Posts Tagged ‘stackoverflow’

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! 🙂

How to Turn Off, Suppress PHP Notices and Warnings – PHP error handling levels via php.ini and PHP source code

Friday, April 25th, 2014

Reading Time: 2minutes

php-logo-disable-warnings-and-notices-in-php-through-htaccess-php-ini-and-php-code

PHP Notices are common to occur after PHP version upgrades or where an obsolete PHP code is moved from Old version PHP to new version. This is common error in web software using Frameworks which have been abandoned by developers.

Having PHP Notices to appear on a webpage is pretty ugly and give a lot of information which might be used by malicious crackers to try to break your site thus it is always a good idea to disable PHP Notices. There are plenty of ways to disable PHP Notices

The easiest way to disable it is globally in all Webserver PHP library via php.ini (/etc/php.ini) open it and make sure display_errors is disabled:

display_errors = 0

or

display_errors = Off

Note that that some claim in PHP 5.3 setting display_errors to Off will not work as expected. Anyways to make sure where your loaded PHP Version display_errors is ON or OFF use phpinfo();

It is also possible to disable PHP Notices and error reporting straight from PHP code you need code like:

 

<?php
// Turn off all error reporting
error_reporting(0);
?>

 

or through code:

 

ini_set('display_errors',0);


PHP has different levels of error reporting, here is complete list of possible error handling variables:

 

 

 

<?php
// Report simple running errors

error_reporting(E_ERROR | E_WARNING | E_PARSE);

// Reporting E_NOTICE can be good too (to report uninitialized
// variables or catch variable name misspellings …)

error_reporting(E_ERROR | E_WARNING | E_PARSE | E_NOTICE);

// Report all errors except E_NOTICE
// This is the default value set in php.ini

error_reporting(E_ALL ^ E_NOTICE);
// Report all PHP errors (see changelog)

error_reporting(E_ALL);
// Report all PHP errors error_reporting(-1);
// Same as error_reporting(E_ALL);

ini_set('error_reporting', E_ALL); ?>

The level of logging could be tuned on Debian Linux via /etc/php5/apache2/php.ini or if necessary to set PHP log level in PHP CLI through/etc/php5/cli/php.ini with:

error_reporting = E_ALL & ~E_NOTICE

 

If you need to remove to remove exact warning or notices from PHP without changing the way  PHPLib behaves is to set @ infront of variable or function that is causing NOTICES or WARNING:
For example:
 

@yourFunctionHere();
@var = …;


Its also possible toDisable PHP Notices and Warningsusing .htaccess file (useful in shared hosting where you don't have access to global php.ini), here is how:

# PHP error handling for development servers
php_flag display_startup_errors off
php_flag display_errors off
php_flag html_errors off
php_flag log_errors on
php_flag ignore_repeated_errors off
php_flag ignore_repeated_source off
php_flag report_memleaks on
php_flag track_errors on
php_value docref_root 0
php_value docref_ext 0
php_value error_log /home/path/public_html/domain/php_errors.log
php_value error_reporting -1
php_value log_errors_max_len 0

This way though PHP Notices and Warnings will be suppressed errors will get logged into php_error.log

How to set a crontab to execute commands on a seconds time interval on GNU / Linux and FreeBSD

Sunday, October 30th, 2011

Reading Time: 2minutes
crontab-execute-cron-jobs-every-second-on-linux-cron-logo
Have you ever been in need to execute some commands scheduled via a crontab, every let’s say 5 seconds?, naturally this is not possible with crontab, however adding a small shell script to loop and execute a command or commands every 5 seconds and setting it up to execute once in a minute through crontab makes this possible.
Here is an example shell script that does execute commands every 5 seconds:

#!/bin/bash
command1_to_exec='/bin/ls';
command2_to_exec='/bin/pwd';
for i in $(echo 1 2 3 4 5 6 7 8 9 10 11); do
sleep 5;
$command1_to_exec; $command2_to_exec;
done

This script will issue a sleep every 5 seconds and execute the two commands defined as $command1_to_exec and $command2_to_exec

Copy paste the script to a file or fetch exec_every_5_secs_cmds.sh from here

The script can easily be modified to execute on any seconds interval delay, the record to put on cron to use with this script should look something like:

# echo '* * * * * /path/to/exec_every_5_secs_cmds.sh' | crontab -

Where of course /path/to/exec_every_5_secs_cmds.sh needs to be modified to a proper script name and path location.

Another way to do the on a number of seconds program / command schedule without using cron at all is setting up an endless loop to run/refresh via /etc/inittab with a number of predefined commands inside. An example endless loop script to run via inittab would look something like:

while [ 1 ]; do
/bin/ls
sleep 5;
done

To run the above sample never ending script using inittab, one needs to add to the end of inittab, some line like:

mine:234:respawn:/path/to/script_name.sh

A quick way to add the line from consone would be with echo:

echo 'mine:234:respawn:/path/to/script' >> /etc/inittab

Of course the proper paths, should be put in:

Then to load up the newly added inittab line, inittab needs to be reloaded with cmd:

# init q

I've also red, some other methods suggested to run programs on a periodic seconds basis using just cron, what I found in stackoverflow.com's  as a thread proposed as a solution is:

* * * * * /foo/bar/your_script
* * * * * sleep 15; /foo/bar/your_script
* * * * * sleep 30; /foo/bar/your_script
* * * * * sleep 45; /foo/bar/your_script

One guy, even suggested a shorted way with cron:

0/15 * * * * * /path/to/my/script