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

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1 Fix MySQL ibdata file size - ibdata1 file growing too large, preventing ibdata1 from eating all your server disk space Author : admin 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. The ibdata1 file, taking up hundreds of gigabytes is likely to be encountered on virtually all Linux distributions which run default MySQL server 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: 1 / 7

2 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 InnoDB 5 MEMORY 584 MyISAM 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 2 / 7

3 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): 3 / 7

4 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 password: mysql> SHOW DATABASES; DROP DATABASE blog; DROP DATABASE sessions; DROP DATABASE wordpress; DROP DATABASE micropcfreak; DROP DATABASE statusnet; 4 / 7

5 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. 5 / 7

6 7. Re-Import previously dumped SQL databases with mysql cli client server:~# cd /root/ 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: 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: SHOW DATABASES; Next lets see what is currently the size of ibdata1, ib_logfile0 and ib_logfile1 6 / 7

7 Powered by TCPDF ( 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! :) 7 / 7