTML transferred:       1093500000 bytes
Requests per second:    1190.19 [#/sec] (mean)
Time per request:       210.051 [ms] (mean)
Time per request:       0.840 [ms] (mean, across all concurrent requests)
Transfer rate:          13194.35 [Kbytes/sec] received

Connection Times (ms)
              min  mean[+/-sd] median   max
Connect:        0   64 921.3      0   45006
Processing:     1  129 376.0     68   18268
Waiting:        1  128 376.0     67   18267
Total:          4  193 1004.5     68   47267

Percentage of the requests served within a certain time (ms)
  50%     68
  66%     78
  75%     85
  80%     90
  90%    131
  95%    525
  98%   1093
  99%   3070
 100%  47267 (longest request)

The job is close to CPU bound and the load grows to close to 7:

00:37:26 up 38 days, 21:13,  2 users,  load average: 6.97, 3.19, 1.28

Let’s be fair here, we served up 100.000 pages in 84 seconds or 1190 pages per second.
Apache may not be extremely fast, but it still does a good job serving up HTML pages (remember, the frontpage is cached using W3 Total Cache)

Let’s engage Varnish and see the difference

Server Software:        Apache/2
Server Hostname:
Server Port:            80

Document Path:          /
Document Length:        10935 bytes

Concurrency Level:      250
Time taken for tests:   24.277115 seconds
Complete requests:      100000
Failed requests:        0
Write errors:           0
Total transferred:      1136834104 bytes
HTML transferred:       1093532805 bytes
Requests per second:    4119.11 [#/sec] (mean)
Time per request:       60.693 [ms] (mean)
Time per request:       0.243 [ms] (mean, across all concurrent requests)
Transfer rate:          45729.86 [Kbytes/sec] received

Connection Times (ms)
              min  mean[+/-sd] median   max
Connect:        0   10  60.8      8    3035
Processing:     3   49  14.7     49     271
Waiting:        0   21  14.2     19     243
Total:         14   60  61.7     56    3064

Percentage of the requests served within a certain time (ms)
  50%     56
  66%     59
  75%     65
  80%     71
  90%     76
  95%     77
  98%     80
  99%     81
 100%   3064 (longest request)


The server had an easier time too

00:52:42 up 38 days, 21:28,  2 users,  load average: 1.70, 0.81, 0.73

Other than showing impressive numbers, please keep in mind that every pageload includes loads of other resources (CSS, images, javascript) that will also be sped up by Varnish cache. Your website will also feel a lot faster to your users and rank higher in performance tests.


As you can see, Varnish really increases performance of your websites. Unfortunately, while Varnish is perfect (really!) the configuration and the real world rarely is. Varnish by default will not cache pages that serve cookies, and for good reason. Cookies usually indicate dynamic content. To make WordPress cachable we drop most of the cookies except for dynamic pages.

Here is a small list of things that will change when using Varnish:

  • Apache logs become useless since not every request hits apache. This is important for bandwidth accounting in controlpanels such as Virtualmin, cPanel etc. Varnish allows logging in the same format as Apache, but does not separate the logs by domain as Apache does. I’ll share a work around in a later post
  • Plugins may break in subtle ways  as they don’t receive cookies correctly or if their pages are cached (for example, completely dynamic user driven pages may need to be excluded).
  • Widgets don’t update properly (for example a hitcounter will not update) I’ll show in a later post how to use “Edge Side Includes (ESI)” to counter this problem.

Next article will discuss how to setup W3 Total Cache with Varnish (don’t worry, it will be easy)