check_mysql has determined that there are corrupted database tables

[calamus]

I recive form cPanel this email and round cube does't work

cPanel & WHM has determined that the following database tables are corrupt:

Database   Error
mysql   mysql.gtid_slave_pos
Error  : Table 'mysql.gtid_slave_pos' doesn't exist in engine
mysql.innodb_index_stats
Error  : Table 'mysql.innodb_index_stats' doesn't exist in engine
mysql.innodb_table_stats
Error  : Table 'mysql.innodb_table_stats' doesn't exist in engine
mysql.slave_master_info
Error  : Table 'mysql.slave_master_info' doesn't exist in engine
mysql.slave_relay_log_info
Error  : Table 'mysql.slave_relay_log_info' doesn't exist in engine
mysql.slave_worker_info
Error  : Table 'mysql.slave_worker_info' doesn't exist in engine
roundcube   roundcube.cache
Error  : Table 'roundcube.cache' doesn't exist in engine
roundcube.cache_index
Error  : Table 'roundcube.cache_index' doesn't exist in engine
roundcube.cache_messages
Error  : Table 'roundcube.cache_messages' doesn't exist in engine
roundcube.cache_shared
Error  : Table 'roundcube.cache_shared' doesn't exist in engine
roundcube.cache_thread
Error  : Table 'roundcube.cache_thread' doesn't exist in engine
roundcube.contactgroupmembers
Error  : Table 'roundcube.contactgroupmembers' doesn't exist in engine
roundcube.contactgroups
Error  : Table 'roundcube.contactgroups' doesn't exist in engine
roundcube.contacts
Error  : Table 'roundcube.contacts' doesn't exist in engine
roundcube.dictionary
Error  : Table 'roundcube.dictionary' doesn't exist in engine
roundcube.identities
Error  : Table 'roundcube.identities' doesn't exist in engine
roundcube.searches
Error  : Table 'roundcube.searches' doesn't exist in engine
roundcube.session
Error  : Table 'roundcube.session' doesn't exist in engine
roundcube.system
Error  : Table 'roundcube.system' doesn't exist in engine
roundcube.users
Error  : Table 'roundcube.users' doesn't exist in engine
horde   horde.content_schema_info
Error  : Table 'horde.content_schema_info' doesn't exist in engine
horde.horde_alarm_schema_info
Error  : Table 'horde.horde_alarm_schema_info' doesn't exist in engine
horde.horde_auth_schema_info
Error  : Table 'horde.horde_auth_schema_info' doesn't exist in engine
horde.horde_cache_schema_info
Error  : Table 'horde.horde_cache_schema_info' doesn't exist in engine
horde.horde_core_schema_info
Error  : Table 'horde.horde_core_schema_info' doesn't exist in engine
horde.horde_dav_collections
Error  : Table 'horde.horde_dav_collections' doesn't exist in engine
horde.horde_dav_objects
Error  : Table 'horde.horde_dav_objects' doesn't exist in engine
horde.horde_dav_schema_info
Error  : Table 'horde.horde_dav_schema_info' doesn't exist in engine
horde.horde_group_schema_info
Error  : Table 'horde.horde_group_schema_info' doesn't exist in engine
horde.horde_histories_modseq
Error  : Table 'horde.horde_histories_modseq' doesn't exist in engine
horde.horde_history_schema_info
Error  : Table 'horde.horde_history_schema_info' doesn't exist in engine
horde.horde_imap_client_data
Error  : Table 'horde.horde_imap_client_data' doesn't exist in engine
horde.horde_imap_client_message
Error  : Table 'horde.horde_imap_client_message' doesn't exist in engine
horde.horde_imap_client_metadata
Error  : Table 'horde.horde_imap_client_metadata' doesn't exist in engine
horde.horde_imap_client_schema_info
Error  : Table 'horde.horde_imap_client_schema_info' doesn't exist in engine
horde.horde_lock_schema_info
Error  : Table 'horde.horde_lock_schema_info' doesn't exist in engine
horde.horde_muvfs
Error  : Table 'horde.horde_muvfs' doesn't exist in engine
horde.horde_perms_schema_info
Error  : Table 'horde.horde_perms_schema_info' doesn't exist in engine
horde.horde_prefs_schema_info
Error  : Table 'horde.horde_prefs_schema_info' doesn't exist in engine
horde.horde_queue_schema_info
Error  : Table 'horde.horde_queue_schema_info' doesn't exist in engine
horde.horde_queue_tasks
Error  : Table 'horde.horde_queue_tasks' doesn't exist in engine
horde.horde_sessionhandler
Error  : Table 'horde.horde_sessionhandler' doesn't exist in engine
horde.horde_sessionhandler_schema_info
Error  : Table 'horde.horde_sessionhandler_schema_info' doesn't exist in engine
horde.horde_syncml_schema_info
Error  : Table 'horde.horde_syncml_schema_info' doesn't exist in engine
horde.horde_token_schema_info
Error  : Table 'horde.horde_token_schema_info' doesn't exist in engine
horde.horde_vfs_schema_info
Error  : Table 'horde.horde_vfs_schema_info' doesn't exist in engine
horde.imp_schema_info
Error  : Table 'horde.imp_schema_info' doesn't exist in engine
horde.ingo_schema_info
Error  : Table 'horde.ingo_schema_info' doesn't exist in engine
horde.ingo_sharesng
Error  : Table 'horde.ingo_sharesng' doesn't exist in engine
horde.ingo_sharesng_groups
Error  : Table 'horde.ingo_sharesng_groups' doesn't exist in engine
horde.ingo_sharesng_users
Error  : Table 'horde.ingo_sharesng_users' doesn't exist in engine
horde.kronolith_events_geo
Error  : Table 'horde.kronolith_events_geo' doesn't exist in engine
horde.kronolith_events_mysqlgeo
Error  : Table 'horde.kronolith_events_mysqlgeo' doesn't exist in engine
horde.kronolith_resources
Error  : Table 'horde.kronolith_resources' doesn't exist in engine
horde.kronolith_schema_info
Error  : Table 'horde.kronolith_schema_info' doesn't exist in engine
horde.kronolith_sharesng
Error  : Table 'horde.kronolith_sharesng' doesn't exist in engine
horde.kronolith_sharesng_groups
Error  : Table 'horde.kronolith_sharesng_groups' doesn't exist in engine
horde.kronolith_sharesng_users
Error  : Table 'horde.kronolith_sharesng_users' doesn't exist in engine
horde.mnemo_schema_info
Error  : Table 'horde.mnemo_schema_info' doesn't exist in engine
horde.mnemo_sharesng
Error  : Table 'horde.mnemo_sharesng' doesn't exist in engine
horde.mnemo_sharesng_groups
Error  : Table 'horde.mnemo_sharesng_groups' doesn't exist in engine
horde.mnemo_sharesng_users
Error  : Table 'horde.mnemo_sharesng_users' doesn't exist in engine
horde.nag_schema_info
Error  : Table 'horde.nag_schema_info' doesn't exist in engine
horde.nag_sharesng
Error  : Table 'horde.nag_sharesng' doesn't exist in engine
horde.nag_sharesng_groups
Error  : Table 'horde.nag_sharesng_groups' doesn't exist in engine
horde.nag_sharesng_users
Error  : Table 'horde.nag_sharesng_users' doesn't exist in engine
horde.rampage_objects
Error  : Table 'horde.rampage_objects' doesn't exist in engine
horde.rampage_tag_stats
Error  : Table 'horde.rampage_tag_stats' doesn't exist in engine
horde.rampage_tagged
Error  : Table 'horde.rampage_tagged' doesn't exist in engine
horde.rampage_tags
Error  : Table 'horde.rampage_tags' doesn't exist in engine
horde.rampage_types
Error  : Table 'horde.rampage_types' doesn't exist in engine
horde.rampage_user_tag_stats
Error  : Table 'horde.rampage_user_tag_stats' doesn't exist in engine
horde.rampage_users
Error  : Table 'horde.rampage_users' doesn't exist in engine
horde.trean_bookmarks
Error  : Table 'horde.trean_bookmarks' doesn't exist in engine
horde.trean_schema_info
Error  : Table 'horde.trean_schema_info' doesn't exist in engine
horde.turba_schema_info
Error  : Table 'horde.turba_schema_info' doesn't exist in engine
horde.turba_sharesng
Error  : Table 'horde.turba_sharesng' doesn't exist in engine
horde.turba_sharesng_groups
Error  : Table 'horde.turba_sharesng_groups' doesn't exist in engine
horde.turba_sharesng_users
Error  : Table 'horde.turba_sharesng_users' doesn't exist in engine
munin_innodb   munin_innodb.sample_table
Error  : Table 'munin_innodb.sample_table' doesn't exist in engine
We recommend that you repair these tables with WHM’s Repair a MySQL/MariaDB Database interface at: example.com:2087/scripts/repairmysqllist If the repair fails, contact cPanel Support for further assistance.

Try repair the table but this is the output:

Repairing roundcube
roundcube.cache
Error    : Table 'roundcube.cache' doesn't exist in engine
status   : Operation failed
roundcube.cache_index
Error    : Table 'roundcube.cache_index' doesn't exist in engine
status   : Operation failed
roundcube.cache_messages
Error    : Table 'roundcube.cache_messages' doesn't exist in engine
status   : Operation failed
roundcube.cache_shared
Error    : Table 'roundcube.cache_shared' doesn't exist in engine
status   : Operation failed
roundcube.cache_thread
Error    : Table 'roundcube.cache_thread' doesn't exist in engine
status   : Operation failed
roundcube.contactgroupmembers
Error    : Table 'roundcube.contactgroupmembers' doesn't exist in engine
status   : Operation failed
roundcube.contactgroups
Error    : Table 'roundcube.contactgroups' doesn't exist in engine
status   : Operation failed
roundcube.contacts
Error    : Table 'roundcube.contacts' doesn't exist in engine
status   : Operation failed
roundcube.cp_schema_version                        OK
roundcube.dictionary
Error    : Table 'roundcube.dictionary' doesn't exist in engine
status   : Operation failed
roundcube.identities
Error    : Table 'roundcube.identities' doesn't exist in engine
status   : Operation failed
roundcube.searches
Error    : Table 'roundcube.searches' doesn't exist in engine
status   : Operation failed
roundcube.session
Error    : Table 'roundcube.session' doesn't exist in engine
status   : Operation failed
roundcube.system
Error    : Table 'roundcube.system' doesn't exist in engine
status   : Operation failed
roundcube.users
Error    : Table 'roundcube.users' doesn't exist in engine
status   : Operation failed

Done.

Please help
Thanks
Piero

Solved for roudcube, horde and munin table width this guide:
blog.triantech.com/tag/check_mysql-has-determined-that-there-are-corrupted-database-tables/

mysql table still corrupted

 

[cPanelMichael]

Hello

Could you let us know the contents of your /etc/my.cnf file?

Thank you.

 

[calamus]

[mysqld]
max_allowed_packet=268435456
open_files_limit=10000

default-storage-engine=MyISAM
innodb_file_per_table=1

default configuration

 

[calamus]

still corrupted mysql table
this is the report sent via email from cpanel


cPanel & WHM has determined that the following database tables are corrupt:

Database Error
mysql mysql.gtid_slave_pos
Error : Table 'mysql.gtid_slave_pos' doesn't exist in engine
mysql.innodb_index_stats
Error : Table 'mysql.innodb_index_stats' doesn't exist in engine
mysql.innodb_table_stats
Error : Table 'mysql.innodb_table_stats' doesn't exist in engine
mysql.slave_master_info
Error : Table 'mysql.slave_master_info' doesn't exist in engine
mysql.slave_relay_log_info
Error : Table 'mysql.slave_relay_log_info' doesn't exist in engine
mysql.slave_worker_info
Error : Table 'mysql.slave_worker_info' doesn't exist in engine

 

[cPanelMichael]

Yes, you will continue to receive that email until the "mysql" database is repaired. Could you let us know of any error messages logged to /var/lib/mysql/$hostname.err when restarting MySQL? Also, have you recently upgraded to MariaDB? Does the "mysql_upgrade" command succeed?

Thank you.

 

[calamus]

Yes, I upgrade to MariaDB afther the problem.

below the log of error file

160413 08:39:17 mysqld_safe mysqld from pid file /var/lib/mysql/srv10.example.com.pid ended
160413 08:39:18 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
2016-04-13  8:39:18 139668595525664 [Note] /usr/sbin/mysqld (mysqld 10.1.13-MariaDB) starting as process 14176 ...
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Using mutexes to ref count buffer pool pages
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: The InnoDB memory heap is disabled
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Memory barrier is not used
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Compressed tables use zlib 1.2.3
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Using Linux native AIO
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Using generic crc32 instructions
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Completed initialization of buffer pool
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Highest supported file format is Barracuda.
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: 128 rollback segment(s) are active.
2016-04-13  8:39:19 139668595525664 [Note] InnoDB: Waiting for purge to start
2016-04-13  8:39:19 139668595525664 [Note] InnoDB:  Percona XtraDB (Experts in Database Performance Management) 5.6.28-76.1 started; log sequence number 42838$
2016-04-13  8:39:19 139668595525664 [Note] Plugin 'FEEDBACK' is disabled.
2016-04-13  8:39:19 139667861141248 [Note] InnoDB: Dumping buffer pool(s) not yet started
2016-04-13  8:39:19 139668595525664 [Note] Server socket created on IP: '::'.
2016-04-13  8:39:19 139668594559744 [Warning] InnoDB: Cannot open table mysql/gtid_slave_pos from the internal data dictionary of InnoDB t$
2016-04-13  8:39:19 139668594559744 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1932: Table 'mysql.g$
2016-04-13  8:39:19 139668595525664 [Note] /usr/sbin/mysqld: ready for connections.
Version: '10.1.13-MariaDB'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MariaDB Server

 

[calamus]

and this is the prompt of mysql restart:

Service Status
   mysql (/usr/sbin/mysqld --basedir=/usr --datadir=/var/lib/mysql --plugin-dir=/usr/lib64/mysql/plugin --user=mysql --log-error=/var/lib/mysql/srv10.example.com.err --open-files-limit=10000 --pid-file=/var/lib/mysql/srv10.example.com.pid) is running as mysql with PID 14176 (pidfile check method).

Startup Log
   Starting MySQL.. SUCCESS!

Log Messages
   2016-04-13  8:39:19 139668595525664 [Note] /usr/sbin/mysqld: ready for connections.
   160413 08:39:18 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
   160413 08:39:17 mysqld_safe mysqld from pid file /var/lib/mysql/srv10.example.com.pid ended

 

[cPanelMichael]

2016-04-13 8:39:19 139668594559744 [Warning] InnoDB: Cannot open table mysql/gtid_slave_pos from the internal data dictionary of InnoDB t$

The following thread is offered for users with InnoDB corruption:

InnoDB Corruption Repair Guide

Please review this thread to determine if any of the steps offered are helpful.

Thank you.