Archive for the ‘MySQL’ Category

How to Set MySQL MariaDB server root user to be able to connect from any host on the Internet / Solution to ‘ ERROR 1045 (28000): Access denied for user ‘root’@’localhost’ (using password: YES) ‘

Tuesday, September 3rd, 2019

Reading Time: 5minutes

How-to-set-up-MariaDB-server-root-admin-user-to-be-able-to-connect-from-any-host-anywhere-mariadb-seal-logo-picture

In this small article, I'll shortly explain on how I setup a Standard default package MariaDB Database server on Debian 10 Buster Linux and how I configured it to be accessible from any hostname on the Internet in order to make connection from remote Developer PC with MySQL GUI SQL administration tools such as MySQL WorkBench / HeidiSQL / Navicat / dbForge  as well as the few set-backs experienced in the process (e.g. what was the reason for ' ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) '  error and its solution.

Setting new or changing old MariaDB (MySQL) root server password

 

I've setup a brand new MariaDB database (The new free OpenSource software fork of MySQL) mariadb-server-10.3 on a Debian 10, right after the OS was installed with the usual apt command:

# apt install mariadb-server

Next tep was to change the root access password which was set to empty pass by default, e.g. connected with mysql CLI locally while logged via SSH on server and run:

MariaDB [(none)]> mysql -u root -p

use mysql;
update user set authentication_string=PASSWORD("MyChosenNewPassword") where User='root';

There was requirement by the customer, that MySQL server is not only accessed locally but be accessed from any IP address from anywhere on the Internet, so next step was to do so.

Allowing access to MySQL server from Anywhere

Allowing access from any host to MariaDB SQL server  is a bad security practice but as the customer is the King I've fulfilled this weird wish too, by changing the listener for MariaDB (MySQL) on Debian 10 codenamed Buster
 
changingthe defaultlistener
to be not the default 127.0.0.1 (localhost) but any listener is done by modifying the bind-address directive in conf /etc/mysql/mariadb.conf.d/50-server.cnf:

root@linux:~# vim /etc/mysql/mariadb.conf.d/50-server.cnf

Then comment out

bind-address  = 127.0.0.1

and  add instead 0.0.0.0 (any listener)

 

bind-address  = 0.0.0.0
root@linux:/etc/mysql/mariadb.conf.d# grep -i bind-address 50-server.cnf
##bind-address            = 127.0.0.1
bind-address    = 0.0.0.0


Then to make the new change effective restart MariaDB (luckily still using the old systemV init script even though systemd is working.
 

root@linux:~# /etc/init.d/mysql restart
[ ok ] Restarting mysql (via systemctl): mysql.service.


To make sure it is properly listening on MySQL defaults TCP port 3306, then as usual used netcat.

root@pritchi:~# netstat -etna |grep -i 3306
tcp        0      0 0.0.0.0:3306            0.0.0.0:*               LISTEN      109        1479917  

 

By the way the exact mariadb.cnf used on this middle-sized front-backend server is here – the serveris planned to be a Apache Web server + Database host with MySQL DB of a middle range to be able to serve few thousand of simultaneous unique customers.

To make sure no firewall is preventing MariaDB to be accessed, I've checked for any reject rules iptables and ipset definitions, e.g.:
 

root@linux:~# iptables -L |gre -i rej

root@linux:~# ipset list

 

Then to double make sure the MySQL is allowed to access from anywhere, used simple telnet from my Desktop Laptop PC (that also runs Debian Linux) towards the server .

hipo@jeremiah:~$ telnet 52.88.235.45 3306
Trying 52.88.235.45…
Connected to 52.88.235.45.
Escape character is '^]'.
[
5.5.5-10.3.15-MariaDB-1
                       rQ}Cs>v\��-��G1[W%O>+Y^OQmysql_native_password
Connection closed by foreign host.

 

As telnet is not supporting the data encryption after TCP proto connect, in a few seconds time, remote server connection is terminated.

 

Setting MySQL user to be able to connect to local server MySQL from any remote hostname


I've connected locally to MariaDB server with mysql -u root -p and issued following set of SQL commands to make MySQL root user be able to connect from anywhere:

 

CREATE USER 'root'@'%' IDENTIFIED BY 'my-secret-pass';
GRANT ALL ON *.* TO 'root'@'localhost';
GRANT ALL ON *.* TO 'root'@'%';

 

Next step, I've took was to try logging in with root (admin) MariaDB superuser from MySQL CLI (Command Line Interface) on my desktop just to find out, I'm facing a nasty error.
 

hipo@jeremiah:~$ mysql -u root -H remote-server-hostname.com -p
Enter password:
ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)


My first guess was something is wrong with my root user created in MySQL's mysql.user table (In MySQL this is the privileges table that stores, how MySQL user credentials are handled by mysqld local OS running process.

 

Changing the MySQL root (admin) password no longer possible on Debian 10 Buster?

 

The standard way ot change the MySQL root password well known via a simple dpkg-reconfigure (provided by Debian's debconf is no longer working so below command produces empty output instead of triggering the good old Ncurses text based interface well-known over the years …

 

root@linux:~# /usr/sbin/dpkg-reconfigure mariadb-server-10.3

 

 

Viewing MariaDB (MySQL) username / password set-up from the CLI

 

To list how this set-privileges looked like I've used following command:

 

MariaDB [mysql]> select * from mysql.user where User = 'root';
+———–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+————————+———————+———-+————+————-+————–+—————+————-+—————–+———————-+———————–+———————–+——————+———+————–+——————–+
| Host      | User | Password                                  | Select_priv | Insert_priv | Update_priv | Delete_priv | Create_priv | Drop_priv | Reload_priv | Shutdown_priv | Process_priv | File_priv | Grant_priv | References_priv | Index_priv | Alter_priv | Show_db_priv | Super_priv | Create_tmp_table_priv | Lock_tables_priv | Execute_priv | Repl_slave_priv | Repl_client_priv | Create_view_priv | Show_view_priv | Create_routine_priv | Alter_routine_priv | Create_user_priv | Event_priv | Trigger_priv | Create_tablespace_priv | Delete_history_priv | ssl_type | ssl_cipher | x509_issuer | x509_subject | max_questions | max_updates | max_connections | max_user_connections | plugin                | authentication_string | password_expired | is_role | default_role | max_statement_time |
+———–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+————————+———————+———-+————+————-+————–+—————+————-+—————–+———————-+———————–+———————–+——————+———+————–+——————–+
| localhost | root | *E6D338325F50177F2F6A15EDZE932D68C88B8C4F | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | Y          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            | Y                      | Y                   |          |            |             |              |             0 |           0 |               0 |                    0 | mysql_native_password |                       | N                | N       |              |           0.000000 |
| %         | root | *E6D338325F50177F2F6A15EDZE932D68C88B8C4F | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | N          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            | Y                      | Y                   |          |            |             |              |             0 |           0 |               0 |                    0 |                       |                       | N                | N       |              |           0.000000 |
+———–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+————————+———————+———-+————+————-+————–+—————+————-+—————–+———————-+———————–+———————–+——————+———+————–+——————–+

 

The hashed (encrypted) password string is being changed from the one on the server, so please don't try to hack me (decrypt it) 🙂
As it is visible from below output the Host field for root has the '%' string which means, any hostname is authorized to be able to connect and login to the MySQL server, so this was not the problem.

After quite some time on reading on what causes
' ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)
',
I've spend some time reading various forum discussions online on the err such as the one on StackOverflow here SuperUser.com's  how to fix access denied for user 'root'@'localhost' and one on askubuntu.com's – ERROR 1045(28000) : Access denied for user 'root@localhost' (using password: no ) and after a while finally got it, thanks to a cool IRC.FREENODE.NET guy nicknamed, hedenface who pointed me I'm that, I'm trying to use the -H flag (Prodice HTML) instead of -h (host_name), it seems somehow I ended up with the wrong memory that the -H stands for hostname, by simply using -h I could again login Hooray!!!

 

root@linux:~$ mysql -u root -h remote-server-host.com -p
Enter password:
Welcome to the MariaDB monitor.  Commands end with ; or \g.
Your MariaDB connection id is 14
Server version: 10.3.15-MariaDB-1 Debian 10

 

Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.


I've further asked the customer to confirm, he can connect also from his Microsoft Windows 10 PC situated on a different LAN network and got his confirmation. Few notes to make here is I've also installed phpmyadmin on the server using phpmyadmin php source code latest version, as in Debian 10 it seems the good old PHP is no longer available (as this crazy developers again made a mess and there is no phpmyadmin .deb package in Debian Buster – but that's a different story I'll perhaps try to document in some small article in future.

Mass substitute WordPress site Old domain URL to new URL in MySQL (MariaDB) database after website migration

Thursday, September 13th, 2018

Reading Time: 5minutes

mass-substitute-old-urls-to-new-urls-when-moving-wordpress-website-migrate-wordpress

Mass substitute WordPress site Old domain URL to new URL in MySQL (MariaDB) database after website migration

If you have just migrated a wordpress blog or site to a new server (domain URL) and you have many articles pointing to the old URL. Out of sudden the new domain will end up with many broken links and that would have a severe negative SEO effect on your website leading to a certain downfall of your number of daily unique visits.

Of course manually changing the URL links is achievable by going through all Published Posts when migrating small websites with 10-20 pages,  however it is an impossible tedious task you would definitely want to avoid when you're migrating large WP based websites with few hundred or thousands of posts / pages,
bacause this would be a few weeks of mindless repeatable job to go through each and every post and substite the broken URLs.

Fortunately with a little bit of SQL magic either through MySQL CLI or PHPMyAdmin (if the website is moved to a shared hosting where you have disabled access to MySQL (MariaDB) default connect tcp port 3306.

Depending on the type of WordPress or Website the old broken URLs might be located in various Database tables.
 

– So when Mass URL substitution is might be required ?


1. You migrate a Website http://what-ever-website.com with (PHP / CSS / HTML / Templates) etc. from Hosting Provider Hostgator.com to UK2.com (because the website target client changed lately to United Kingdom customers) to http://what-ever-website.co.uk and the site is moved to a new domain beacause of Business rebranding
 

2. Other reason for changing internal URLs from one URL to another might be if you're migrating your website from HTTP to HTTPS for security.

3. You are restructuring file storage / image directories on the server or due to migration of files to external CDN (Content Delivery Network).
For example (http://your-server.com/images/ , http://your-server.com/files )  URLs pointing to old website location subdirectory has to be changed to the new one (http://your-server.com/img/ , http://your-server.com/data)

 

– So what is the automated approach to solve the task of Mass URL substitution across WP site ?

 

  •  Create full backup of all your website database and double-check the backup (try to restore on a test (home) server or other hosting account to make sure the backup is consistent and restore would work normally if necessery
     
  • You can Create Backup either with mysqldump command tool manually … with the right command arguments or use some kind of script such as My tiny mysqlbackupper.sh shell script which I shared under my previous article Make daily MySQL on Linux backup with Shell Script  via PhpMyAdmin.


2. Change old website URL to new one directly from Database using MySQL text client
 

To change incorrect URL with the new correct one the general query to run is:

 

update TABLE_NAME set FIELD_NAME = replace(FIELD_NAME, ‘find string’, ‘replace string’);

 

To change old website URL to the new website URL across every table within the wordpress database use below queries:
 

hipo@linux:~$ mysql -u root -p
Enter password:

 

USE blog;

 

UPDATE wp_options SET option_value = replace(option_value, 'Existing (old) URL', 'New URL') WHERE option_name = 'home' OR option_name = 'siteurl';

UPDATE wp_posts SET post_content = replace(post_content, 'Existing (old)URL', 'New URL');

UPDATE wp_postmeta SET meta_value = replace(meta_value,'Existing (old) URL','New URL');

UPDATE wp_usermeta SET meta_value = replace(meta_value, 'Existing (old) URL','New URL');

UPDATE wp_links SET link_url = replace(link_url, 'Existing (old) URL','New URL');

UPDATE wp_comments SET comment_content = replace(comment_content , 'Existing (old) URL','New URL');


3. Replace Old website URL to New one after migration using PHPMyAdmin web interface
 

If you don't have access  ssh shell, you can also run the queries via PhpMyAdmin to do so:

1. Open PHPMyadmin URL Panel in browser and login with your user / pass

2. Choose the wordpress database of the wordpress site / blog

3. Select SQL tab and in the panel type on above given SQL queries
 

web-hosting-phpmyadmin-sql-query-tab-screenshot-how-to-run-sql-queries-via-phpmyadmin

If you're lazy to type there is also a web based SQL queries generator tool for moving websites to a new domain


4. Using Search and Replace WordPress plugin to do the old URL to new URL (strings) transition
 

If you have never used SQL queries and you're totally new to it and don't want to risk breaking up something there is also a bunch of wordpress plugins available that do the URL string substitution throughout each wordpress table in a WP databaseone such WordPress plugin is Search and Replace I have written earlier an article Change string in all WordPress Posts with Search and Replace plugin.


5. Problems with data-serialization
 

If you do a simple search and replace of Old domain urls to New ones, using above given commands and you still end up with some broken links on WP Pages that might be due to data-serialization issues (for the cause of issues check out what is data serialization).
Data serialization in wordpress terms is an array of PHP encrypted data that contains the actual URL, thus a simple search and replace as explained above if URLs use data-serialization would not work. There are available tools online that does URL search and replace operation through  "serialize-data sensitively" if you stuck with data-serializatoin caused issues.

Besides that for there are written scripts that does URL substitution to a WordPress or Joomla websites so an alternative to above WP plugin to replace the URL after migration is to use one of the scripts available a very famous one that will do pain-free all URL / string substitutions inside your WP, Drupal,  Joomla databses isinterconnect/it.
 

Few closure words
 

As a system administrator and webmaster I have migrated wordpress installations many times with the need to change the old URLs to a new ones for both customer websites and my own wordpress based. On many ocassions because of lack of attention and hurry, I've messed up things.
The moral I got out of this is when you're doing a WordPress migration just like everything you have to be very attentive and do everything step by step slowly and have a good idea on what you're doing in advance …

Even as a person who had overall idea on how MySQL Server works and have experience in writting SQL queries, I have to confess I've  made mistakes during URL substitution operations when doing it via the MySQL CLI every now and then.

Thus I would recommend you better use some of the many plugins for wordpress and script tools (few of which I mentioned above), especially if you're not having at least few years with some kind of UNIX variation / Linux / MySQL.

MySQL crashes after upgrade from MySQL to MariaDB and how to fix it

Tuesday, August 21st, 2018

Reading Time: 3minutes

how-to-fix-crashing-mysql-after-upgrade-to-mariadb-database-mariadb-logo.png

If you have recently upgraded your Debian / Ubuntu / CentOS Linux Server to the latest RPM / DEB packages as part of the upgrade you might have noticed the upgrade of MySQL Community Server  (which was bought by Oracle Corporation few years ago) is automatically upgradedto MariaDB (which is a MySQL fork made by the original developers of MySQL and guaranteed to stay open source. Just to name some of the Notable users include Wikipedia, WordPress.com and Google.).

You might have noticed MariaDB's restart script which is still under /etc/init.d/mysql  won't start and a quick check in /var/log/mysql.err | /var/log/mysql.log
shows errors of /usr/bin/mysqld crashing with errors like:

140502 14:13:05 [Note] Plugin 'FEDERATED' is disabled.
InnoDB: Log scan progressed past the checkpoint lsn 108 1057948207
140502 14:13:06  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files…
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer…
InnoDB: Doing recovery: scanned up to log sequence number 108 1058059648
InnoDB: 1 transaction(s) which must be rolled back or cleaned up
InnoDB: in total 15 row operations to undo
InnoDB: Trx id counter is 0 562485504
140502 14:13:06  InnoDB: Starting an apply batch of log records to the database…
InnoDB: Progress in percents: 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
InnoDB: Starting in background the rollback of uncommitted transactions
140502 14:13:06  InnoDB: Rolling back trx with id 0 562485192, 15 rows to undo
140502 14:13:06  InnoDB: Started; log sequence number 108 1058059648
140502 14:13:06  InnoDB: Assertion failure in thread 1873206128 in file ../../../storage/innobase/fsp/fsp0fsp.c line 1593
InnoDB: Failing assertion: frag_n_used > 0
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.1/en/forcing-recovery.html
InnoDB: about forcing recovery.
140502 14:13:06 – mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
We will try our best to scrape up some info that will hopefully help diagnose
the problem, but since we have already crashed, something is definitely wrong
and this may fail.

key_buffer_size=16777216
read_buffer_size=131072
max_used_connections=0
max_threads=151
threads_connected=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 345919 K
bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

thd: 0x0
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong…
stack_bottom = (nil) thread_stack 0x30000
140502 14:13:06 [Note] Event Scheduler: Loaded 0 events
140502 14:13:06 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.1.41-3ubuntu12.10'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  (Ubuntu)
/usr/sbin/mysqld(my_print_stacktrace+0x2d) [0xb7579cbd]
/usr/sbin/mysqld(handle_segfault+0x494) [0xb7245854]
[0xb6fc0400]
/lib/tls/i686/cmov/libc.so.6(abort+0x182) [0xb6cc5a82]
/usr/sbin/mysqld(+0x4867e9) [0xb74647e9]
/usr/sbin/mysqld(btr_page_free_low+0x122) [0xb74f1622]
/usr/sbin/mysqld(btr_compress+0x684) [0xb74f4ca4]
/usr/sbin/mysqld(btr_cur_compress_if_useful+0xe7) [0xb74284e7]
/usr/sbin/mysqld(btr_cur_pessimistic_delete+0x332) [0xb7429e72]
/usr/sbin/mysqld(btr_node_ptr_delete+0x82) [0xb74f4012]
/usr/sbin/mysqld(btr_discard_page+0x175) [0xb74f41e5]
/usr/sbin/mysqld(btr_cur_pessimistic_delete+0x3e8) [0xb7429f28]
/usr/sbin/mysqld(+0x526197) [0xb7504197]
/usr/sbin/mysqld(row_undo_ins+0x1b1) [0xb7504771]
/usr/sbin/mysqld(row_undo_step+0x25f) [0xb74c210f]
/usr/sbin/mysqld(que_run_threads+0x58a) [0xb74a31da]

/usr/sbin/mysqld(trx_rollback_or_clean_all_without_sess+0x3e3) [0xb74ded43]
/lib/tls/i686/cmov/libpthread.so.0(+0x596e) [0xb6f9f96e]
/lib/tls/i686/cmov/libc.so.6(clone+0x5e) [0xb6d65a4e]
The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.

Any recommendations?
mysql

I hoped to solve the /usr/bin/mysqldsegfault error with server reboot as I though the problem is caused by the fact libc library was updated, but even a reboot did not solve it.

I've investigated online for a solution and found following MySQL corruption and recovery article.

The solution outlined there is very simple and comes to adding the line:
 

innodb_force_recovery = 1


to /etc/mysql/my.cnf

Assuming the mysql server is not running before restarting mariadb server.

1. Make a backup (Dump) of all MySQL tables

mysql:~# mysqldump -A > dump.sql

2. Drop all databases which need recovery.
You can do that from mysql cli or phpmyadmin

3. Stop mysqld.

mysql:~# /etc/init.d/mysql restart

4.  Remove /var/lib/mysql/ib*

mysql:~# rm -rf /var/lib/mysql/ib*

5. Comment out innodb_force_recovery in /etc/mysql/my.cnf

6. Restart mysqld. Look at mysql error log.
If everything is fine and you have problems with broken or missing databases the best thing next is to stop again mariadb and

7. Restore databases from the dump

mysql:~# mysql < dump.sql

 

 

 

Check is MySQL dropping connections or how to check drop out SQL problems and debug problems with slow queries

Thursday, October 26th, 2017

Reading Time: 2minutes

mysql-dropping-connections-how-to-check-command-drop-out-sql-problems-and-debugging-slow-queries

If you have migrated a website or you recently upgraded MySQL and you face occasional problems with dropped connections to remote Web site or application it is likely that the problem is rooted either in Apache being unable to handle multiple connections, e.g. you will get a lot of 503 errors in log or MySQL dropping connections due to someout or MySQL / PHP bug that occurs after packages upgrade.

So how to check is MySQL dropping connections?

Use below command one liner shell script and check for Aborted conncetions a relatively high number is indication MySQL is dropping connections from PHP script or local / remote application such as SOAP or XSLT connects.
 

# echo 'show global status' | mysql -u root -p |grep -i connect
Enter password:
Aborted_connects    710
Connections    49537
Max_used_connections    76
Ssl_client_connects    0
Ssl_connect_renegotiates    0
Ssl_finished_connects    0
Threads_connected    1

Another indicator for MySQL dropping connections is if you find MySQL to have many slow queries, that would mean the slow queries won't be processed on time and there will be consequential connection drop outs.
 

# echo 'show global status' | mysql -u root -p |grep -i slow
Enter password:
Slow_launch_threads    0
Slow_queries    120237


If you find any you can use some MySQL / MariaDB monitoring script such as (mytop / mtop – for more on monitoring MySQL queries in real time I recommend you check out my previous article Monitoring MySQL queries and debugging performance (slow queries))

Fix MySQL ibdata file size – ibdata1 file growing too large, preventing ibdata1 from eating all your server disk space

Thursday, April 2nd, 2015

Reading Time: 4minutes

fix-solve-mysql-ibdata-file-size-ibdata1-file-growing-too-large-and-preventing-ibdata1-from-eating-all-your-disk-space-innodb-vs-myisam

If you're a webhosting company hosting dozens of various websites that use MySQL with InnoDB  engine as a backend you've probably already experienced the annoying problem of MySQL's ibdata1 growing too large / eating all server's disk space and triggering disk space low alerts. Theibdata1 file, taking up hundreds of gigabytes is likely to be encountered on virtually all Linux distributions which run default MySQL server <= MySQL 5.6 (with default distro shipped my.cnf). The excremental ibdata1 raise appears usually due to a application software bug on how it queries the database. In theory there are no limitation for ibdata1 except maximum file size limitation set for the filesystem (and there is no limitation option set in my.cnf) meaning it is quite possible that under certain conditionsibdata1 grow over time can happily fill up your server LVM (Storage) drive partitions.

Unfortunately there is no way to shrink the ibdata1 file and only known work around (I found) is to set innodb_file_per_table option in my.cnf to force the MySQL server create separate *.ibd files under datadir (my.cnf variable) for each freshly created InnoDB table.
 

1. Checking size of ibdata1 file

On Debian / Ubuntu and other deb based Linux servers datadir is /var/lib/mysql/ibdata1

server:~# du -hsc /var/lib/mysql/ibdata1
45G     /var/lib/mysql/ibdata1
45G     total


2. Checking info about Databases and Innodb storage Engine

server:~# mysql -u root -p
password:

mysql> SHOW DATABASES;
+——————–+
| Database           |
+——————–+
| information_schema |
| bible              |
| blog               |
| blog-sezoni        |
| blogmonastery      |
| daniel             |
| ezmlm              |
| flash-games        |


Next step is to get some understanding about how many existing InnoDB tables are present within Database server:

 

mysql> SELECT COUNT(1) EngineCount,engine FROM information_schema.tables WHERE table_schema NOT IN ('information_schema','performance_schema','mysql') GROUP BY engine;
+————-+——–+
| EngineCount | engine |
+————-+——–+
|         131 | InnoDB |
|           5 | MEMORY |
|         584 | MyISAM |
+————-+——–+
3 rows in set (0.02 sec)

To get some more statistics related to InnoDb variables set on the SQL server:
 

mysqladmin -u root -p'Your-Server-Password' var | grep innodb


Here is also how to find which tables use InnoDb Engine

mysql> SELECT table_schema, table_name
    -> FROM INFORMATION_SCHEMA.TABLES
    -> WHERE engine = 'innodb';

+————–+————————–+
| table_schema | table_name               |
+————–+————————–+
| blog         | wp_blc_filters           |
| blog         | wp_blc_instances         |
| blog         | wp_blc_links             |
| blog         | wp_blc_synch             |
| blog         | wp_likes                 |
| blog         | wp_wpx_logs              |
| blog-sezoni  | wp_likes                 |
| icanga_web   | cronk                    |
| icanga_web   | cronk_category           |
| icanga_web   | cronk_category_cronk     |
| icanga_web   | cronk_principal_category |
| icanga_web   | cronk_principal_cronk    |


3. Check and Stop any Web / Mail / DNS service using MySQL

server:~# ps -efl |grep -E 'apache|nginx|dovecot|bind|radius|postfix'

Below cmd should return empty output, (e.g. Apache / Nginx / Postfix / Radius / Dovecot / DNS etc. services are properly stopped on server).

4. Create Backup dump all MySQL tables with mysqldump

Next step is to create full backup dump of all current MySQL databases (with mysqladmin):

server:~# mysqldump –opt –allow-keywords –add-drop-table –all-databases –events -u root -p > dump.sql
server:~# du -hsc /root/dump.sql
940M    dump.sql
940M    total

 

If you have free space on an external backup server or remotely mounted attached (NFS or SAN Storage) it is a good idea to make a full binary copy of MySQL data (just in case something wents wrong with above binary dump), copy respective directory depending on the Linux distro and install location of SQL binary files set (in my.cnf).
To check where are MySQL binary stored database data (check in my.cnf):

server:~# grep -i datadir /etc/mysql/my.cnf
datadir         = /var/lib/mysql

If server is CentOS / RHEL Fedora RPM based substitute in above grep cmd line /etc/mysql/my.cnf with /etc/my.cnf

if you're on Debian / Ubuntu:

server:~# /etc/init.d/mysql stop
server:~# cp -rpfv /var/lib/mysql /root/mysql-data-backup

Once above copy completes, DROP all all databases except, mysql, information_schema (which store MySQL existing user / passwords and Access Grants and Host Permissions)

5. Drop All databases except mysql and information_schema

server:~# mysql -u root -p
password:

 

mysql> SHOW DATABASES;

DROP DATABASE blog;
DROP DATABASE sessions;
DROP DATABASE wordpress;
DROP DATABASE micropcfreak;
DROP DATABASE statusnet;

          etc. etc.

ACHTUNG !!!DON'T execute!DROP database mysql; DROP database information_schema; !!! – cause this might damage your User permissions to databases

6. Stop MySQL server and add innodb_file_per_table and few more settings to prevent ibdata1 to grow infinitely in future

server:~# /etc/init.d/mysql stop

server:~# vim /etc/mysql/my.cnf
[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G

Delete files taking up too much space –ibdata1 ib_logfile0 and ib_logfile1

server:~# cd /var/lib/mysql/
server:~#  rm -f ibdata1 ib_logfile0 ib_logfile1
server:~# /etc/init.d/mysql start
server:~# /etc/init.d/mysql stop
server:~# /etc/init.d/mysql start
server:~# ps ax |grep -i mysql

 

You should get no running MySQL instance (processes), so above ps command should return blank.
 

7. Re-Import previously dumped SQL databases with mysql cli client

server:~# cd /root/
server:~# mysql -u root -p < dump.sql

Hopefully import should went fine, and if no errors experienced new data should be in.

Altearnatively if your database is too big and you want to import it in less time to mitigate SQL downtime, instead import the database with:

server:~# mysql -u root -p
password:
mysql>  SET FOREIGN_KEY_CHECKS=0;
mysql> SOURCE /root/dump.sql;
mysql> SET FOREIGN_KEY_CHECKS=1;

 

If something goes wrong with the import for some reason, you can always copy over sql binary files from /root/mysql-data-backup/ to /var/lib/mysql/
 

8. Connect to mysql and check whether databases are listable and re-check ibdata file size

Once imported login with mysql cli and check whther databases are there with:

server:~# mysql -u root -p
SHOW DATABASES;

Next lets see what is currently the size of ibdata1, ib_logfile0 and ib_logfile1
 

server:~# du -hsc /var/lib/mysql/{ibdata1,ib_logfile0,ib_logfile1}
19M     /var/lib/mysql/ibdata1
1,1G    /var/lib/mysql/ib_logfile0
1,1G    /var/lib/mysql/ib_logfile1
2,1G    total

Now ibdata1 will grow, but only contain table metadata. Each InnoDB table will exist outside of ibdata1.
To better understand what I mean, lets say you have InnoDB table named blogdb.mytable.
If you go into /var/lib/mysql/blogdb, you will see two files
representing the table:

  •     mytable.frm (Storage Engine Header)
  •     mytable.ibd (Home of Table Data and Table Indexes for blogdb.mytable)

Now construction will be like that for each of MySQL stored databases instead of everything to go to ibdata1.
MySQL 5.6+ admins could relax as innodb_file_per_table is enabled by default in newer SQL releases.


Now to make sure your websites are working take few of the hosted websites URLs that use any of the imported databases and just browse.
In my case ibdata1 was 45GB after clearing it up I managed to save 43 GB of disk space!!!

Enjoy the disk saving! 🙂

MySQL: How to check user privileges and allowed hosts to connect with mysql cli

Wednesday, April 2nd, 2014

Reading Time: 3minutes

how-to-check-user-privileges-and-allowed-hosts-to-connect-with-mysql-cli

On a project there are some issues with root admin user unable to access the server from remote host and the most probable reason was there is no access to the server from that host thus it was necessary check mysql root user privilegse and allowed hosts to connect, here SQL query to do it:
 

mysql> select * from `user` where  user like 'root%';
+——————————–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+———-+————+————-+————–+—————+————-+—————–+———————-+
| Host                           | User | Password                                  | Select_priv | Insert_priv | Update_priv | Delete_priv | Create_priv | Drop_priv | Reload_priv | Shutdown_priv | Process_priv | File_priv | Grant_priv | References_priv | Index_priv | Alter_priv | Show_db_priv | Super_priv | Create_tmp_table_priv | Lock_tables_priv | Execute_priv | Repl_slave_priv | Repl_client_priv | Create_view_priv | Show_view_priv | Create_routine_priv | Alter_routine_priv | Create_user_priv | Event_priv | Trigger_priv | ssl_type | ssl_cipher | x509_issuer | x509_subject | max_questions | max_updates | max_connections | max_user_connections |
+——————————–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+———-+————+————-+————–+—————+————-+—————–+———————-+
| localhost                      | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | Y          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            |          |            |             |              |             0 |           0 |               0 |                    0 |
| server737                        | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | Y          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            |          |            |             |              |             0 |           0 |               0 |                    0 |
| 127.0.0.1                      | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | Y          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            |          |            |             |              |             0 |           0 |               0 |                    0 |
| server737.server.myhost.net | root | *5A07790DCF43FC89820A93CAF7B03DE3F43A10D9 | Y           | Y           | Y           | Y           | Y           | Y         | Y           | Y             | Y            | Y         | Y          | Y               | Y          | Y          | Y            | Y          | Y                     | Y                | Y            | Y               | Y                | Y                | Y              | Y                   | Y                  | Y                | Y          | Y            |          |            |             |              |             0 |           0 |               0 |                    0 |
| server4586                        | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | N           | N           | N           | N           | N           | N         | N           | N             | N            | N         | N          | N               | N          | N          | N            | N          | N                     | N                | N            | N               | N                | N                | N              | N                   | N                  | N                | N          | N            |          |            |             |              |             0 |           0 |               0 |                    0 |
| server4586.myhost.net              | root | *5A07790DCF43AC89820F93CAF7B03DE3F43A10D9 | N           | N           | N           | N           | N           | N         | N           | N             | N            | N         | N          | N               | N          | N          | N            | N          | N                     | N                | N            | N               | N                | N                | N              | N                   | N                  | N                | N          | N            |          |            |             |              |             0 |           0 |               0 |                    0 |
+——————————–+——+——————————————-+————-+————-+————-+————-+————-+———–+————-+—————+————–+———–+————+—————–+————+————+————–+————+———————–+——————+————–+—————–+——————+——————+—————-+———————+——————–+——————+————+————–+———-+————+————-+————–+—————+————-+—————–+———————-+
6 rows in set (0.00 sec)

mysql> exit


Here is query explained:

select * from `user` where  user like 'root%'; query means:

select * – show all
from `user` – from user database
where user like 'root%' – where there is match in user column to any string starting with 'root*',
 

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

Monday, July 16th, 2012

Reading Time: 2minutes

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 😉

‘host-name’ is blocked because of many connection errors; unblock with ‘mysqladmin flush-hosts’

Sunday, May 20th, 2012

Reading Time: 3minutes

mysql-logo-host-name-blocked-because-of-many-connection-errors
My home run machine MySQL server was suddenly down as I tried to check my blog and other sites today, the error I saw while trying to open, this blog as well as other hosted sites using the MySQL was:

Error establishing a database connection

The topology, where this error occured is simple, I have two hosts:

1. Apache version 2.0.64 compiled support externally PHP scripts interpretation via libphp – the host runs on (FreeBSD)

2. A Debian GNU / Linux squeeze running MySQL server version 5.1.61

The Apache host is assigned a local IP address 192.168.0.1 and the SQL server is running on a host with IP 192.168.0.2

To diagnose the error I've logged in to 192.168.0.2 and weirdly the mysql-server was appearing to run just fine:
 

debian:~# ps ax |grep -i mysql
31781 pts/0 S 0:00 /bin/sh /usr/bin/mysqld_safe
31940 pts/0 Sl 12:08 /usr/sbin/mysqld –basedir=/usr –datadir=/var/lib/mysql –user=mysql –pid-file=/var/run/mysqld/mysqld.pid –socket=/var/run/mysqld/mysqld.sock –port=3306
31941 pts/0 S 0:00 logger -t mysqld -p daemon.error
32292 pts/0 S+ 0:00 grep -i mysql

Moreover I could connect to the localhost SQL server with mysql -u root -p and it seemed to run fine. The error Error establishing a database connection meant that either something is messed up with the database or 192.168.0.2 Mysql port 3306 is not properly accessible.

My first guess was something is wrong due to some firewall rules, so I tried to connect from 192.168.0.1 to 192.168.0.2 with telnet:
 

freebsd# telnet 192.168.0.2 3306
Trying 192.168.0.2…
Connected to jericho.
Escape character is '^]'.
Host 'webserver' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'
Connection closed by foreign host.

Right after the telnet was initiated as I show in the above output the connection was immediately closed with the error:

Host 'webserver' is blocked because of many connection errors; unblock with 'mysqladmin flush-hosts'Connection closed by foreign host.

In the error 'webserver' is my Apache machine set hostname. The error clearly states the problems with the 'webserver' apache host unable to connect to the SQL database are due to 'many connection errors' and a fix i suggested with mysqladmin flush-hosts

To temporary solve the error and restore my normal connectivity between the Apache and the SQL servers I logged I had to issue on the SQL host:

mysqladmin -u root -p flush-hostsEnter password:

Thogh this temporar fix restored accessibility to the databases and hence the websites errors were resolved, this doesn't guarantee that in the future I wouldn't end up in the same situation and therefore I looked for a permanent fix to the issues once and for all.

The permanent fix consists in changing the default value set for max_connect_error in /etc/mysql/my.cnf, which by default is not too high. Therefore to raise up the variable value, added in my.cnf in conf section [mysqld]:

debian:~# vim /etc/mysql/my.cnf
...
max_connect_errors=4294967295

and afterwards restarted MYSQL:

debian:~# /etc/init.d/mysql restart
Stopping MySQL database server: mysqld.
Starting MySQL database server: mysqld.
Checking for corrupt, not cleanly closed and upgrade needing tables..

To make sure the assigned max_connect_errors=4294967295 is never reached due to Apache to SQL connection errors, I've also added as a cronjob.

debian:~# crontab -u root -e
00 03 * * * mysqladmin flush-hosts

In the cron I have omitted the mysqladmin -u root -p (user/pass) input options because for convenience I have already stored the mysql root password in /root/.my.cnf

Here is how /root/.my.cnf looks like:

debian:~# cat /root/.my.cnf
[client]
user=root
password=a_secret_sql_password

Now hopefully, this would permanently solve SQL's 'failure to accept connections' due to too many connection errors for future.

Speed up WordPress / Joomla CMS and MySQL server on Linux with tmpfs ram file system / Decrease Website pageload times with RAM caching

Wednesday, March 4th, 2015

Reading Time: 9minutes

speed-up-accelerate-wordpress-joomla-drupal-cms-and-mysql-server-with-tmpfs_ramfs_decrease-pageload-times-with-ram-caching
As a WordPress blog owner and an sys admin that has to deal with servers running a lot of WordPress / Joomla / Droopal and other custom CMS installed on servers, performoing slow or big enough to put a significant load on servers
and I love efficiency and hardware cost saving is essential for my daily job, I'm constantly trying to find new ways to optimize Customer Website (WordPress) and rest of sites in order to utilize better our servers and improve our clients sites speed (and hence satisfaction). 

There is plenty of little things to do on servers but probably among the most crucial ones which we use nowadays that save us a lot of money is tmpfs, and earlier (ramfs) – previously known as shmfs).
TMPFS is a (Temporary File Storage Facility) Linux kernel technology based on ramfs (used by Linux kernel initrd / initramfs on boot time in order to load and store the Linux kernel in memory, before system hard disk partition file systems are mounted) which is heavily used by virtually all modern popular Linux distributions. 

Using ramfs (cramfs variation – Compressed ROM filesystem) has been used to store different system environment kernel and Desktop components of many Linux environment / applications and used by a lot of the Linux BootCD such as the most famous (Klaus Knopper's) KNOPPIX LiveCD and Trinity Rescue Kit Linux (TRK uses /dev/shm which btw can be seen on most modern Linux distros and is actually just another mounted tmpfs).
If you haven't tried Live Linux yet try it out as me and a lot of sysadmins out there use some kind of LiveLinux at least few times on yearly basis  to Recover Unbootable Linux servers after some applied remote Updates as well as for Rescuing (Save) Data from Linux server failing to properly boot because of hard disk (bad blocks) failures. As I said earlier TMPFS is also used on almost any distribution for the /dev/ filesystem which is kept in memory.

You can see which tmpfs partitions is used on your Linux server with:

 

debian-server:~# mount |grep -i tmpfs
tmpfs on /lib/init/rw type tmpfs (rw,nosuid,mode=0755)
udev on /dev type tmpfs (rw,mode=0755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)

 

Above is an output from a standard Debian Linux server. On CentOS 7 standard mounted tmpfs are as follows:

 

[root@centos ~]# mount |grep -i tmpfs
devtmpfs on /dev type devtmpfs (rw,nosuid,seclabel,size=1016332k,nr_inodes=254083,mode=755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,seclabel)
tmpfs on /run type tmpfs (rw,nosuid,nodev,seclabel,mode=755)
tmpfs on /sys/fs/cgroup type tmpfs (rw,nosuid,nodev,noexec,seclabel,mode=755)

 

[root@centos ~]# df -h|grep -i tmpfs
devtmpfs                 993M     0  993M   0% /dev
tmpfs                   1002M   92K 1002M   1% /dev/shm
tmpfs                   1002M  8.8M  993M   1% /run
tmpfs                   1002M     0 1002M   0% /sys/fs/cgroup

The /run tmpfs mounted directory is also to be seen also on latest Ubuntus and Fedoras and is actually the good old /var/run ( where applications keep there pids and some small app related files) stored in tmpfs filesystem stored in memory.

If you're wondering what is /dev/shm and why it appears mounted on every single Linux Server / Desktop you've ever used this is a special filesystem shared memory which various running programs (processes) can use to transfer data quick and efficient between each other to preven the slow disk swapping. People using Linux for the rest 15 years should remember /dev/shm has been a target of a lot of kernel exploits as historically it had a lot of security issues.

While writting this article I've just checked about KNOPPIX developed amd just for info as of time of writting this distro has already 1000+ programs on CD version and 2600+ packages / application on DVD version.
Nowadays Knoppixis mostly used mostly as USB Live Flash drive as a lot of people are dropping CD / DVD use (many servers doesn't have a CD / DVD Drive) and for USB Live Flash Linux distros tmpfs is also key technology used as this gives the end user an amazing fast experience (Desktop applications run much fasten on Live USBs when tmpfs is used than when the slow 7200 RPM HDDs are used).

Loading big parts of the distribution within RAM (with tmpfs from Linux Kernel 2.4+ onwards) is also heavily used by a lot of Cluster vendors in most of Clustered (Cloud) Linux based environemnts, cause TMPFS gives often speeds up improvements to x30 times and decreases greatly I/O HDD. FreeBSD users will be happy to know that TMPFS is already ported and could be used on from FreeBSD 7.0+ onward.

In this small article I will give you example use on how I use tmpfs to speed up our WordPress Websites which use WP Caching plugins such as W3 Total Cache and WP Super Cache
and Hyper Cache / WP Super Cache disk caching and MySQL server as a Database backend.
Below example is wordpress specific but since it can be easily applied to JoomlaDrupal or any other CMS out there that uses mySQL server to make a lot of CPU expensive memory hungry(LEFT JOIN) queries which end up using a slow 7200 RPM hard disk.


 

1. Preparing tmpfs partitions for WordPress File Cache directory
 

If you want to give tmpfs a test drive, I recommend you try to create / mount a 20 Megabyte partition. To create a tmpfs partition you don't need to use a tool like mkfs.ext3 / mkfs.ext4 as TMPFS is in reality a virtual filesystem that is mapped in the server system physical RAM (volatile memory). TMPFS is very nice because if you run out of free RAM system starts a combination of RAM use + some Hard disk SWAP 
The great thing about TMPFS is it never uses all of the available RAM and SWAP, which would not halt your server if TMPFS partition gets filled, but instead you will start getting the usual "Insufficient Disk Space", just like with a physical HDD parititon. RAMFS cares much less about server compared to TMPFS, because if RAMFS is historically older.

ramfsfile systems cannot be limited in size like a disk base file system which is limited by it’s capacity, thus ramfswill continue using memory storage until the system runs out of RAM and likely crashes or becomes unresponsive. This is a problem if the application writing to the file system cannot be limited in total size, so in my opinion you better stay away from RAMFS except you have a good idea what you're doing. Another disadvantage of RAMFS compared to TMPFS is you cannot see the size of the file system in df and it can only be estimated by looking at the cached entry in free.

Note that before proceeding to use TMPFS or RAMFS you should know besides having advantages, there are certain serious disadvantage that if the server using tmpfs (in RAM) to store files crashes the customer might loose his data, therefore using RAM filesystems on Production servers is best to be used just for caching folders which are regularly synchronized with (rsync) to some folder to assure no data will be lost on server reboot or crash.

Memory of fast storage areas are ideally suited for applications which need repetitively small data areas for caching or using as temporary space such as Jira (Issue and Proejct Tracking Software) Indexing  As the data is lost when the machine reboots the tmpfsstored data must not be data of high importance as even scheduling backups cannot guarantee that all the data will be replicated in the even of a system crash.

To test mounting a tmpfs virtual (memory stored) filesystem issue:
 

mount -t tmpfs tmpfs -o size=256m /mnt/tmpfs


If you want to test mount a ramfs instead:

 

 mount -t ramfs -o size=256m ramfs /mnt/ramfs

 

debian-server:~#  mount |grep -i -E "ramfs|tmpfs"
tmpfs on /lib/init/rw type tmpfs (rw,nosuid,mode=0755)
udev on /dev type tmpfs (rw,mode=0755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /mnt/tmpfs type tmpfs (rw,size=256m)
ramfs on /mnt/ramfs type tmpfs (rw,size=256m)

 

Once mounted tmpfs can be used in the same way as any ext4 / reiserfs filesystem. In the same way to make mounts permanent, its necessery to add a line to /etc/fstab

To illustrate better a tmpfs use case on my blog running WordPress with W3TotalCache (W3TC) plugin cache folder in /var/www/blog/wp-content/w3tc to get advantage of tmpfs to store w3tc files.

a) Stop Apache

On Debian
 

debian-server:~# /etc/init.d/apache stop


On CentOS 
 

[root@centos ~]# /etc/init.d/httpd stop


b) Move w3tc dir to w3tc-bak

 

debian-server:~# cd /var/www/blog/wp-content/
debian-server:~# mv w3tc w3tc-bak

 

c) Create w3tc directory
 

debian-server:/var/www/blog/wp-content# mkdir w3tc
debian-server:/var/www/blog/wp-content# chown -R www-data:www-data w3tc


d) Add tmpfs record to /etc/fstab

My W3TC Cache didn't grow bigger than 2Gigabytes so I create a 2Giga directory for it by adding following in /etc/fstab 
 

debian-server:~# vim /etc/fstab

 

tmpfs /var/www/blog/wp-content/w3tc tmpfs defaults,size=2g,noexec,nosuid,uid=33,gid=33,mode=1755 0 0


You might also want to add the nr_inodes (option) to tmpfs while mounting. nr_inodes is the maximum inode for instance. Default is half the number of your physical RAM pages, (on a machine with highmem) the number of lowmem RAM page, some common option that should work is nr_inodes=5k, if you're unsure what this option does you can safely skip it 🙂

e) Mount new added tmpfs folder

Then to mount the newly added filesystem issue:
 

mount -a


Or if you're on a CentOS / RHEL server use httpd Apache user instead and whenever you have docroot and wordpress installed.

 

[root@centos ~]# chown -R apache:apache: w3tc


If you're using Apache SuPHP use whatever the UID / GID is proper.

On CentOS you will need to set proper UID and GID (UserID / GroupID), to find out which ones to to use check in /etc/passwd:
 

[root@centos ~]# grep -i apache /etc/passwd
apache:x:48:48:Apache:/var/www:/sbin/nologin


f) Move old w3tc cache from w3tc-bak to w3tc

 

debian-server:/var/www/blog/wp-content# mv w3tc-bak/* w3tc/

 

g) Start again Apache

On Debian:

 

debian-server:~# /etc/init.d/apache2 start

 


On CentOS:
 

[root@centos~]# /etc/init.d/httpd start

h) Keeping w3tc cache site folder synced

As I said earlier the biggest problem with caching (the reason why many hosting providers) and site admins refuse to use it is they might loose some data, to prevent data loss or at least mitigate the data loss to few minutes intervals it is a good idea to synchronize tmpfs kept folders somewhere to disk with rsync.

To achieve that use a cronjob like this:
 

debian-server:~# crontab -u root -e
*/5 * * * * /usr/bin/ionice -c3 -n7 /usr/bin/nice -n 19 /usr/bin/rsync -ah –stats –delete /var/www/blog/wp-content/w3tc/ /backups/tmpfs/cache/ 1>/dev/null


Note that you will need to have the /backups/tmpfs/cache folder existing, create it with:

 

debian-server:~# mkdir -p /backups/tmpfs/cache


You will also need to add a rsync synchronization from backupped folder to tmpfs (in case if the server gets accidently rebooted because it hanged or power outage), place in

/etc/rc.local

 

ionice -c3 -n7 nice -n 19 rsync -ahv –stats –delete /backups/tmpfs/cache/ /var/www/blog/wp-content/w3tc/ 1>/dev/null


(somewhere before exit 0) line
 

0 05 * * * /usr/bin/ionice -c3 -n7 /bin/nice -n 19 /usr/bin/rsync -ah –stats –delete /var/www/blog/wp-content/w3tc/ /backups/tmpfs/cache/ 1>/dev/null

 

 

2. Preparing tmpfs partitions for MySQL server temp File Cache directory


Its common that MySQL servers had to serve a lot of long and heavy SQL JOIN Queries mostly by related posts WP plugins such as (Zemanta Related Posts) and Contextual Related posts though MySQLs are well optimized  to work as much as efficient using mysql tuner (tuning primer) still often SQL servers get a lot of temp tables created to disk (about 25% to 30%) of all SQL queries use somehow HDD to serve queries and as this is very slow and there is file lock created the overall MySQL performance becomes sluggish at times to fix (resolve) that without playing with SQL code to optimize the slow queries the best way I found is by using TMPFS as MySQL temp folder.

To do so I create a TMPFS usually the size of 256 MB because this is usually enough for us, but other hosting companies might want to add bigger virtual temp disk:

a) Add tmpfs new dir to /etc/fstab

In /etc/fstab add below record with vim editor:
 

debian-server:~# vim /etc/fstab

 

tmpfs /var/mysqltmp tmpfs rw,gid=111,uid=108,size=256M,nr_inodes=10k,mode=0700 0 0

 

Note that the uid / and gid 105 and 114 are taken again from /etc/passwd

On Debian

debian-server:~# grep -i mysql /etc/passwd
mysql:x:108:111:MySQL Server,,,:/var/lib/mysql:/bin/false


On CentOS
 

[root@centos ~]# grep -i mysql /etc/passwd
mysql:x:27:27:MySQL Server:/var/lib/mysql:/bin/bash


b) Create folder /var/mysqltmp or whenever you want to place the tmpfs memory kept SQL folder

 

debian-server:~# mkdir /var/mysqltmp
debian-server:~# chown mysql:mysql /var/mysqltmp

 

debian-server:~# mount|grep -i tmpfs
tmpfs on /lib/init/rw type tmpfs (rw,nosuid,mode=0755)
udev on /dev type tmpfs (rw,mode=0755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /var/www/blog/wp-content/w3tc type tmpfs (rw,noexec,nosuid,size=2g,uid=33,gid=33,mode=1755)
tmpfs on /var/mysqltmp type tmpfs (rw,gid=108,uid=111,size=256M,nr_inodes=10k,mode=0700)


c) Add new path to tmpfs created folder in my.cnf 

Then  edit /etc/mysql/my.cnf

 

debian-server:~# vim /etc/mysql/my.cnf

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /var/mysqltmp

 

On CentOS edit and change tmpdir in same way within /etc/my.cnf


d) Finally Restart Apache and MySQL to make mysql start using new set tmpfs memory kept folder

On Debian:
 

debian-server:~# /etc/init.d/apache2 stop; /etc/init.d/mysql restart; /etc/init.d/apache2 start

On CentOS:
 

[root@centos ~]# /etc/init.d/httpd stop; /etc/init.d/mysqld restart; /etc/initd/httpd start


Now monitor your server and check your pagespeed increase for me such an optimization usually improves site performance so site becomes +50% faster, to see the difference you can test your website before applying tmpfs caching for site and after that by using Google PageInsight (PageSpeed) Online Test. Though this example is for MySQL and WordPress you can easily adopt the same for Joomla if you have Joomla Caching enabled to some folder, same goes for any other CMS such as Drupal that can take use of Disk Caching. Actually its a small secret of many Hosting providers that allow clients to create sites via CPanel and Kloxo this tmpfs optimizations are already used for sites and by this the provider is able to offer better website service on lower prices. VPS hosting providers also use heavy caching. A lot of people are using TMPFS also to accelerate Sites that have enabled Google Pagespeed as Cacher and accelerator, as PageSpeed module puts a heavy HDD I/O load that can easily stone the server. Many admins also choose to use TMPFS for  /tmp, /var/run, and /var/lock directories as this leads often to significant overall server services operations improvement.
Once you have tmpfs enabled, It is a good idea to periodically monitor your SWAP used space with (df -h), because if you allocate bigger tmpfs partitions than your physical memory and tmpfs's full size starts to be used your machine will start swapping heavily and this could have a very negative performance affect.
 

debian-server:~# df -h|grep -i tmpfs
tmpfs            3,9G     0   3,9G   0% /lib/init/rw
tmpfs            3,9G     0   3,9G   0% /dev/shm
tmpfs            2,0G  1,4G   712M  66% /var/www/blog/wp-content/w3tc
tmpfs            256M     0   256M   0% /mnt/tmpfs
tmpfs            256M  236K   256M   1% /var/mysqltmp

The applications of tmpfs to accelerate services is up to your imagination, so I will be glad to hear from other admins on any interesting other application or problems faced while using TMPFS.

 Enjoy! 🙂

Create SSH Tunnel to MySQL server to access remote filtered MySQL port 3306 host through localhost port 3308

Friday, February 27th, 2015

Reading Time: 3minutes

create_ssh_tunnel_to-mysql_server-to-access-remote-filtered-mysql-on-port-3306-secure_ssh_traffic
On our Debian / CentOS / Ubuntu Linux and Windows servers we're running multiple MySQL servers and our customers sometimes need to access this servers.
This is usually problem because MySQL Db  servers are running in a DMZ Zone with a strong firewall and besides that for security reasons SQLs are configured to only listen for connections coming from localhost, I mean in config files across our Debian Linux servers and CentOS / RHEL Linux machines the /etc/mysql/my.cnf and /etc/my.cnf the setting for bind-address is 127.0.0.1:
 

[root@centos ~]# grep -i bind-address /etc/my.cnf 
bind-address            = 127.0.0.1
##bind-address  = 0.0.0.0


For source code developers which are accessing development SQL servers only through a VPN secured DMZ Network there are few MySQL servers witha allowed access remotely from all hosts, e.g. on those I have configured:
 

[root@ubuntu-dev ~]# grep -i bind-address /etc/my.cnf 

bind-address  = 0.0.0.0


However though clients insisted to have remote access to their MySQL Databases but since this is pretty unsecure, we decided not to configure MySQLs to listen to all available IP addresses / network interfaces. 
MySQl acess is allowed only through PhpMyAdmin accessible via Cleint's Web interface which on some servers is CPanel  and on other Kloxo (This is open source CPanel like very nice webhosting platform).

For some stubborn clients which wanted to have a mysql CLI and MySQL Desktop clients access to be able to easily analyze their databases with Desktop clients such as MySQL WorkBench there is a "hackers" like work around to create and use a MySQL Tunnel to SQL server from their local Windows PCs using standard OpenSSH Linux Client from Cygwin,  MobaXterm which already comes with the SSH client pre-installed and has easy GUI interface to create SSH tunnels or eventually use Putty's Plink (Command Line Interface) to create the tunnel

Anyways the preferred and recommended (easiest) way to achieve a tunnel between MySQL and local PC (nomatter whether Windows or Linux client system) is to use standard ssh client and below command:
 

ssh -o ServerAliveInterval=10 -M -T -M -N -L 3308:localhost:3306 your-server.your-domain.com


By default SSH tunnel will keep opened for 3 minutes and if not used it will automatically close to get around this issue, you might want to raise it to (lets say 15 minutes). To do so in home directory user has to add in:
 

~/.ssh/config

ServerAliveInterval 15
ServerAliveCountMax 4


Note that sometimes it is possible ven though ssh tunnel timeout value is raised to not take affect if there is some NAT (Network Adress Translation) with low timeout setting on a firewall level. If you face constant SSH Tunnel timeouts you can use below bash few lines code to auto-respawn SSH tunnel connection (for Windows users use MobaXterm or install in advance bash shell cygwin package):
 

while true
do
 
ssh -o ServerAliveInterval=10 -M -T -M -N -L 3308:localhost:3306 your-server.your-domain.com
  sleep 15
done


Below is MySQLBench screenshot connected through server where this blog is located after establishing ssh tunnel to remote mysql server on port 3308 on localhost

mysql-workbench-database-analysis-and-management-gui-tool-convenient-for-data-migratin-and-queries-screenshot-

There is also another alternative way to access remote firewall filtered mysql servers without running complex commands to Run a tunnel which we recommend for clients (sql developers / sql designers) by using HeidiSQL (which is a useful tool for webdevelopers who has to deal with MySQL and MSSQL hosted Dbs).

heidisql-show-host_processlist-screenshot

To connect to remote MySQL server through a Tunnel using Heidi:

mysql_connection_configuration-heidi-mysql-gui-connect-tool

 

In the ‘Settings’ tab

1. In the dropdown list of ‘Network type’, please select SSH tunnel

2. Hostname/IP: localhost (even you are connecting remotely)

3. Username & Password: your mysql user and password

Next, in the tab SSH Tunnel:

1. specify plink.exe or you need to download it and specify where it’s located

2. Host + port: the remote IP of your SSH server(should be MySQL server as well), port 22 if you don’t change anything

3. Username & password: SSH username (not MySQL user)

 

heidi-connection_ssh_tunnel_configuration-heidi-sql-tool-screenshot