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
SELECTstatement: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.
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 documentation.
Note: for Windows, see the following article: How to fix InnoDB corruption cases for the MySQL databases on Plesk for Windows?
There are several ways to recover a failed MySQL database:
Firstly, connect to the server using SSH.
-
Stop the affected MySQL service:
# service mysql stop
-
Back up all the MySQL data storage files. By default, they are located in
/var/lib/mysql/For example:
# mkdir /root/mysql_backup
# cp -a /var/lib/mysql/* /root/mysql_backup/ -
Set the
innodb_force_recoveryvalue under the[mysqld]section in the MySQL configuration file. This option will allow you to start MySQL service and create all databases dump.For example:
# vi /etc/my.cnf
[mysqld]
innodb_force_recovery = 2 -
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If the service fails to start, set the parameter
innodb_force_recoveryto greater value and try starting MySQL again.
Value of the parameterinnodb_force_recoverycan be from 1 to 6.Warning: Only set
innodb_force_recoveryto a value greater than 0 in an emergency situation, so that you can start InnoDB and dump your tables. Values of 4 or greater can permanently corrupt data files. Therefore, increase this value incrementally, as necessary. Please see more details in the official MySQL Documentation. -
If the service fails to start with an error like:
CONFIG_TEXT: InnoDB: Waiting for the background threads to start
Add directive
innodb_purge_threadsaccording to the following article: Unable to start MySQL service: InnoDB: Waiting for the background threads to start -
If the service continues failing to start, jump directly to the 3rd Section of this article: Restore from a backup
-
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Try to dump 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 the dump fails with an error like:
CONFIG_TEXT: Incorrect information in file: './psa/APSApplicationItems.frm' when using LOCK TABLES"`
then increase
innodb_force_recoveryvalue, 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 unable to dump the databases, then try using method II (Copy table content) or III (Restore from the backup) which are described below. -
Remove all the MySQL data storage files except the
mysqlfolder. For example:# rm -rf `ls -d /var/lib/mysql/* | grep -v "/var/lib/mysql/mysql"`
-
Remove the
innodb_force_recoveryoption from the MySQL configuration file. -
Restart the MySQL service:
# service mysqld restart
-
Check the MySQL log file for any errors.
-
Restore databases from the dumps made on the 5th step. 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 instructions above did not help, the only remaining method is to restore the databases from backups. Do not forget to remove the innodb_force_recovery option from the MySQL configuration file before restore.
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To restore Plesk-related databases (psa, apsc, horde) see How to backup/restore a Plesk database dump article. For example:
# ls -tl /var/lib/psa/dumps
-rw------- 1 root root 141960 Aug 8 01:03 mysql.daily.dump.0.gz
-rw------- 1 root root 141925 Aug 7 01:03 mysql.daily.dump.1.gz
# zcat /var/lib/psa/dumps/mysql.daily.dump.0.gz | MYSQL_PWD=`cat /etc/psa/.psa.shadow` mysql -u admin psa -
To restore customer's databases from Plesk backup see the Restoring Data from Backup Archives section in the Administrator's Guide.
Note: If timeouts are encountered when restoring databases, set the
wait_timeoutvalue in the MySQL configuration file and restart the MySQL service. For example:# vi /etc/my.cnf
[mysqld]
wait_timeout = 1800
Comments
9 comments
Hi:
What information must content the file /root/db_list.txt ?
Regards
@Pedro Telmo,
Hi! After executing the following command:
it should contain the names of all databases that are stored on MySQL server.
Yes Artyom.
Alisa Kasyanova add this line after my comment :)
Thanks
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.'
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...
@Mskumar Blaze
Hello!
I would suggest contacting MySQL Technical Support regarding this issue as they are experts in their product.
Thanks Leonid!
This article was a lifesaver. Worked great and the problem was fixed.
Me funcionó correctamente, gracias !!!
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.
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