Posts Tagged ‘Database’

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 pc-freak.net – paste.pc-freak.net (p.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  ! 🙂

Oracle: Get database, tables and instances access permissions

Thursday, January 30th, 2014

Oracle user get permissions of table database and instances access
If you are logged in to Oracle SQL server with sqlplus and you're not sure to which Database, Tables, Object instances you have permissions to below 2 queries will be of use:

SQL> SELECT DISTINCT OWNER, OBJECT_NAME  FROM ALL_OBJECTS  WHERE OBJECT_TYPE = 'TABLE';

Query lists all queries in a Oracle table schema. Alternavite shorter way to do the query is via:

SQL> SELECT table_name FROM user_tables;

SQL> SELECT * FROM TAB;

Shows your own schema's all tables and views.

Other oracle useful query is the Oracle equivalent of MySQL SHOW TABLES;

SQL> SELECT table_name FROM user_tables;

It will also output info only for logged in user credentials, if you're logged in as oracle database administrator (DBA role) account and you would like to check what Instances are owned by any user lets say user GEORGI query should be;

SQL> SELECT DISTINCT OWNER, OBJECT_NAME  FROM ALL_OBJECTS  WHERE OBJECT_TYPE = 'TABLE' AND OWNER = 'GEORGI;

Other way to do it is via:

SQL> SELECT Table_Name from All_Tables WHERE OWNER = 'YOURSCHEMA';


How to completely disable Replication in MySQL server 5.1.61 on Debian GNU / Linux

Monday, July 16th, 2012

Replication_mysql_disable

Some time ago on one of the Database MySQL servers, I've configured replication as it was required to test somethings. Eventually it turned out replication will be not used (for some reason) it was too slow and not fitting our company needs hence we needed to disable it.

It seemed logical to me that, simply removing any replication related directives from my.cnf and a restart of the SQL server will be enough to turn replication off on the Debian Linux host. Therefore I proceeded removed all replication configs from /etc/my/my.cnf and issued MySQL restart i. e.:

sql-server:~# /etc/init.d/mysql restart
....

This however didn't turned off replication,as I thought and in phpmyadminweb frontend interface, replication was still appearing to be active in the replication tab.

Something was still making the SQL server still act as an Replication Slave Host, so after a bit of pondering and trying to remember, the exact steps I took to make the replication work on the host I remembered that actually I issued:

mysql> START SLAVE;

Onwards I run:

mysql> SHOW SLAVE STATUS;
....

and found in the database the server was still running in Slave Replication mode

Hence to turn off the db host run as a Slave, I had to issue in mysql cli:

mysql> STOP SLAVE;
Query OK, 0 rows affected, 1 warning (0.01 sec)
mysql> RESET SLAVE;
Query OK, 0 rows affected, 1 warning (0.01 sec)

Then after a reload of SQL server in memory, the host finally stopped working as a Slave Replication host, e.g.

sql-server:~# /etc/init.d/mysql restart
....

After the restart, to re-assure myself the SQL server is no more set to run as MySQL replication Slave host:

mysql> SHOW SLAVE STATUS;
Empty set (0.00 sec)

Cheers 😉

How to add a new MySQL user to have INSERT,UPDATE,DELETE permissions to a Database

Tuesday, October 25th, 2011

I needed to add a newly created MySQL user with no access to any database with no special permissions (user is created from phpmyadmin) with some permissions to a specific database which is used for the operation of a website, here are the MySQL CLI client commands I issued to make it work:

# mysql -u root -p
mysql> GRANT ALL ON Sql_User_DB.* TO Sql_User@localhost;
mysql> FLUSH PRIVILEGES;

Where in the Example Sql_User_DB is my example database to which the user is granted access and my sample user is Sql_User .
Note that without FLUSH PRIVILEGES; new privileges might not be active. 

To test further if all is fine login with Sql_User and try to list database tables.

$ mysql -u Sql_User -p
password:
mysql> USE Sql_User_DB;
mysql> SHOW TABLES;
...

How to fix clamd “ERROR: LOCAL: Socket file /tmp/clamd.socket is in use by another process.”

Monday, May 23rd, 2011

One of the Qmail server installations I’m taking care of’s clamd antivirus process started loading the system heavily.
After a bit of log reading and investigation I’ve found the following error in my /var/log/clamd/current

@400000004dda1e1815cf03f4 ERROR: LOCAL: Socket file /tmp/clamd.socket is in use by another process.

I’ve noticed in my process list that actually I do have two processes clamd :

11608 ? Sl 0:05 /usr/local/sbin/clamd
11632 ? S 0:00 /usr/bin/multilog t /var/log/clamd
16013 ? Sl 0:06 /usr/local/sbin/clamd

It appeared that for some weird reason one of the clamd process was failing to connect constantly to the clam server socket /tmp/clamd.socket and each time it tried to connect and failed to connect to the socket the system gets about 5% of extra load …

Resolving the issues was a piece of cake, all I had to do is stop the clamd server delete the /tmp/clamd.socket and relaunch the clamd server.

Here is exactly the commands I issued:

debian:~# cd /service/
debian:/service# svc -a clamd
debian:/service# svc -h clamd
debian:/service# svc -d clamd
debian:/service# rm -f /tmp/clamd.socket
debian:/service# svc -u clamd

Afterwards the clamd extra load went out and in /var/log/clamd/current I can see clamd loads fine without errors, e.g.:

Listening daemon: PID: 16013
MaxQueue set to: 150
No stats for Database check - forcing reload
Reading databases from /usr/local/share/clamav
Database correctly reloaded (966822 signatures)
SelfCheck: Database status OK.
...