Archive for the ‘MySQL’ Category

How to get a list and Backup (Save Enabled Plugins) / Restore Enabled (Active) plugins in WordPress site with SQL query

Wednesday, January 14th, 2015

get-list-and-backup-restore-enabled-active-plugins-only-in-wordpress-with-sql-mysql-query

Getting a snapshot of all active plugins and keeping it for future in case if you install some broken plugin and you have to renable all enabled plugins from scratch is precious thing in WordPress.

… It is really annoying when you decide to try to enable few new plugins and out of a sudden your WordPress site / blog starts hanging (when accessed in browser)…

To fix it you have to Disable All Plugins and Re-enable all that used to work. However if you don't keep a copy of the plugins which were previously working and you're like me and have 109 plugins installed of which only 50 are in (Active) state / used. It could take you a day or two until you come up with a similar list to the ones you previously used … Thanksfully there is some prevention you can take by dumping a list of all plugins that are currently active and in later time only enable those in the list.

 

# mysql -u root -p
Enter password:

mysql> USE blog_db;

Here is the output I get in the moment:
 

mysql> DESCRIBE wp_options;
+————–+———————+——+—–+———+—————-+
| Field        | Type                | Null | Key | Default | Extra          |
+————–+———————+——+—–+———+—————-+
| option_id    | bigint(20) unsigned | NO   | PRI | NULL    | auto_increment |
| option_name  | varchar(64)         | NO   | UNI |         |                |
| option_value | longtext            | NO   |     | NULL    |                |
| autoload     | varchar(20)         | NO   |     | yes     |                |
+————–+———————+——+—–+———+—————-+

 

mysql> SELECT * FROM wp_options WHERE option_name = 'active_plugins';

|        38 | active_plugins | a:50:{i:0;s:45:"add-to-any-subscribe/add-to-any-subscribe.php";i:1;s:19:"akismet/akismet.php";i:2;s:43:"all-in-one-seo-pack/all_in_one_seo_pack.php";i:3;s:66:"ambrosite-nextprevious-post-link-plus/ambrosite-post-link-plus.php";i:4;s:49:"automatic-tag-selector/automatic-tag-selector.php";i:5;s:27:"autoptimize/autoptimize.php";i:6;s:35:"bm-custom-login/bm-custom-login.php";i:7;s:45:"ckeditor-for-wordpress/ckeditor_wordpress.php";i:8;s:47:"comment-info-detector/comment-info-detector.php";i:9;s:27:"comments-statistics/dcs.php";i:10;s:31:"cyr2lat-slugs/cyr2lat-slugs.php";i:11;s:49:"delete-duplicate-posts/delete-duplicate-posts.php";i:12;s:45:"ewww-image-optimizer/ewww-image-optimizer.php";i:13;s:34:"feedburner-plugin/fdfeedburner.php";i:14;s:39:"feedburner-widget/widget-feedburner.php";i:15;s:63:"feedburner_feedsmith_plugin_2.3/FeedBurner_FeedSmith_Plugin.php";i:16;s:21:"feedlist/feedlist.php";i:17;s:39:"force-publish-schedule/forcepublish.php";i:18;s:50:"google-analytics-for-wordpress/googleanalytics.php";i:19;s:81:"google-sitemap-generator-ultimate-tag-warrior-tags-addon/UTWgoogleSitemaps2_1.php";i:20;s:36:"google-sitemap-generator/sitemap.php";i:21;s:24:"headspace2/headspace.php";i:22;s:29:"my-link-order/mylinkorder.php";i:23;s:27:"php-code-widget/execphp.php";i:24;s:43:"post-plugin-library/post-plugin-library.php";i:25;s:35:"post-to-twitter/post-to-twitter.php";i:26;s:28:"profile-pics/profile-pic.php";i:27;s:27:"redirection/redirection.php";i:28;s:42:"scripts-to-footerphp/scripts-to-footer.php";i:29;s:29:"sem-dofollow/sem-dofollow.php";i:30;s:33:"seo-automatic-links/seo-links.php";i:31;s:23:"seo-slugs/seo-slugs.php";i:32;s:41:"seo-super-comments/seo-super-comments.php";i:33;s:31:"similar-posts/similar-posts.php";i:34;s:21:"sociable/sociable.php";i:35;s:44:"strictly-autotags/strictlyautotags.class.php";i:36;s:16:"text-control.php";i:37;s:19:"tidy-up/tidy_up.php";i:38;s:37:"tinymce-advanced/tinymce-advanced.php";i:39;s:33:"tweet-old-post/tweet-old-post.php";i:40;s:33:"w3-total-cache/w3-total-cache.php";i:41;s:44:"widget-settings-importexport/widget-data.php";i:42;s:54:"wordpress-23-related-posts-plugin/wp_related_posts.php";i:43;s:23:"wp-minify/wp-minify.php";i:44;s:27:"wp-optimize/wp-optimize.php";i:45;s:33:"wp-post-to-pdf/wp-post-to-pdf.php";i:46;s:29:"wp-postviews/wp-postviews.php";i:47;s:55:"wp-simple-paypal-donation/wp-simple-paypal-donation.php";i:48;s:46:"wp-social-seo-booster/wpsocial-seo-booster.php";i:49;s:31:"wptouch-pro-3/wptouch-pro-3.php";} | yes      |

Copy and paste this CVS format data to a text file or a Word document for later reference ..

To restore back to normal only active WordPress plugins, first launch following SQL query to disable all enabled wordpress plugins:

UPDATE wp_options SET option_value = 'a:0:{}' WHERE option_name = 'active_plugins';

To restore above "backupped" list of active WP plugins you have to copy paste the saved content and paste it into above UPDATE query substituting option_value=' ' with the backupped string.

P.S. – This query should work on WordPress 3.x on older wordpress ver 2.x use instead:

UPDATE wp_options SET option_value = ' ' WHERE option_name = 'active_plugins';

Because pasting the backupped Active plugins list CSV is a messy and unreadable from command line it is recommended for clarity to use PHPMyAdmin frontend (whenever it is available) on server. This little hint is a real time-saver and saves a lot of headaches. Before proceeding to any Db UPDATE SQL queries always backup your Blog database, with time structure of WordPress data changes!, so in future releases this method might not be working, however if it helped you and works on your version please drop a comment with WordPress version on which this helped you.

Enjoy! 🙂

 

WordPress Plugins to monitor and debug WP enabled plugins – Find Errors / Warnings and Remove WP problematic plugins slowing down your Website (blog) database

Thursday, February 19th, 2015

plugins-to-monitor-debug-wordpress-enabled-plugins-how-to-track-find-errors-and-warnings-and-remove-problematic-wp-extensions-that-slow-down-your-website

Recent days, I'm spending a lot of time again trying to optimize my wordpress blog. Optimizing WP for better efficiency is becoming harder and harder task day by day as the website file content data is growing along with SQL databases. Moreover situation gets even worse because the number of plugins enabled on my blog is incrementally growing with time because, there is more and more goodies I'd like to add.
Optimizing WordPress to run for Speed on a server is a whole a lot of art and its a small universe in itself, because as of time of writting this post the count (number) of WordPress available PLUGINS is 36,197 ! 

1. Manually Tracking WordPress  Plugins causing Slow SQL Queries (MySQL bottleneck) issues directly using console / SSH

Because of its open source development and its nice modular design wordpress has turned into a standard for building small, middle sized and large websites (some WordPress based blogs and sites have from 50 000 to 100 000 unique pages!). My blog is still a small WordPress site with only 1676 posts, so I still haven't reached the high volume traffic optimization requirements but still even though I have a relatively good server hardware  8GB RAM / (2×2.70 Ghz Intel CPU) / 500 GB (7400 RPM HDD) at times I see Apache Webservers is unable to properly serve coming requests because of MySQL database (LEFT JOIN) requests being slow to serve (taking up to few seconds to complete) and creating a MySQL table lock, putting all the rest SQL queries to stay in a long unserved queues line, I've realized about this performance issue by using a a mysql cli (command) client and few commands and console command (tool) called mytop (also known as mtop). MyTop refreshes every 3 seconds, so the slow query will immediately stay on screen to view moer info about it press "f" and type the  in query ID.

mysql-top-running-on-gnu-linux-server-tracking-sql-queries-in-console-screenshot.png

mysql-top-running-on-gnu-linux-server-tracking-sql-queries-in-console-screenshot2

Finally it is very useful to run  for a while MySQL server logging to /var/log/mysql/slow-query.log:
Slow query is enabled (on my Debian 7 Wheezy host) by adding to /etc/mysql/my.cnf
after conf section

 

vim /etc/mysql/my.cnf
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error logging goes to syslog due to /etc/mysql/conf.d/mysqld_safe_syslog.cnf.
#
# Here you can see queries with especially long duration

 

Paste:

 

slow_query_log = 1
slow_query_log_file = /var/log/mysql/slow-query.log
long_query_time = 2
log-queries-not-using-indexes

 

And then to make new mysql configuration load restarted mysql server:

 

debian-server:~# /etc/init.d/mysql restart
Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld ..
Checking for tables which need an upgrade, are corrupt or were
not closed cleanly..

 

Leaving mysql-slow.log to be enabled for 30 minutes to an 1 hrs is a good time to track most problematic slow queries and based on this queries, I took parts of  SQL UPDATE / SELECT / INSERT etc. Db queries which was problematic and grepped throughout /var/www/blog/wp-content/plugin files in order to determine which WordPress Plugin is triggering the slow query, causing blog to hang when too many clients try to see it in browser.

My main problematic SQL query having long execution time  (about 2 to 3 seconds!!!) most commonly occuring in slow-query.log was:

 

SELECT DISTINCT post_title, ID, post_type, post_name FROM wp_posts wposts LEFT JOIN wp_postmeta wpostmeta ON wposts.ID = wpostmeta.post_id LEFT JOIN wp_term_relationships ON (wposts.ID = wp_term_relationships.object_id) LEFT JOIN wp_term_taxonomy ON (wp_term_relationships.term_taxonomy_id = wp_term_taxonomy.term_taxonomy_id) WHERE (post_type='page' OR (wp_term_taxonomy.taxonomy = 'category' AND wp_term_taxonomy.term_id IN(11))) AND post_status = 'publish' AND LENGTH(post_title)>=5 ORDER BY LENGTH(post_title) ASC LIMIT 500

Because above query uses SQL Column names and Tables which are not hard coded in PHP code, to find out which plugins is most probably to launch this complex LEFT JOIN query, I used a quick bash one-liner:

 

# cd /var/www/blog/wp-content/plugins

 

# for i in $(grep -rli 'SELECT DISTINCT' *); do grep -rli 'LEFT JOIN' $i; done 
./seo-automatic-links/seo-links.php
./wp-postviews/wp-postviews.php
./yet-another-related-posts-plugin/classes/YARPP_Cache_Tables.php

 

I wanted to put less load on CPU during grep so looked for string only in .PHP extensioned files with:

 

 # for i in $(find . -iname '*.php' -exec grep -rli 'SELECT DISTINCT' '{}' \;); do grep -rli 'LEFT JOIN' $i; done
./seo-automatic-links/seo-links.php
./wp-postviews/wp-postviews.php
./yet-another-related-posts-plugin/classes/YARPP_Cache_Tables.php


As you can see the complex query is being called from PHP file belonging to one of 3 plugins

  • SEO Automatic Links – this is SEO Smart Links WP plugin (Does internal bliog interlinking in order to boast SEA)
  • WP PostViews – WordPress Post Views plugin (Which allows me to show how many times an article was read in WP Widget menu)
  • Yet Another Related Posts – Which is WP plugin I installed / enabled to show Related posts down on each blog post


2. Basic way to optimize MySQL slow queries (EXPLAIN / SHOW CREATE TABLE)

Now as I have a basic clue on plugins locking my Database, I disabled them one by one while keeping enabled mysql slow query log and viewing queries in mytop and I figure out that actually all of the plugins were causing a short time overheat (lock) on server Database because of LEFT JOINs. Though I really like what this plugins are doing, as they boast SEO and attract prefer to disable them for now and have my blog all the time responsible light fast instead of having a little bit better Search Engine Optimization (Ranking) and loosing many of my visitors because they're annoyed to wait until my articles open

Before disabling I tried to optimize the queries using MySQL EXPLAIN command + SHOW CREATE TABLE (2 commands often used to debug slow SQL queries and find out whether a Column needs to have added INDEX-ing to boast MySQL query).

Just in case if you decide to give them a try here is example on how they're used to debug problematic SQL query:
 

  1. mysql> explain SELECT DISTINCT post_title, ID, post_type, post_name
  2.     -> FROM wp_posts wposts LEFT JOIN wp_postmeta wpostmeta
  3.     -> ON wposts.ID = wpostmeta.post_id LEFT JOIN wp_term_relationships
  4.     -> ON (wposts.ID = wp_term_relationships.object_id) LEFT JOIN wp_term_taxonomy
  5.     -> ON (wp_term_relationships.term_taxonomy_id = wp_term_taxonomy.term_taxonomy_id)
  6.     -> WHERE (post_type='page'
  7.     -> OR (wp_term_taxonomy.taxonomy = 'category'
  8.     -> AND wp_term_taxonomy.term_id IN(11,15,17)))
  9.     -> AND post_status = 'publish'
  10.     -> AND LENGTH(post_title)>=5
  11.     -> ORDER BY LENGTH(post_title) ASC
  12.     -> LIMIT 500;
  13. +—-+————-+———————–+——–+——————+———+———+———————————————+——+———————————————-+
  14. | id | select_type | table                 | type   | possible_keys    | key     | key_len | ref                                         | rows | Extra                                        |
  15. +—-+————-+———————–+——–+——————+———+———+———————————————+——+———————————————-+
  16. |  1 | SIMPLE      | wposts                | ALL    | type_status_date | NULL    | NULL    | NULL                                        | 1715 | Using where; Using temporary; Using filesort |
  17. |  1 | SIMPLE      | wpostmeta             | ref    | post_id          | post_id | 8       | blog.wposts.ID                              |   11 | Using index; Distinct                        |
  18. |  1 | SIMPLE      | wp_term_relationships | ref    | PRIMARY          | PRIMARY | 8       | blog.wposts.ID                              |   19 | Using index; Distinct                        |
  19. |  1 | SIMPLE      | wp_term_taxonomy      | eq_ref | PRIMARY          | PRIMARY | 8       | blog.wp_term_relationships.term_taxonomy_id |    1 | Using where; Distinct                        |
  20. +—-+————-+———————–+——–+——————+———+———+———————————————+——+———————————————-+
  21. 4 rows in set (0.02 sec)
  22.  
  23. mysql>
  24.  

     

     

  1. mysql> show create table wp_posts;
  2. +———-+————————–+
  3. | Table    | Create Table                                                                                                                                                                                                                                                                                                                                                                                                                                 |
  4. +———-+————————–+
  5. | wp_posts | CREATE TABLE `wp_posts` (
  6.   `ID` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
  7.   `post_author` bigint(20) unsigned NOT NULL DEFAULT '0',
  8.   `post_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
  9.   `post_date_gmt` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
  10.   `post_content` longtext NOT NULL,
  11.   `post_title` text NOT NULL,
  12.   `post_excerpt` text NOT NULL,
  13.   `post_status` varchar(20) NOT NULL DEFAULT 'publish',
  14.   `comment_status` varchar(20) NOT NULL DEFAULT 'open',
  15.   `ping_status` varchar(20) NOT NULL DEFAULT 'open',
  16.   `post_password` varchar(20) NOT NULL DEFAULT '',
  17.   `post_name` varchar(200) NOT NULL DEFAULT '',
  18.   `to_ping` text NOT NULL,
  19.   `pinged` text NOT NULL,
  20.   `post_modified` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
  21.   `post_modified_gmt` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
  22.   `post_content_filtered` longtext NOT NULL,
  23.   `post_parent` bigint(20) unsigned NOT NULL DEFAULT '0',
  24.   `guid` varchar(255) NOT NULL DEFAULT '',
  25.   `menu_order` int(11) NOT NULL DEFAULT '0',
  26.   `post_type` varchar(20) NOT NULL DEFAULT 'post',
  27.   `post_mime_type` varchar(100) NOT NULL DEFAULT '',
  28.   `comment_count` bigint(20) NOT NULL DEFAULT '0',
  29.   PRIMARY KEY (`ID`),
  30.   KEY `post_name` (`post_name`),
  31.   KEY `type_status_date` (`post_type`,`post_status`,`post_date`,`ID`),
  32.   KEY `post_parent` (`post_parent`),
  33.   KEY `post_author` (`post_author`),
  34.   FULLTEXT KEY `post_related` (`post_title`,`post_content`)
  35. ) ENGINE=MyISAM AUTO_INCREMENT=12033 DEFAULT CHARSET=utf8 |
  36. +———-+———————-+
  37. 1 row in set (0.00 sec)
  38.  
  39. mysql>
  40.  


By the way above output is a paste from the the new PasteBin Open Source (Stikked powered) service I started on www.pc-freak.net – paste.www.pc-freak.net (p.www.pc-freak.net) 🙂

Before I took final decision to disable slow WP plugins, I've experimented a bit trying to add INDEX to Table Column (wposts) in hope that this would speed up SQL queries with:

 

mysql> ALTER TABLE TABLE_NAME ADD INDEX (wposts);

 

But this didn't improve query speed even on the contrary it make execution time worse.

3. Tracking WordPress Plugin PHP Code Execution time and Plugins causing Slow SQL Queries (MySQL bottleneck) issues through WP itself

Well fine, I'm running my own hosted Blog and WordPress sites, but for people who have wordpress sites on shared hosting, there is usually no SSH (Terminal) Access to server, those people will be happy to hear there are 2 Free easy installable WordPress plugins which can be used to Debug Slow WordPress Plugins SQL Queries as well as plugin to Track which plugin takes most time to execute, this are:
 

 

a) P3 Plugin Performance Profiler  

runs a scan over your site to determine what resources your plugins are using, and when, during a standard page request. P3 PPP Can even create reports in a beatiful Excel like Pie chart sheet.

p3-plugin-performance-profiler-godaddy-screenshot-debian-gnu-linux-wordpress-website

Another useful thing to see with P3 PPP is Detailed Timeline it shows when the plugins are being loaded during new page request so you can see if there is a certain sequence in time when a plugin slows down the website.

detailed_timeline-wordpress-p3-performance-plugin-on-website-screenshot

The pictures says it all as P3 PPP is Godaddy's work, congrats to GoDaddy, they've done great job.

 

b) WordPress memory Viewer WP plugins

Is useful to check how much memory each of WordPress plugin is taking on user (visitor) request.
Memory Viewer is allows you to view WordPress’ memory utilization at several hooks during WordPress’ execution. It also shows a summary of MySQL Queries that have ran as well as CPU time.
To use it download it to plugins/ folder as usual enable it from:

Installed Plugins -> (Inactive) -> Memory Viewer (Enable)

To see statistics from Memory Viewer open any post from your blog website and scroll down to the bottom you will notice the statistics, showing up there, like on below screenshot.

wordpress-memory-viewer-plugin-debian-gnu-linux-hosted-website-show-which-plugin-component-eats-most-memory-in-wordprses-blog
 

Though WP Memory Viewer is said to work only up to WP version 3.2.1, I've tested it and it works fine on my latest stable WordPress 4.1 based blog.

c) WordPress Query Monitor

wordpress-query-monitor-plugin-to-monitor-track-and-optimize-problems-with-sql-caused-by-wp-plugins.png
 

Query Monitor is a debugging plugin for anyone developing with WordPress but also very helpful for anyone who want to track issues with plugins who use the database unefficient.
It has some advanced features not available in other debugging plugins, including automatic AJAX debugging and the ability to narrow down things by plugin or theme.
You can view plenty of precious statistics on how enabled plugins query the database server, here is a short overview on its Database Queries capabilities:

  • Shows all database queries performed on the current page
  • Shows affected rows and time for all queries
  • Show notifications for slow queries and queries with errors
  • Filter queries by query type (SELECT, UPDATE, DELETE, etc)
  • Filter queries by component (WordPress core, Plugin X, Plugin Y, theme)
  • Filter queries by calling function
  • View aggregate query information grouped by component, calling function, and type
  • Super advanced: Supports multiple instances of wpdb on one page
  • Once enabled from Plugins you will see it appear as a new menu on bottom Admin raw.

An important note to make here is latest Query Monitor extension fails when loaded on current latest Wordpress 4.1, to use it you will have to download and useolder Query Monitor plugin version 2.6.8 you can download it from here

d) Debug Bar

If you want you want a Memory Viewer like plugin for more complex used components memory debugging, reporting if (WP_DEBUG is set in wp-config.php) also check out Debug Bar .
For me Debug Bar was very useful because it show me depreciated functions some plugins used, so I substituted the obsoleted function with new one.

 

debug-bar-debug-wordpress-plugins-memory-use-screenshot-website


4. Server Hardware hungry (slow) WordPress plugins that you better not use

While spending time to Google for some fixes to WP slow query plugins – I've stumbled upon this post giving a good list with WordPress Plugins better off not to use because they will slow down your site
This is a publicly well known list of WP plugins every WordPress based site adminstrator should avoid, but until today I didn't know so my assumption is you don't know either ..

Below plugins are extremely database intensive mentioned in article that we should better (in all cases!) avoid:

  • Dynamic Related Posts
  • SEO Auto Links & Related Posts
  • Yet Another Related Posts Plugin
  • Similar Posts
  • Contextual Related Posts
  • Broken Link Checker — Overwhelms even our robust caching layer with an inordinate amount of HTTP requests.
  • MyReviewPlugin — Slams the database with a fairly significant amount of writes.
  • LinkMan — Much like the MyReviewPlugin above, LinkMan utilizes an unscalable amount of database writes.
  • Fuzzy SEO Booster — Causes MySQL issues as a site becomes more popular.
  • WP PostViews — Inefficiently writes to the database on every page load. To track traffic in a more scalable manner, both the stats module in Automattic’s Jetpack plugin and Google Analytics work wonderfully.
  • Tweet Blender — Does not play nicely with our caching layer and can cause increased server load.


A good Complete list of known WordPress slow plugins that will hammer down your wordpress performance is here

There are few alternatives to this plugins and when I have some free time I will download and test their alternatives but for now I plan the plugins to stay disabled.
 

For the absolute WP Performance Optimization Freaks, its good to check out the native way to Debug a wordpress installation through using few embedded
variables

 

define('WP_DEBUG', true);
define('WP_DEBUG', false);
define('WP_DEBUG_LOG', true);
define('WP_DEBUG_DISPLAY', false);
define('SAVEQUERIES', true);

 

An article describing how you can use native WP debug variables is here


Happy Optimizing  ! 🙂

How to deb upgrade PHP 5.3.3-7 / MySQL Server 5.1 to PHP 5.4.37 MySQL 5.5 Server on Debian 6.0 / 7.0 Squeeze / Wheezy GNU / Linux

Thursday, February 12th, 2015

how-to-deb-upgrade-mysql-server-5.1-to-mysql-5.5-php-5.3-to-php-5.4-5.5-upgrade-howto-on-old-stable-debian-squeeze-wheezy

I've been still running Debian Squeeze 6.0 GNU / Linux on few of the Linux / Apache / MySQL servers I'm administrating and those servers are running few Wordperss / Joomla websites which lately face severe MySQL performance issues. I tried to optimize using various mysql performance optimization scripts such as mysql-tuner.pl, Tuning-primer.sh and Percona Toolkit – a collection of advanced command-line tools for system administrators and tech / support staff to perform a variety of MySQL and system tasks that are too difficult or complex to perform manually. Though with above tools and some my.cnf tunizations I managed to achieve positive performance improvement results with above optimizations, still I didn't like how MyQSL served queries and since the SQL server is already about 5 years old (running version 5.1) and the PHP on sever is still at 5.3 branch, I was advised by my dear colleague Anatoliy to try version update as a mean to improve SQLserver performance. I took seriously the suggestion to try upgrade as a mean to resolve performance issues in this article I will explain in short what I had to do to make MySQL upgrade a success

Of course to try keep deb installed software versions as fresh as possible possible deb packagse, I'm already using Debian Back Ports (for those who hear it a first time Debian Backports is a special repository for Stable versioned Debian Desktop and Servers  – supporting stable releases of Debian Linux) which allows you to keep install packages versions less outdated (than default installable software which usually are way behind latest stable package versions with 2-5 years).

If you happen to administer Stable Debian servers and you never used BackPorts I warmly recommend it as it often includes security patches of packages part of Debian stable releases that reached End Of Support (EOS) and already too old even for security updates to be issued by respective Debian Long Term Suport (LTS) repositories.

If you're like me and still in situation to manage remotely Debian 6.0 Squeeze and its the first time you hear about BackPorts and Debian LTShttps://wiki.debian.org/LTS/ to start using those two add to your /etc/apt/sources.list below 3 lines

Open with vim editor and press shift+G to go to last line of file and then press I to enter INSERT mode, once you're done to save, press (ESC) then press : and type x! in short key combination for exit and save setting in vim is 
 

Esc + :x! 

 

debian-server:~# vim /etc/apt/sources.list
deb http://http.debian.net/debian squeeze-lts main contrib non-free
deb-src http://http.debian.net/debian squeeze-lts main contrib non-free
deb http://http.debian.net/debian-backports squeeze-backports main

If you haven't been added a security updates line in /etc/apt/sources.list make sure you add also:

 

deb http://security.debian.org/ squeeze/updates main contrib non-free
deb-src http://security.debian.org/ squeeze/updates main contrib non-free


Then to apply latest security updates and packages from LTS / Backports repository run the usual:

 

debian-server:~# apt-get update && apt-get –yes upgrade
….

If you need to search a package or install something from just added backports repository use:

 

debian-server:~# apt-cache -t squeeze-backports search "mysql-server"
auth2db – Powerful and eye-candy IDS logger, log viewer and alert generator
torrentflux – web based, feature-rich BitTorrent download manager
cacti – Frontend to rrdtool for monitoring systems and services
mysql-server-5.1 – MySQL database server binaries and system database setup
mysql-server-core-5.1 – MySQL database server binaries
mysql-server – MySQL database server (metapackage depending on the latest version)

 

To install specific packages only with all their dependencies from Backports while keeping rest of packages from Debian Stable:

 

debian-server:~# apt-get install -t squeeze-backports "package_name"

In same way you can also search or install specific packages from LTS repo:

 

debian-server:~# apt-get search -t squeeze-lts "package_name"

debian-server:~# apt-get install -t squeeze-lts "package_name"

Latest mysql available from Debian BackPorts and LTS is still quite old 5.1.73-1+deb6u1 therefore I made an extensive research online on how can I easily update MySQL 5.1 to MySQL 5.5 / 5.6 on Debian Stable Linux.
 

Luckily there were already DotDeb deb repositories for Debian LAMP (Linux / Apache  / MySQL / PHP / Nginx ) running servers prepared in order to keep the essential Webserver services up2date even long after distro official support is over. I learned about existence of this repo thanks to a Ryan Tate's post who updates his LAMP stack on TurnKey Linux which by the way is based on slightly modified official stable Debian Linux releases packages

To start using DotDeb repos add in /etc/apt/sources.list (depending whereh you're on Squeeze or Wheeze Debian):

 

deb http://packages.dotdeb.org squeeze all
deb-src http://packages.dotdeb.org squeeze all

or for Debian Wheezy add repos:

 

deb http://packages.dotdeb.org wheezy all
deb-src http://packages.dotdeb.org wheezy all

 

I was updating my DebianLatest MySQL / PHP / Apache release to Latest ones on (6.0.4) Squeeze so added above squeeze repos:

Before refreshing list of package repositories, to authenticate repos issue:

 

debian-server:~# wget -q http://www.dotdeb.org/dotdeb.gpg
debian-server:~# apt-key add dotdeb.gpg

Once again to update my packages from newly added DodDeb repository

 

debian-server:~# apt-get update

Before running the SQL upgrade to insure myself, I dumped all databases with:

 

debian-server:~# mysqldump -u root -p -A > /root/dump.sql

Finally I was brave enough to run apt-get dist-upgrade to update with latest LAMP packages

 

debian-server:~# apt-get dist-upgrade
Reading package lists… Done
Building dependency tree
Reading state information… Done
Calculating upgrade… Done
The following packages will be REMOVED:
  mysql-client-5.1 mysql-server mysql-server-5.1
The following NEW packages will be installed:
  libaio1 libmysqlclient18 mysql-client-5.5 mysql-client-core-5.5 python-chardet python-debian
The following packages will be upgraded:
  curl krb5-multidev libapache2-mod-php5 libc-bin libc-dev-bin libc6 libc6-dev libc6-i386 libcurl3 libcurl3-gnutls libcurl4-openssl-dev libevent-1.4-2
  libgssapi-krb5-2 libgssrpc4 libjasper1 libk5crypto3 libkadm5clnt-mit7 libkadm5srv-mit7 libkdb5-4 libkrb5-3 libkrb5-dev libkrb53 libkrb5support0 libmysqlclient-dev
  libxml2 libxml2-dev locales mysql-client mysql-common ntp ntpdate php-pear php5 php5-cgi php5-cli php5-common php5-curl php5-dev php5-gd php5-imagick php5-mcrypt
  php5-mysql php5-odbc php5-recode php5-sybase php5-xmlrpc php5-xsl python-reportbug reportbug unzip

50 upgraded, 6 newly installed, 3 to remove and 0 not upgraded.
Need to get 51.7 MB of archives.
After this operation, 1,926 kB of additional disk space will be used.
Do you want to continue [Y/n]? Y

As you see from above output above command updates Apache webservers / PHP and PHP related modules, however it doesn't update MySQL installed version, to update also MySQL server 5.1 to MySQL server 5.5

 

debian-server:~#  apt-get install –yes mysql-server mysql-server-5.5

You will be prompted with the usual Debian ncurses text blue interface to set a root password to mysql server, just set it the same as it used to be on old upgraded MySQL 5.1 server.

Well now see whether mysql has properly restarted with ps auxwwf

 

debian-server:~#  ps axuwwf|grep -i sql
root     22971  0.0  0.0 112360   884 pts/11   S+   15:50   0:00  |                   \_ grep -i sql
root     19436  0.0  0.0 115464  1556 pts/1    S    12:53   0:00 /bin/sh /usr/bin/mysqld_safe
mysql    19837  4.0  2.3 728192 194552 pts/1   Sl   12:53   7:12  \_ /usr/sbin/mysqld –basedir=/usr –datadir=/var/lib/mysql –plugin-dir=/usr/lib/mysql/plugin –user=mysql –pid-file=/var/run/mysqld/mysqld.pid –socket=/var/run/mysqld/mysqld.sock –port=3306
root     19838  0.0  0.0 110112   700 pts/1    S    12:53   0:00  \_ logger -t mysqld -p daemon.error

In my case it was running, however if it fails to run try to debug what is going wrong on initialization by manually executing init script /etc/init.d/mysql stop; /etc/init.d/mysql start and look for errors. You can also manually try to run mysqld_safe from console if it is not running run:

 

debian-server:~# /usr/bin/mysqld_safe &

This should give you a good hint on why it is failing to run
 

One more thing left is to check whether php modules load correctly to do so issue:

 

debian-server:~# php -v
Failed loading /usr/lib/php5/20090626/xcache.so:  /usr/lib/php5/20090626/xcache.so: cannot open shared object file: No such file or directory

Failed loading /usr/lib/php5/20090626/xdebug.so:  /usr/lib/php5/20090626/xdebug.so: cannot open shared object file: No such file or directory


You will likely get an exception (error) like above.
To solve the error, reinstall xcache and xcache-debug debs

 

debian-server:~# apt-get purge php5-xcache php5-xdebug

Now PHP + MySQL + Apache environment should be running much smootly.

debian-squeeze-wheeze-update-install-mysql-sevver5.55-620x344-howto

Upgrading the MySQL server / PHP library to MySQL server 5.6 / PHP 5.5 on Wheeze Linux is done in very much analogous ways all you have to do is change the repositories with above wheeze 7.0 ones and to follow the process as described in this article. I haven't tested update on Wheezy yet, so if you happen to try my article with wheezy reports and got a positive upgrade result please drop a comment.

Mysqlreport a tiny script intended to make easy-to-read MySQL status reports

Wednesday, February 13th, 2008

mysqlreport-tiny-shell-script-to-make-easy-to-read-mysql-queries-and-usage-reports-debug-mysql-console
Check this out. Mysqlreport is a small script intended to Make easy-to-read MySQL status reports.It has also a nice manual explaining every variable it returns. Check it out here .From yesterday I feel a little sich just like I guess I’ve catched a flu. I’m still looking for a what kind of laptop to buy.
Everybody says a different thing.
A friend of mine who sells laptop says Gigabyte is a good choice, still I’m uncertain about that.I personally like Thinkpads but unfortunately thinkpads comes with OS installed on them and also I don’t like it that IBM Thinkpads (e.g. nowhere days Lenovo Thinkpads) at least the cheaper ones come with Integrated ATI video.
I’m thinking of a Dell as a possibility but still I’min doubt which one to take … For all those who doesn’t know IBM/Lenovo has three major series of Thinkpads the “r” series “t” series from Terminator :), and the “x” series. x series thinkpads are a way smaller than “r” and “t” series. As I’ve heard from friends and other sources online “t” series are rock solid and had a titanium backing. A good thing about Thinkpads to note is that the batter life of “r” and “z” series is 3.5 h 🙂 What I can afford is to spend no more than 1600 lv. (something like 1200 USD) for a laptop. The Dell models I liked were Inspiron 1520 but unfortunately they come with integrated wifi card which is dell and has no support for Linux/BSD (I need the computer to run FBSD/linux).Ofcourse I can always use NDIS and use the windows driver under linux/BSD but this is not the ideaEND—–

Allowing MySQL users access from all hosts – Fixing mysql ERROR 1045 (28000): Access denied for user ‘root’@’remote-admin.com’ (using password: YES)

Friday, June 20th, 2014

mysql_allow_access-from-remote-any-host-fix-access-error-after-sql-migration

I recently migrated MySQL database server from host A to host B (remotesystemadministration.com), because I wanted to have the mysql database server on a separate machine (have separation of server running services and have a dedicated mysql server).

MySQL server host (running on localhost previously was set from my mysql config my.cnf to listen and serve connections on localhost with

bind-address = 127.0.0.1

). MySQL is used by a Tomcat running Java application on localhost and my task was to set the Tomcat to use the MySQL database remotely to MySQL host B (new remote hostname where MySQL is moved is  remotesystemadminsitration.com and is running on IP 83.228.93.76).

Migration from MySQL Db server 1 (host A) to MySQL Db server 2 (host B) is done by binary copying the mysql database directory which in this case is (as it is a Debian server installed MySQL), the standard directory where mysql stores its database data is /var/lib/mysql ( datadir = /var/lib/mysql in /etc/mysql/my.cnf)

Binary copying of data from MySQL db (host A) to MySQL Db (host B) is done with rsync

After migrating and trying to login on migrated mysql  database on remotesystemadministration.net with mysql cli client:

remotesysadmin:~$ mysql -u root -p

I got following error:
 

ERROR 1045 (28000): Access denied for user 'root'@'remotesystemadministration.com' (using password: YES)


To fix the issue I had to login remotely from old migration server mysql (host A) cli:

mysql:~$ mysql -u root -p -h remotesystemadministration.com

and  run SQL commands:

GRANT ALL PRIVILEGES ON *.* TO 'root'@'remotesystemadministration.com' WITH GRANT OPTION;
GRANT USAGE ON *.* TO 'root'@'remotesystemadministration.com' IDENTIFIED BY 'secret-mysql-pass';
FLUSH PRIVILEGES;

Query OK, 0 rows affected (0.03 sec)
Query OK, 0 rows affected (0.00 sec)
Query OK, 0 rows affected (0.00 sec)


Another way to solve the problem is to add the root user to be able to connect from any host (Enable MySQL root access from all host), to do so issue:

GRANT ALL PRIVILEGES ON *.* TO 'root'@'%' IDENTIFIED BY 'password';
FLUSH PRIVILEGES;

Note: In newer version of MySQL, flush privileges could be omitted.

Another approach if you want to substitute access from localhost for all users and enable all users to be able to authenticate to mysql remotely is to execute SQL Query:

UPDATE USER SET host='%' WHERE host='localhost';

Allowing all users to be able to connect from anywhere on the internet is a very bad security practice anyways, if you already have a tight firewall setup and you can only access the server via specific remote IP addresses allowing MySQL access from all hosts / ips should be ok.

Fix MySQL connection error – Host ” is blocked because of many connection errors; unblock with ‘mysqladmin flush-hosts’

Wednesday, July 2nd, 2014

fix-mysql-too-many-connection-errors-explained

If you get a MySQL error like:

Host '' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'

This most likely means your PHP / Java whatever programming language application connecting to MySQL is failing to authenticate with the application created (existing) or that the application is trying too many connections to MySQL in a rate where MySQL server can't serve all the requests.

Some common errors for Too many Connection errors are:
 

  • Networking Problem
  • Server itself could be down
  • Authentication Problems
  • Maximum Connection Errors allowed.

The value of the max_connection_errors system variable determines how many successive interrupted connection requests are permitted to myqsl server.
 

Well anyways if you get the:

Host '' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'

You can consider this a sure sign application connections to MySQLis logging a lot of error connections, for some reason.
This error could also appear on very busy websites where high amount of separete connections are used – I've seen the error occur on PHP websites whether mysql_pconnect(); is selected in favour of the prooved working mysql_connect();

The first thing to do before changing / increasing default set of max connection errors is to check how many max connection errors are set within MySQL?

For that connect with MySQL CLI and issue:
 

mysql> SHOW VARIABLES LIKE '%error%';


+——————–+————————————————————-+
| Variable_name      | Value                                                           |
+——————–+————————————————————-+
| error_count        | 0                                                                     |
| log_error          | /var/log/mysql//mysqld.log                                |
| max_connect_errors | 10000                                                      |
| max_error_count    | 64                                                               |
| slave_skip_errors  | OFF                                                             |
+——————–+————————————————————-+


A very useful mysql cli command in debugging max connection errors reached problem is

mysql> SHOW PROCESSLIST;

 

To solve the error, try to tune in /etc/my.cnf, /etc/mysql/my.cnf or wherever my.cnf is located:

[mysqld]
max_connect_errors
variable

and

wait_timeout var. Some reasonable variable size would be:

max_connect_errors = 100000
wait_timeout = 60

If such (anyways) high values is still not high enough you can raise mysql config connection timeout

 

to

max_connect_errors = 100000000

Also if you want to try raise max_connect_errors var without making it permanenty (i.e. remember var setting after MySQL service restart), set it from MySQL cli with:

SET GLOBAL max_connect_errors


If you want to keep the set default max_connection_errors and fix it temporary, you can try to follow the error

Host '' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'

suggestion and issue in root console:

mysqladmin flush-hosts

Same could also be done from MySQL Cli with cmd:
 

FLUSH HOSTS;

Make MySQL existing users to have access from any or particular host after SQL migration

Tuesday, July 1st, 2014

make_mysql_existing_users_have-access-from-any-or-particular-host-after-SQL-migration
Recently I've done a migration of MySQL server from host A (running and configured to serve requests on (localhost – 127.0.0.1) to host B (server2.host.com)
There are already existing users in mysql which are allowed to only access the database server from localhost as until now the applciation was sending SQL queries straight on localhost. Now the architecture has to change to use the MySQL Database remotely.

Hence I've migrated the MySQL server by dumping all the existing the databases on MySQL host A  with:

mysqldump -u root -p --all-databases > alldbs_dump.sql


And then importing the databases on host B with

mysql -u root -p < alldbs_dump.sql

Though this migrated the data from Host A to Host B, still the application on Host A was failing to succesfully use its data from database on Host B, because of inability to properly authenticate. It couldn't authenticate because MySQL on Host B's users are not configured to have access from IP address of Host A, but only allowed the application users to be able to connect on localhost..

I've used following SQL CLI query to check Hosts allowed to connect to MySQL (in this case localhost):

# mysql -u root -p
mysql> use mysql;
mysql> select * from user where user like '%eameiotest%' and Host='localhost';

 

To fix that I logged on MySQL server on Host B with mysql cli and issued for each of the users the application was using:

UPDATE mysql.user SET Host='%' WHERE Host='localhost' AND User='eameiotest';
 

UPDATE mysql.user SET Host='%' WHERE Host='localhost' AND User='eameiotest2';
 

UPDATE mysql.user SET Host='%' WHERE Host='localhost' AND User='eameiotest3';

 

On execution, If you get errors like:
 

ERROR 1062 (23000): Duplicate entry '%-eameiotest' for key 'PRIMARY'


Don't think that there is no solution, as I've read some threads online claiming the only way to get around this issue is to dump mysql database and re-import it, this is not necessery. There is a work around to this MySQL bug.

To work-around the error, you will first have to set the user allowed access host to empty – ' ' :

 

UPDATE mysql.user SET Host='' WHERE Host='localhost' AND User='eameiotest';
 

UPDATE mysql.user SET Host='' WHERE Host='localhost' AND User='eameiotest2';
 

UPDATE mysql.user SET Host='' WHERE Host='localhost' AND User='eameiotest3';


And re-issue again commands:
 

UPDATE mysql.user SET Host='%' WHERE Host='localhost' AND User='eameiotest';
 

UPDATE mysql.user SET Host='%' WHERE Host='localhost' AND User='eameiotest2';
 

UPDATE mysql.user SET Host='%' WHERE Host='localhost' AND User='eameiotest3';


You might want to also issue:
 

GRANT ALL PRIVILEGES ON yourdatabase-name.* TO 'eameiotest1'@'server-host';

GRANT ALL PRIVILEGES ON yourdatabase-name.* TO 'eameiotest2'@'server-host';

GRANT ALL PRIVILEGES ON yourdatabase-name.* TO 'eameiotest3'@'server-host';
 

This should have solve the app connection issues, Cheers 🙂

 

 

Manually deleting spam comments from WordPress blogs and websites to free disk space and optimize MySQL

Monday, November 24th, 2014

WordPress-delete_spam_comments_manually_with_sql_query_to-optimize_mysql-and-free-disk-space
If you're a web-hosting company or a web-development using WordPress to build multitudes of customer blogs or just an independent blogger or sys-admin with a task to optimize a server's MySQL allocated storage  / performance on triads of WordPress-es a a good tip that would help is to removing wp_comments marked as spam.

Even though sites might be protected of thousands of spam message daily caught by WP anti-spam plugin Akismet, spam caught messages aer forwarder by Akismet to WP's Spam filter and kept wp_comments table with comments_approved column  record 'spam'.

Therefore you will certainly gain of freeing disk space uselessly allocated by spam messages into current MySQL server storage dir (/var/lib/mysql   /usr/local/mysql/data – the directory where my.cnf tells the server to keep its binary data .MYI, .MYD, .frm files) as well as save a lot of disk space by excluding the useless spam messages from SQL daily backup archives.

Here is how to remove manually spam comments from a WordPress blog under database (wp_blog1);

mysql> use wp_blog1;
mysql> describe wp_comments;
+———————-+———————+——+—–+———————+—————-+
| Field | Type | Null | Key | Default | Extra |
+———————-+———————+——+—–+———————+—————-+
| comment_ID | bigint(20) unsigned | NO | PRI | NULL | auto_increment |
| comment_post_ID | bigint(20) unsigned | NO | MUL | 0 | |
| comment_author | tinytext | NO | | NULL | |
| comment_author_email | varchar(100) | NO | | | |
| comment_author_url | varchar(200) | NO | | | |
| comment_author_IP | varchar(100) | NO | | | |
| comment_date | datetime | NO | | 0000-00-00 00:00:00 | |
| comment_date_gmt | datetime | NO | MUL | 0000-00-00 00:00:00 | |
| comment_content | text | NO | | NULL | |
| comment_karma | int(11) | NO | | 0 | |
| comment_approved | varchar(20) | NO | MUL | 1 | |
| comment_agent | varchar(255) | NO | | | |
| comment_type | varchar(20) | NO | | | |
| comment_parent | bigint(20) unsigned | NO | MUL | 0 | |
| user_id | bigint(20) unsigned | NO | | 0 | |
+———————-+———————+——+—–+———————+—————-+


The most common and quick way useful for scripting (whether you have to do it for multiple blogs with separate dbs) is to delete all comments being filled as 'Spam'.

To delete all messages which were filled by Akismet's spam filter with high probabily being a spam issue from mysql cli interface:

DELETE FROM wp_comments WHERE comment_approved = 'spam';


For Unread (Unapproved) messages the value of comment_approved field are 0 or 1, 0 if the comment is Red and Approved and 1 if still it is to be marked as read (and not spam).
If a wordpress gets heavily hammered with mainly spam and the probability that unapproved message is different from spam is low and you want to delete any message waiting for approvel as not being spam from wordpress use following SQL query:

DELETE FROM wp_comments WHERE comment_approved = 0;

Another not very common you might want to do is delete only all apprved comments:

DELETE FROM wp_comments WHERE comment_approved = 1;

For old installed long time unmaintained blogs (with garbish content), it is very likely that 99% of the messages might be spam and in case if there are already >= 100 000 spam messages and you don't have the time to inspect 100 000 spam comments to get only some 1000 legitimate and you want to delete completely all wordpress comments for a blog in one SQL query use:

TRUNCATE wp_comments;

Another scenario if you know a blog has been maintained until certain date and comments were inspected and then it was left unmaintained for few years without any spam detect and clear plugin like Akismet, its worthy to delete all comments starting from the date wordpress site stopped to be maintained:

DELETE FROM wp_comments WHERE comment_date > '2008-11-20 05:00:10' AND comment_date <= '2014-11-24 00:30:00'

Monitoring MySQL server queries and debunning performance (slow query) issues with native MySQL commands and with mtop, mytop

Thursday, May 10th, 2012

If you're a Linux server administrator running MySQL server, you need to troubleshoot performance and bottleneck issues with the SQL database every now and then. In this article, I will pinpoint few methods to debug basic issues with MySQL database servers.

1. Troubleshooting MySQL database queries with native SQL commands

a)One way to debug errors and get general statistics is by logging in with mysql cli and check the mysql server status:

# mysql -u root -p
mysql> SHOW STATUS;
+-----------------------------------+------------+
| Variable_name | Value |
+-----------------------------------+------------+
| Aborted_clients | 1132 |
| Aborted_connects | 58 |
| Binlog_cache_disk_use | 185 |
| Binlog_cache_use | 2542 |
| Bytes_received | 115 |
.....
.....
| Com_xa_start | 0 |
| Compression | OFF |
| Connections | 150000 |
| Created_tmp_disk_tables | 0 |
| Created_tmp_files | 221 |
| Created_tmp_tables | 1 |
| Delayed_errors | 0 |
| Delayed_insert_threads | 0 |
| Delayed_writes | 0 |
| Flush_commands | 1 |
.....
.....
| Handler_write | 132 |
| Innodb_page_size | 16384 |
| Innodb_pages_created | 6204 |
| Innodb_pages_read | 8859 |
| Innodb_pages_written | 21931 |
.....
.....
| Slave_running | OFF |
| Slow_launch_threads | 0 |
| Slow_queries | 0 |
| Sort_merge_passes | 0 |
| Sort_range | 0 |
| Sort_rows | 0 |
| Sort_scan | 0 |
| Table_locks_immediate | 4065218 |
| Table_locks_waited | 196 |
| Tc_log_max_pages_used | 0 |
| Tc_log_page_size | 0 |
| Tc_log_page_waits | 0 |
| Threads_cached | 51 |
| Threads_connected | 1 |
| Threads_created | 52 |
| Threads_running | 1 |
| Uptime | 334856 |
+-----------------------------------+------------+
225 rows in set (0.00 sec)

SHOW STATUS; command gives plenty of useful info, however it is not showing the exact list of queries currently processed by the SQL server. Therefore sometimes it is exactly a stucked (slow queries) execution, you need to debug in order to fix a lagging SQL. One way to track this slow queries is via enabling mysql slow-query.log. Anyways enabling the slow-query requires a MySQL server restart and some critical productive database servers are not so easy to restart and the SQL slow queries have to be tracked "on the fly" so to say.
Therefore, to check the exact (slow) queries processed by the SQL server (without restarting it), do
 

mysql> SHOW processlist;
+——+——+—————+——+———+——+————–+——————————————————————————————————+
| Id | User | Host | db | Command | Time | State | Info |
+——+——+—————+——+———+——+————–+——————————————————————————————————+
| 609 | root | localhost | blog | Sleep | 5 | | NULL |
| 1258 | root | localhost | NULL | Sleep | 85 | | NULL |
| 1308 | root | localhost | NULL | Query | 0 | NULL | show processlist |
| 1310 | blog | pcfreak:64033 | blog | Query | 0 | Sending data | SELECT comment_author, comment_author_url, comment_content, comment_post_ID, comment_ID, comment_aut |
+——+——+—————+——+———+——+————–+——————————————————————————————————+
4 rows in set (0.00 sec)
mysql>

SHOW processlist gives a good view on what is happening inside the SQL.

To get more complete information on SQL query threads use the full extra option:

mysql> SHOW full processlist;

This gives pretty full info on running threads, but unfortunately it is annoying to re-run the command again and again – constantly to press UP Arrow + Enter keys.

Hence it is useful to get the same command output, refresh periodically every few seconds. This is possible by running it through the watch command:

debian:~# watch "'show processlist' | mysql -u root -p'secret_password'"

watch will run SHOW processlist every 2 secs (this is default watch refresh time, for other timing use watch -n 1, watch -n 10 etc. etc.

The produced output will be similar to:

Every 2.0s: echo 'show processlist' | mysql -u root -p'secret_password' Thu May 10 17:24:19 2012

Id User Host db Command Time State Info
609 root localhost blog Sleep 3 NULL1258 root localhost NULL Sleep 649 NULL1542 blog pcfreak:64981 blog Query 0 Copying to tmp table \
SELECT p.ID, p.post_title, p.post_content,p.post_excerpt, p.pos
t_date, p.comment_count, count(t_r.o
1543 root localhost NULL Query 0 NULL show processlist

Though this "hack" is one of the possible ways to get some interactivity on what is happening inside SQL server databases and tables table. for administering hundred or thousand SQL servers running dozens of queries per second – monitor their behaviour few times aday using mytop or mtop is times easier.

Though, the names of the two tools are quite similar and I used to think both tools are one and the same, actually they're not but both are suitable for monitoring sql database execution in real time.

As a sys admin, I've used mytop and mtop, on almost each Linux server with MySQL server installed.
Both tools has helped me many times in debugging oddities with sql servers. Therefore my personal view is mytop and mtop should be along with the Linux sysadmin most useful command tools outfit, still I'm sure many administrators still haven't heard about this nice goodies.

1. Installing mytop on Debian, Ubuntu and other deb based GNU / Linux-es

mytop is available for easy install on Debian and across all debian / ubuntu and deb derivative distributions via apt.

Here is info obtained with apt-cache show

debian:~# apt-cache show mytop|grep -i description -A 3
Description: top like query monitor for MySQL
Mytop is a console-based tool for monitoring queries and the performance
of MySQL. It supports version 3.22.x, 3.23.x, 4.x and 5.x servers.
It's written in Perl and support connections using TCP/IP and UNIX sockets.

Installing the tool is done with the trivial:

debian:~# apt-get --yes install mytop
....

mtop used to be available for apt-get-ting in Debian Lenny and prior Debian releases but in Squeeze onwards, only mytop is included (probably due to some licensing incompitabilities with mtop??).

For those curious on how mtop / mytop works – both are perl scripts written to periodically connects to the SQL server and run commands similar to SHOW FULL PROCESSLIST;. Then, the output is parsed and displayed to the user.

Here how mytop running, looks like:

MyTOP showing queries running on Ubuntu 8.04 Linux - Debugging interactively top like MySQL

2. Installing mytop on RHEL and CentOS

By default in RHEL and CentOS and probably other RedHat based Linux-es, there is neither mtop nor mytop available in package repositories. Hence installing the tools on those is only available from 3rd parties. As of time of writting an rpm builds for RHEL and CentOS, as well as (universal rpm distros) src.rpm package is available on http://pkgs.repoforge.org/mytop/. For the sake of preservation – if in future those RPMs disappear, I made a mirror of mytop rpm's here

Mytop rpm builds depend on a package perl(Term::ReadKey), my attempt to install it on CentOS 5.6, returned following err:

[root@cenots ~]# rpm -ivh mytop-1.4-2.el5.rf.noarch.rpm
warning: mytop-1.4-2.el5.rf.noarch.rpm: Header V3 DSA signature: NOKEY, key ID 6b8d79e6
error: Failed dependencies:
perl(Term::ReadKey) is needed by mytop-1.4-2.el5.rf.noarch

The perl(Term::ReadKey package is not available in CentOS 5.6 and (probably other centos releases default repositories so I had to google perl(Term::ReadKey) I found it on http://rpm.pbone.net/ package repository, the exact url to the rpm dependency as of time of writting this post is:

ftp://ftp.pbone.net/mirror/yum.trixbox.org/centos/5/old/perl-Term-ReadKey-2.30-2.rf.i386.rpm

Quickest, way to install it is:

[root@centos ~]# rpm -ivh ftp://ftp.pbone.net/mirror/yum.trixbox.org/centos/5/old/perl-Term-ReadKey-2.30-2.rf.i386.rpmRetrieving ftp://ftp.pbone.net/mirror/yum.trixbox.org/centos/5/old/perl-Term-ReadKey-2.30-2.rf.i386.rpmPreparing... ########################################### [100%]
1:perl-Term-ReadKey ########################################### [100%]

This time mytop, install went fine:

[root@centos ~]# rpm -ivh mytop-1.4-2.el5.rf.noarch.rpm
warning: mytop-1.4-2.el5.rf.noarch.rpm: Header V3 DSA signature: NOKEY, key ID 6b8d79e6
Preparing... ########################################### [100%]
1:mytop ########################################### [100%]

To use it further, it is the usual syntax:

mytop -u username -p 'secret_password' -d database

CentOS Linux MyTOP MySQL query benchmark screenshot - vpopmail query

3. Installing mytop and mtop on FreeBSD and other BSDs

To debug the running SQL queries in a MySQL server running on FreeBSD, one could use both mytop and mtop – both are installable via ports:

a) To install mtop exec:

freebsd# cd /usr/ports/sysutils/mtop
freebsd# make install clean
....

b) To install mytop exec:

freebsd# cd /usr/ports/databases/mytop
freebsd# make install clean
....

I personally prefer to use mtop on FreeBSD, because once run it runs prompts the user to interactively type in the user/pass

freebsd# mtop

Then mtop prompts the user with "interactive" dialog screen to type in user and pass:

Mtop interactive type in username and password screenshot on FreeBSD 7.2

It is pretty annoying, same mtop like syntax don't show user/pass prompt:

freebsd# mytop
Cannot connect to MySQL server. Please check the:

* database you specified "test" (default is "test")
* username you specified "root" (default is "root")
* password you specified "" (default is "")
* hostname you specified "localhost" (default is "localhost")
* port you specified "3306" (default is 3306)
* socket you specified "" (default is "")
The options my be specified on the command-line or in a ~/.mytop
config file. See the manual (perldoc mytop) for details.
Here's the exact error from DBI. It might help you debug:
Unknown database 'test'

The correct syntax to run mytop instead is:

freebsd# mytop -u root -p 'secret_password' -d 'blog'

Or the longer more descriptive:

freebsd# mytop --user root --pass 'secret_password' --database 'blog'

By the way if you take a look at mytop's manual you will notice a tiny error in documentation, where the three options –user, –pass and –database are wrongly said to be used as -user, -pass, -database:

freebsd# mytop -user root -pass 'secret_password' -database 'blog'
Cannot connect to MySQL server. Please check the:

* database you specified "atabase" (default is "test")
* username you specified "ser" (default is "root")
* password you specified "ass" (default is "")
* hostname you specified "localhost" (default is "localhost")
* port you specified "3306" (default is 3306)
* socket you specified "" (default is "")a
...
Access denied for user 'ser'@'localhost' (using password: YES)

Actually it is interesting mytop, precededed historically mtop.
mtop was later written (probably based on mytop), to run on FreeBSD OS by a famous MySQL (IT) spec — Jeremy Zawodny .
Anyone who has to do frequent MySQL administration tasks, should already heard Zawodny's name.
For those who haven't, Jeremy used to be a head database administrators and developer in Yahoo! Inc. some few years ago.
His website contains plenty of interesting thoughts and writtings on MySQL server and database management
 

Tracking graphically MySQL, Apache and Network performance in web with Munin on Debian Linux

Saturday, March 19th, 2011

munin_monitor_cpu_network_hard_drive_apache_mysql_performance-in-web-on-linux_logo

Munin is great software for surveillance software for your MySQL, Apache, Qmail, Postfix and many other of the classical daemon services which most of the Linux, BSD servers online are running on.

1. Munin on Debian Linux is really easy to be installed and comes to executing:

debian:~# apt-get install munin munin-node munin-plugins-extra

2. Link /var/www/munin/ to some VirtualHost or ServerHost
For instance if your munin is to be placed on the domain www.pc-freak.net.net which has the DocumentRoot of /var/www

debian:~# cd /var/www
debian:/var/www# ln -sf /var/www/munin munin

3. Add some extra MySQL related plugins

To check whole list of pmunin plugins you can enable check in /etc/munin/plugins directory

Lets say our Munin will be providing statistics mainly for MySQL, enable this bunch of plugins:

cd /etc/munin/plugins
ln -s /usr/share/munin/plugins/mysql_ mysql_
ln -s /usr/share/munin/plugins/mysql_bytes mysql_bytes
ln -s /usr/share/munin/plugins/mysql_innodb mysql_innodb
ln -s /usr/share/munin/plugins/mysql_isam_space_ mysql_isam_space_
ln -s /usr/share/munin/plugins/mysql_queries mysql_queries
ln -s /usr/share/munin/plugins/mysql_slowqueries mysql_slowqueries
ln -s /usr/share/munin/plugins/mysql_threads mysql_threads


Though above command would enable mysql monitoring it will be not working out of the box. You will find in munin logs error like:

Missing dependency Cache::Cache at /usr/share/munin/plugins/mysql_ line 716."

To fix this install libcache-perl and libcache-cache-perl

apt-get install --yes libcache-perl libcache-cache-perl
 

Then regenerate munin plugin configuration issue cmd:

munin-node-configure --suggest --shell | sh

and restart Munin-node server

service munin-node restart
 

Munin Node should be able login to the MySQL server using the Debian System Maintenance user however if you should need to create a custom user you can add the following configuration to:
 

/etc/munin/plugin-conf.d/munin-node

 

[mysql*]
    user root
    env.mysqluser muninmonitor
    env.mysqlpassword Your-Secret-Password

4. Edit Munin config

Make sure you have at least the following variables enabled in /etc/munin/munin.conf
 

 dbdir  /var/lib/munin
 htmldir /var/cache/munin/www
 logdir /var/log/munin
 rundir  /var/run/munin

 tmpldir    /etc/munin/templates

includedir /etc/munin/munin-conf.d

[localhost.localdomain]
    address 127.0.0.1
    use_node_name yes

 

5. Add Munin Alias or Virtualhost

To make Munin Accessible from Webserver you need to at least add an alias create a file
/etc/apache2/conf.d/munin with following content:

vim /etc/apache2/conf.d/munin

Alias /munin /var/cache/munin/www

<Directory /var/cache/munin/www>
        Order allow,deny
        #Allow from localhost 127.0.0.0/8 ::1
        Allow from all
        Options None
        php_value engine off

    <IfModule mod_expires.c>
        ExpiresActive On
        ExpiresDefault M310
    </IfModule>

</Directory>


If you want to access Munin from Apache subdomain create it lets say you want to access it via stats.www.pc-freak.net, use following config file:

vi /etc/apache2/sites-enabled/stats.www.pc-freak.net
 

<VirtualHost *>
   ServerAdmin hipo@www.pc-freak.net
   ServerName stats.www.pc-freak.net
   DocumentRoot /var/cache/munin/www
   <Directory />
       Options FollowSymLinks
       #AllowOverride All
       php_value engine off
   </Directory>
   LogLevel debug
   CustomLog /var/log/apache2/munin/access.log combined
   ErrorLog /var/log/apache2/munin/error.log
   ServerSignature On
<Directory /var/cache/munin/www>
        Order allow,deny
        #Allow from localhost 127.0.0.0/8 ::1
        Allow from all
        Options FollowSymlinks
        #AllowOverride All
        php_value engine off

</Directory>

</VirtualHost>

 


6. Restart Apache;

debian:~# /etc/init.d/apache2 restart

Now to access the newly installed munin point your favorite browser to (either the subdirectory configured for access or the Virtualhost subdomain):

https://www.pc-freak.net/munin/
or
http://munin.www.pc-freak.net

eth0-network-traffic-munin-server-statistics

connections_through_firewall-statistics-munin-debian-linux
7. Protecting Munin with a password

As it could be a security leak to expose statistics regarding your server (Disk I/O, Memory, Load Avarage, Apache, MySQL Postfix) operations it is good security practice to protect munin with a password.

I've earlied blogged on how to protect your server munin web-statistics wtih an htaccess password (read it here)


munin-cup-statistics-by-day-and-by-month-screenshot

Happy Monitoring