Issue Cannot login, mysqld won't start

[maniot]

hello,

Without interfering on the server, i find myself with a server that doesn't respond any more. Cannot login to Plesk, i get this error:
ERROR: Zend_Db_Adapter_Exception: SQLSTATE[HY000] [2002] No such file or directory
When i try to start mysqld i'm getting this error: MySQl Daemon failed to start.
Mysqld.log looks like:

2017-04-21T10:18:44.612799Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-04-21T10:18:44.616117Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.17) starting as process 1061 ...
2017-04-21T10:18:44.622210Z 0 [Warning] option 'innodb-buffer-pool-size': signed value 2097152 adjusted to 5242880
2017-04-21T10:18:44.622971Z 0 [Note] InnoDB: PUNCH HOLE support available
2017-04-21T10:18:44.622992Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-04-21T10:18:44.623002Z 0 [Note] InnoDB: Uses event mutexes
2017-04-21T10:18:44.623010Z 0 [Note] InnoDB: GCC builtin __sync_synchronize() is used for memory barrier
2017-04-21T10:18:44.623017Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-04-21T10:18:44.623032Z 0 [Note] InnoDB: Using Linux native AIO
2017-04-21T10:18:44.623496Z 0 [Note] InnoDB: Number of pools: 1
2017-04-21T10:18:44.623695Z 0 [Note] InnoDB: Not using CPU crc32 instructions
2017-04-21T10:18:44.626252Z 0 [Note] InnoDB: Initializing buffer pool, total size = 5M, instances = 1, chunk size = 5M
2017-04-21T10:18:44.627490Z 0 [Note] InnoDB: Completed initialization of buffer pool
2017-04-21T10:18:44.628420Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2017-04-21T10:18:44.642537Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2017-04-21T10:18:44.642774Z 0 [Note] InnoDB: The user has set SRV_FORCE_NO_LOG_REDO on, skipping log redo
2017-04-21T10:18:44.643684Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2017-04-21T10:18:44.643769Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2017-04-21T10:18:44.695509Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2017-04-21T10:18:44.699216Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2017-04-21T10:18:44.699256Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2017-04-21T10:18:44.701659Z 0 [Note] InnoDB: 5.7.17 started; log sequence number 0
2017-04-21T10:18:44.701704Z 0 [Note] InnoDB: !!! innodb_force_recovery is set to 6 !!!
2017-04-21T10:18:44.702173Z 0 [Note] Plugin 'FEDERATED' is disabled.
2017-04-21T10:18:44.714659Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2017-04-21T10:18:44.716740Z 0 [Note] InnoDB: Buffer pool(s) load completed at 170421 12:18:44
2017-04-21T10:18:44.718875Z 0 [Warning] System table 'plugin' is expected to be transactional.
2017-04-21T10:18:44.720330Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2017-04-21T10:18:44.720607Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2017-04-21T10:18:44.721181Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2017-04-21T10:18:44.721349Z 0 [Note] IPv6 is available.
2017-04-21T10:18:44.721392Z 0 [Note]   - '::' resolves to '::';
2017-04-21T10:18:44.721467Z 0 [Note] Server socket created on IP: '::'.
2017-04-21T10:18:44.727218Z 0 [Warning] Failed to open optimizer cost constant tables

2017-04-21T10:18:44.728457Z 0 [ERROR] Fatal error: mysql.user table is damaged. Please run mysql_upgrade.
2017-04-21T10:18:44.728676Z 0 [ERROR] Aborting

I've tried to find a solution but everything i tried failed. The only thing i received was an email that states that there was an error updating the key for Plesk.
Best regards,
Niek

 

[Bitpalast]

Your MySQL installation is corrupt. You can try to fix it with mysql_upgrade, but not very likely to succeed. You can try "plesk repair installation", too, but as this is MySQL 5.7 and a database issue, not a Plesk issue, I doubt that will fix it. Maybe leave this to Plesk support? Not sure however, whether they will do it, because it's not really a Plesk thing.

 

[maniot]

Hi Peter,
I imagined already that this has something to do with a corrupt MySQL. I already tried mysql_upgrade but this gives me the same 2002 error.
As i'm a beginner i need all the help i get to get the server going again.
regards,
Niek

 

[Bitpalast]

Have you considered to file a case with Plesk support?

 

[maniot]

Hi Peter,
I don't know if Plesk support will take the case as my plesk version is provided with my hosting account. I think i remember i filed some years ago a case which was refused for that reason. I should turn to my hosting provider, which however is not very cooperative to help.
I also tried your suggestion with the plesk repair utility, but this gives the same mysqld error
Thanks for time.
Regards,
Niek

 

[maniot]

I still cannot acces Plesk, neither i can get to work Mysql due to an error in the database. So i went looking to see whether i could restore a backup of the psa database. I found that the database back ups are in /var/lib/psa/dumps . I saw that there were only small back ups after 19 February. (the date i upgraded from 12.5 to Onyx. would it be possible to use a back-up to restore Plesk?

 

[Pankaj K]

another way to recover from this thing is stop mysql on your current server and then copy the mysql directory to another server where same mysql version is installed. Then try to start the mysql on another test server with your existing mysql directory there you can take dumps of all your databases to take backup of the databases