Issue Upgrade broke MySQL

[John Guva]

I updated yesterday to the latest version.

All seem to have gone well, except a few minutes later I was greeted with this message when trying to login into plesk
or when navigating to a site:

Server Error
500
Zend_Db_Adapter_Exception
SQLSTATE[HY000] [2002] No such file or directory

Type Zend_Db_Adapter_Exception
Message SQLSTATE[HY000] [2002] No such file or directory
File Abstract.php
Line 144

I then noticed MySQL is dead.

mysqld dead but subsys locked

Trying to restart MySQL shows this:
service mysqld restart
Stopping mysqld: [ OK ]
MySQL Daemon failed to start.
Starting mysqld: [FAILED]

Below error log attached.
Now, I've googled my fingers open and have pretty much tried any suggestion that I could find. None have worked.
I am unable to contact Plesk support as my license has been obtained through a 3rd party reseller.
The 3rd party reseller is clueless.

I need some help please - Thanks

2018-11-29T16:05:19.037546Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-11-29T16:05:19.040005Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.24) starting as process 4826 ...
2018-11-29T16:05:19.044148Z 0 [Note] InnoDB: PUNCH HOLE support available
2018-11-29T16:05:19.044169Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-11-29T16:05:19.044176Z 0 [Note] InnoDB: Uses event mutexes
2018-11-29T16:05:19.044181Z 0 [Note] InnoDB: GCC builtin __sync_synchronize() is used for memory barrier
2018-11-29T16:05:19.044203Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2018-11-29T16:05:19.044208Z 0 [Note] InnoDB: Using Linux native AIO
2018-11-29T16:05:19.044522Z 0 [Note] InnoDB: Number of pools: 1
2018-11-29T16:05:19.044673Z 0 [Note] InnoDB: Using CPU crc32 instructions
2018-11-29T16:05:19.046680Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2018-11-29T16:05:19.057621Z 0 [Note] InnoDB: Completed initialization of buffer pool
2018-11-29T16:05:19.060360Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2018-11-29T16:05:19.072666Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2018-11-29T16:05:19.088213Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2018-11-29T16:05:19.088428Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2018-11-29T16:05:19.117282Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-11-29T16:05:19.118774Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2018-11-29T16:05:19.118785Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2018-11-29T16:05:19.119543Z 0 [Note] InnoDB: Waiting for purge to start
2018-11-29T16:05:19.169693Z 0 [Note] InnoDB: 5.7.24 started; log sequence number 1221427332
2018-11-29T16:05:19.170646Z 0 [Note] Plugin 'FEDERATED' is disabled.
2018-11-29T16:05:19.189655Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2018-11-29T16:05:19.190032Z 0 [Note] InnoDB: Buffer pool(s) load completed at 181129 18:05:19
2018-11-29T16:05:19.191071Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2018-11-29T16:05:19.191263Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2018-11-29T16:05:19.191298Z 0 [Note] IPv6 is available.
2018-11-29T16:05:19.191343Z 0 [Note]   - '::' resolves to '::';
2018-11-29T16:05:19.191363Z 0 [Note] Server socket created on IP: '::'.
2018-11-29T16:05:19.191416Z 0 [ERROR] Unix socket lock file is empty /var/lib/mysql/mysql.sock.lock.
2018-11-29T16:05:19.191423Z 0 [ERROR] Unable to setup unix socket lock file.
2018-11-29T16:05:19.191426Z 0 [ERROR] Aborting

2018-11-29T16:05:19.191434Z 0 [Note] Binlog end
2018-11-29T16:05:19.191479Z 0 [Note] Shutting down plugin 'ngram'
2018-11-29T16:05:19.191487Z 0 [Note] Shutting down plugin 'ARCHIVE'
2018-11-29T16:05:19.191490Z 0 [Note] Shutting down plugin 'partition'
2018-11-29T16:05:19.191493Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2018-11-29T16:05:19.191496Z 0 [Note] Shutting down plugin 'MyISAM'
2018-11-29T16:05:19.191506Z 0 [Note] Shutting down plugin 'CSV'
2018-11-29T16:05:19.191511Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2018-11-29T16:05:19.191514Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-11-29T16:05:19.191517Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-11-29T16:05:19.191520Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-11-29T16:05:19.191523Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-11-29T16:05:19.191526Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-11-29T16:05:19.191528Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-11-29T16:05:19.191531Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-11-29T16:05:19.191534Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-11-29T16:05:19.191537Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-11-29T16:05:19.191539Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-11-29T16:05:19.191542Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-11-29T16:05:19.191545Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-11-29T16:05:19.191548Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-11-29T16:05:19.191551Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-11-29T16:05:19.191553Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-11-29T16:05:19.191556Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2018-11-29T16:05:19.191559Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2018-11-29T16:05:19.191562Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-11-29T16:05:19.191564Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-11-29T16:05:19.191567Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-11-29T16:05:19.191570Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-11-29T16:05:19.191573Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-11-29T16:05:19.191576Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-11-29T16:05:19.191578Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-11-29T16:05:19.191581Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-11-29T16:05:19.191584Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2018-11-29T16:05:19.191587Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-11-29T16:05:19.191599Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-11-29T16:05:19.191602Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2018-11-29T16:05:19.191605Z 0 [Note] Shutting down plugin 'InnoDB'
2018-11-29T16:05:19.191689Z 0 [Note] InnoDB: FTS optimize thread exiting.
2018-11-29T16:05:19.191793Z 0 [Note] InnoDB: Starting shutdown...
2018-11-29T16:05:19.292043Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2018-11-29T16:05:19.292229Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 181129 18:05:19
2018-11-29T16:05:20.800204Z 0 [Note] InnoDB: Shutdown completed; log sequence number 1221427351
2018-11-29T16:05:20.803257Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2018-11-29T16:05:20.803272Z 0 [Note] Shutting down plugin 'MEMORY'
2018-11-29T16:05:20.803283Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-11-29T16:05:20.803373Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2018-11-29T16:05:20.803380Z 0 [Note] Shutting down plugin 'sha256_password'
2018-11-29T16:05:20.803384Z 0 [Note] Shutting down plugin 'mysql_native_password'
2018-11-29T16:05:20.803541Z 0 [Note] Shutting down plugin 'binlog'
2018-11-29T16:05:20.803784Z 0 [Note] /usr/sbin/mysqld: Shutdown complete

 

[trialotto]

@John Guva

You have some warning notifications that you should take care of in a later stage, first focus on the error notifications.

Please note that your previous attempts to repair the database can be complicating things to a large degree.

First, simply stop the MySQL server explicitly, run the command: service mysql stop

Second, copy the entire /var/lib/mysql directory to another directory, for instance /mysql-bk

Third, remove the /var/lib/mysql/mysql.sock.lock file and try to restart mysql with the command: service mysql start

Next, provide the output of the command "service mysql status" and provide the output of the relevant mysql logs, otherwise nobody here can help you.

Regards.........