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How to fix InnoDB corruption cases for the MySQL databases on Plesk for Linux?

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Taras Ermoshin
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Plesk for Linux FR:PPM-2077 kb: how-to ABT: Group A

Applicable to:

  • Plesk for Linux

Symptoms

  • The following error is shown in Plesk:

    PLESK_INFO: ERROR: PleskMainDBException
    MySQL query failed: Incorrect information in file: './psa/misc.frm'

    PLESK_INFO: ERROR: PleskDBException: Unable to connect to database: mysql_connect(): No such file or directory /var/run/mysqld/mysqld.sock (Error code: 2002). Please check that database server is started and accessible. (Abstract.php:69)

    PLESK_INFO: ERROR: Zend_Db_Adapter_Exception: SQLSTATE[HY000] [2002] No such file or directory

    PLESK_INFO: ERROR: Zend_Db_Adapter_Exception: SQLSTATE[HY000] [2002] Connection refused:
    0: /usr/local/psa/admin/externals/Zend/Db/Adapter/Pdo/Abstract.php:144

  • Domain overview page on Domains > example.com is not accessible:

    CONFIG_TEXT: 500 Server Error
    Type SB_Facade_Exception_Generic
    Message
    File generic.php
    Line 33

  • Opening WordPress Toolkit results in the following error:

    PLESK_INFO: Server Error 500 Zend_Db_Adapter_Exception
    Type Zend_Db_Adapter_Exception
    Message SQLSTATE[HY000] [2002]
    No such file or directory
    File Abstract.php Line 144

  • Plesk upgrade fails with the following error:

    PLESK_INFO: DATABASE ERROR!!!
    Database psa database found, but version undefined

  • A table cannot be properly queried with the SELECT statement:

    MYSQL_LIN: select * from db_example.misc;
    ERROR 1033 (HY000): Incorrect information in file: './db_example/misc.frm'

  • The following information can be found in the MySQL log file /var/log/mysql/error.log, /var/log/mysqld.log, or /var/log/mariadb/mariadb.log:

    CONFIG_TEXT: 150704 19:09:27 InnoDB: Waiting for the background threads to start
    150704 19:09:28 InnoDB: Error: tablespace size stored in header is 3712 pages, but
    150704 19:09:28 InnoDB: the sum of data file sizes is only 3072 pages
    150704 19:09:28 InnoDB: Cannot start InnoDB. The tail of the system tablespace is
    150704 19:09:28 InnoDB: missing. Have you edited innodb_data_file_path in my.cnf in an
    150704 19:09:28 InnoDB: inappropriate way, removing ibdata files from there?
    150704 19:09:28 InnoDB: You can set innodb_force_recovery=1 in my.cnf to force
    150704 19:09:28 InnoDB: a startup if you are trying to recover a badly corrupt database.

    CONFIG_TEXT: InnoDB: Assertion failure in thread 3876 in file ha_innodb.cc line 17352
    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/5.6/en/forcing-innodb-recovery.html
    InnoDB: about forcing recovery.

    CONFIG_TEXT: InnoDB: Assertion failure in thread 140154354255616 in file trx0purge.c line 848
    InnoDB: Failing assertion: purge_sys->purge_trx_no <= purge_sys->rseg->last_trx_no
    InnoDB: We intentionally generate a memory trap.

    CONFIG_TEXT: InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery

    CONFIG_TEXT: [ERROR] InnoDB: Attempted to open a previously opened tablespace. Previous tablespace database/table uses space ID: 882 at filepath

    CONFIG_TEXT: [Note] InnoDB: Starting crash recovery.
    [ERROR] InnoDB: Tablespace 11904 was not found at ./example_db/example1.ibd.
    [ERROR] InnoDB: Set innodb_force_recovery=1 to ignore this and to permanently lose all changes to the tablespace.
    [ERROR] InnoDB: Tablespace 11905 was not found at ./example_db/example2.ibd.
    [ERROR] InnoDB: Cannot continue operation.

    CONFIG_TEXT: InnoDB: Database page corruption on disk or a failed file read of page 660. A table cannot be properly queried with the SELECT statement - additional possible output: MariaDB [psa]> select * from db_example.misc;
    ERROR 2006 (HY000): MySQL server has gone away No connection. Trying to reconnect...

    CONFIG_TEXT: [ERROR] InnoDB: Missing MLOG_CHECKPOINT at 4083146667 between the checkpoint 4083146667 and the end 4083146240.
    [ERROR] InnoDB: Plugin initialization aborted with error Generic error
    [Note] InnoDB: Starting shutdown...
    [ERROR] Plugin 'InnoDB' init function returned error.
    [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.

    CONFIG_TEXT: [Note] InnoDB: Starting crash recovery from checkpoint LSN=353990497915
    [Warning] InnoDB: Ignoring a doublewrite copy of page [page id: space=0, page number=9679] with future log sequence

Cause

InnoDB corruption.

Most InnoDB corruptions are hardware-related. Corrupted page writes can be caused by power failures or bad memory. The issue also can be caused by using network-attached storage (NAS) and allocating InnoDB databases on it.

Resolution

Note: Since the MySQL service's control, logs and configuration file's location is different on the different operating systems, this article provides general command examples only. Check the following article for additional information regarding MySQL on different operating systems
[Linux] Local MySQL server for all databases
For additional information, check your operating system and MySQL/MariaDB documentation.

Note: for Plesk on Windows, see the following article: How to fix InnoDB corruption cases for the MySQL databases on Plesk for Windows?

  1. Connect to the server using SSH.

  2. Stop the affected MySQL service and the service plesk-web-socket to prevent it from attempting to start MySQL:

    # service mysql stop || service mariadb stop && service plesk-web-socket stop

  3. Back up all the MySQL data storage files. By default, they are located in the directory /var/lib/mysql/.

    For example:

    # cp -a /var/lib/mysql /root/mysql_backup

  4. Add the parameter innodb_force_recovery to the section [mysqld] of the MySQL configuration file. This option allows starting MySQL service in the recovery mode and try creating dumps of databases.

    For example:

    # vi /etc/my.cnf
    [mysqld]
    innodb_force_recovery = 2

  5. Start the MySQL service.

    • If the service fails to start, set the value of the parameter innodb_force_recovery to a greater value and try starting MySQL again.
      Value of the parameter innodb_force_recovery can be from 1 to 6.

      Warning: Only set innodb_force_recovery to a value greater than 0 in an emergency situation, so that you can start InnoDB and dump databases. Values of 4 or greater can permanently corrupt data files. Therefore, increase this value incrementally, as necessary. See more details in the official MySQL Documentation.

    • If the service fails to start with an error like:

      InnoDB: Waiting for the background threads to start

      Then add the parameter innodb_purge_threads as described in the following article: Unable to start MySQL service: InnoDB: Waiting for the background threads to start.

    • If the service fails to start even with innodb_force_recovery set to the highest possible value of 6, restore the databases from backups/dumps using steps from the below section Restore databases from backups and do not apply steps 6-8.

    Restore databases from backups

    1. Check which engine (MyISAM or InnoDB) is used by the database mysql and proceed based on the output of this command:

      # ls -l /var/lib/mysql/mysql/*.ibd

      • If the output is empty (MyISAM engine is used):

        1.1.1. Remove all the MySQL data storage files except the mysql folder. For example:

        # rm -rf `ls -d /var/lib/mysql/* | grep -v "/var/lib/mysql/mysql"`

        1.1.2. Remove the option innodb_force_recovery from the MySQL configuration file.

        1.1.3. Restart the MySQL service:

        # service mysqld restart

      • If the output is not empty and contains .ibd files (InnoDB engine is used):

        ​1.2.1. Remove all files and directories from the MySQL data directory. For example:

        # rm -rf /var/lib/mysql/*

        1.2.2. Remove the option innodb_force_recovery from the MySQL configuration file.

        1.2.3. Create an empty mysql database using ONE of the below commands:

        # mysql_install_db --force

        # mysqld --initialize

        # mysql_secure_installation

        Note: the exact command depends on the installed MySQL/MariaDB version, check MySQL/MariaDB documentation for information on this.

        1.2.4. Set correct ownership for the MySQL data directory:

        # chown -R mysql:mysql /var/lib/mysql

        1.2.5. Add the parameter skip-grant-tables to the MySQL configuration file and restart MySQL to apply the change:

        # service mysqld restart

    2. Restore the database mysql and Plesk system databases (psa, apsc, roundcubemail, horde, phpmyadmin) from a daily/pre-upgrade dump.

    3. Remove the parameter skip-grant-tables from the MySQL configuration file (if it was added in step 1.2.5) and restart MySQL to apply the change:

      # service mysqld restart

    4. Restore websites' databases from a Plesk backup (instructions can be found either in the documentation or in the knowledge base article) or from manually created dumps.

      Note: If timeouts are encountered when restoring databases, set the wait_timeout value in the MySQL configuration file and restart the MySQL service. For example:

      # vi /etc/my.cnf
      ​[mysqld]
      ​wait_timeout = 1800

  6. Try dumping all databases:

    # MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql -Ns -uadmin psa -Ne"show databases" | grep -v information_schema | grep -v performance_schema > /root/db_list.txt
    # mkdir /root/db_backup/
    # cat /root/db_list.txt | while read i; do MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysqldump -uadmin "$i" --routines --databases > /root/db_backup/"$i".sql; echo $i; sleep 5; done

    • If dumping fails with an error like:

      Incorrect information in file: './psa/APSApplicationItems.frm' when using LOCK TABLES"

      then increase the value of innodb_force_recovery, restart MySQL service, and try to dump the databases again. It is better to dump databases one by one, separately. In that case, there is no need to go through restore of all databases once again if restore failed for some reason.
      If creating a dump of some or all databases fails, then the only remaining method is to restore databases as described in the section Restore databases from backups in step 5, do not apply steps 7-8 in this case.

  7. Check which engine (MyISAM or InnoDB) is used by the database mysql and proceed based on the output of this command:

    # ls -l /var/lib/mysql/mysql/*.ibd

    If the output is empty (MyISAM engine is used)

    7.1. Remove all the MySQL data storage files except the mysql folder. For example:

    # rm -rf `ls -d /var/lib/mysql/* | grep -v "/var/lib/mysql/mysql"`

    7.2. Remove the option innodb_force_recovery from the MySQL configuration file.

    7.3. Restart the MySQL service:

    # service mysqld restart

    7.4. Check the MySQL log file for any errors.

    7.5. Restore databases from the dumps made in step 6. For example:

    # for db in `cat /root/db_list.txt`; do echo -e "Importing $db..."; MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql -uadmin < /root/db_backup/$db.sql; done

    If the output is not empty and contains .ibd files (InnoDB engine is used)

    7.1. Remove all files and directories from the MySQL data directory. For example:

    # rm -rf /var/lib/mysql/*

    7.2. Remove the option innodb_force_recovery from the MySQL configuration file.

    7.3. Create an empty mysql database using ONE of the below commands:

    # mysql_install_db --force

    # mysqld --initialize

    # mysql_secure_installation

    Note: the exact command depends on the installed MySQL/MariaDB version, check MySQL/MariaDB documentation for information on this.

    7.4. Set correct ownership for the MySQL data directory:

    # chown -R mysql:mysql /var/lib/mysql

    7.5. Add the parameter skip-grant-tables to the MySQL configuration file and restart MySQL to apply the change:

    # service mysqld restart

    7.6. Restore databases from the dumps made in step 6. For example:

    # for db in `cat /root/db_list.txt`; do echo -e "Importing $db..."; MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql -uadmin < /root/db_backup/$db.sql; done

    7.7. Remove the parameter skip-grant-tables from the MySQL configuration file and restart MySQL to apply the change:

    # service mysqld restart

  8. Start the service plesk-web-socket:

    # service plesk-web-socket start

Comments

12 comments

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  • Avatar
    Pedro Telmo

    Hi:

    What information must content the file /root/db_list.txt ?

    Regards

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  • Avatar
    Artyom Baranov

    @Pedro Telmo,

    Hi! After executing the following command:

    # mysql -Ns -uadmin -p`cat /etc/psa/.psa.shadow` -e"SHOW DATABASES" > db_list.txt

    it should contain the names of all databases that are stored on MySQL server.

    -1
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  • Avatar
    Pedro Telmo (Edited )

    Yes Artyom.

    Alisa Kasyanova add this line after my comment :)

    Thanks

    0
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  • Avatar
    Mskumar Blaze

    2018-02-21T14:59:14.908905Z 12 [ERROR] Plugin group_replication reported: 'Fatal error during the Recovery process of Group Replication. The server will leave the group.'

    0
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  • Avatar
    Mskumar Blaze

    I have some doubt I have configured innodb cluster (3 cluster) after I created I’ll be going to stop group replication in (cluster2) then I had to rejoin cluster2 after I rejoined cluster2 status as recovering after some times it’s going to show missing. My cluster1-(primary) log status Warning] Plugin group_replication reported: 'Members removed from the group: 608781bce352:3306'
    2018-02-21T14:59:16.115814Z 0 [Note] Plugin group_replication reported: 'Group membership changed to d5e07af19ef5:3306, 812606eb6abb:3306 on view 15191888786747824:12.'
    2018-02-21T15:00:13.434470Z 148 [Note] Aborted connection 148 to db: 'unconnected' user: 'mysql_innodb_cluster_r1721619408' host: 'cluster2.willing' (failed on flush_net())
    2018-02-21T15:16:48.046190Z 141 [Note] Aborted connection 141 to db: 'unconnected' user: 'root' host: 'd5e07af19ef5' (Got an error reading communication packets)

    My cluster2 log status Warning] Plugin group_replication reported: 'Members removed from the group: 608781bce352:3306'
    2018-02-21T14:59:16.115814Z 0 [Note] Plugin group_replication reported: 'Group membership changed to d5e07af19ef5:3306, 812606eb6abb:3306 on view 15191888786747824:12.'
    2018-02-21T15:00:13.434470Z 148 [Note] Aborted connection 148 to db: 'unconnected' user: 'mysql_innodb_cluster_r1721619408' host: 'cluster2.willing' (failed on flush_net())
    2018-02-21T15:16:48.046190Z 141 [Note] Aborted connection 141 to db: 'unconnected' user: 'root' host: 'd5e07af19ef5' (Got an error reading communication packets). I got confused kindly help me please...

    0
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  • Avatar
    Ivan Postnikov

    @Mskumar Blaze

    Hello!

    I would suggest contacting MySQL Technical Support regarding this issue as they are experts in their product.

    0
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  • Avatar
    Iman GM

    Thanks Leonid!

    This article was a lifesaver. Worked great and the problem was fixed. 

    1
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  • Avatar
    Carlos Domingo Arias González

    Me funcionó correctamente, gracias !!!

    1
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  • Avatar
    Bendert Feenstra

    Absolute lifesaver!! Had a VPS installation with multiple hosted sites that could not start the mysql service all of a sudden (or to be more precise MariaDB). Was hesitant to try this; not that I didn't trust it, just had hopes that restarting would resolve this. Very glad that after 3 hours of trying other things I followed the Force InnoDB recovery description above. All hosted sites are now up and running again as if nothing happened.

    0
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  • Avatar
    Del C (Edited )

    I would recommend changing the dump line to: 

    cat /root/db_list.txt | while read i; do MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysqldump -uadmin "$i" --routines --hex-blob --databases > /root/db_backup/"$i".sql; echo $i; sleep 5; done

    Adding --hex-blob will dump binary columns using hexadecimal notation. If you don't, then depending on your db contents, on import you will get an error similar to: Mysql ERROR at line 1153: Unknown command '\'

    1
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  • Avatar
    Taras Ermoshin

    Hi @Del C!

    Thanks for sharing, this information may be useful to other Pleskians!

    2
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  • Avatar
    Tom Robak

    step mysqld --initialize error

    any ideas what to do now?

     

    [root@s1 ~]# mysqld --initialize
    2022-07-02 11:21:29 0 [Note] libgovernor.so found
    2022-07-02 11:21:29 0 [Note] All governors functions found too
    2022-07-02 11:21:29 0 [Note] Governor connected
    2022-07-02 11:21:29 0 [Note] All governors lve functions found too
    2022-07-02 11:21:29 0 [Note] mysqld (mysqld 10.5.10-MariaDB-cll-lve) starting as process 104650 ...
    mysqld: Please consult the Knowledge Base to find out how to run mysqld as root!
    2022-07-02 11:21:29 0 [ERROR] Aborting
    0
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