Innodb issue is preventing MySQL from starting For some reason mysqld refused to start after I rebooted my server. Now when I try to start it I will get the following error:


  [root@vps1 ~]# service mysqld restart  ERROR! MySQL server PID file
  could not be found! Starting MySQL. ERROR! The server quit without
  updating PID file (/var/lib/mysql/vps1.xxx.eu.pid).


When  I checked the mysql error log I found the following

140923 05:23:02 mysqld_safe mysqld from pid file /var/lib/mysql/vps1.xxx.eu.pid ended
140923 05:23:07 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
2014-09-23 05:23:08 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2014-09-23 05:23:08 4024 [Note] Plugin 'FEDERATED' is disabled.
2014-09-23 05:23:08 4024 [Note] InnoDB: Using atomics to ref count buffer pool pages
2014-09-23 05:23:08 4024 [Note] InnoDB: The InnoDB memory heap is disabled
2014-09-23 05:23:08 4024 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2014-09-23 05:23:08 4024 [Note] InnoDB: Memory barrier is not used
2014-09-23 05:23:08 4024 [Note] InnoDB: Compressed tables use zlib 1.2.3
2014-09-23 05:23:08 4024 [Note] InnoDB: Using Linux native AIO
2014-09-23 05:23:08 4024 [Note] InnoDB: Using CPU crc32 instructions
2014-09-23 05:23:08 4024 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2014-09-23 05:23:08 4024 [Note] InnoDB: Completed initialization of buffer pool
2014-09-23 05:23:08 4024 [Note] InnoDB: Highest supported file format is Barracuda.
2014-09-23 05:23:08 4024 [Note] InnoDB: The log sequence numbers 0 and 0 in ibdata files do not match the log sequence number 63528574 in the ib_logfiles!
2014-09-23 05:23:08 4024 [Note] InnoDB: Database was not shutdown normally!
2014-09-23 05:23:08 4024 [Note] InnoDB: Starting crash recovery.
2014-09-23 05:23:08 4024 [Note] InnoDB: Reading tablespace information from the .ibd files...
2014-09-23 05:23:08 4024 [ERROR] InnoDB: Attempted to open a previously opened tablespace. Previous tablespace mysql/slave_worker_info uses space ID: 5 at filepath: ./mysql/slave_worker_info.ibd. Cannot open tablespace datumklok_web/wp3_postmeta which uses space ID: 5 at filepath: ./datumklok_web/wp3_postmeta.ibd
2014-09-23 05:23:08 7f667c224720  InnoDB: Operating system error number 2 in a file operation.
InnoDB: The error means the system cannot find the path specified.
InnoDB: If you are installing InnoDB, remember that you must create
InnoDB: directories yourself, InnoDB does not create them.
InnoDB: Error: could not open single-table tablespace file ./datumklok_web/wp3_postmeta.ibd
InnoDB: We do not continue the crash recovery, because the table may become
InnoDB: corrupt if we cannot apply the log records in the InnoDB log to it.
InnoDB: To fix the problem and start mysqld:
InnoDB: 1) If there is a permission problem in the file and mysqld cannot
InnoDB: open the file, you should modify the permissions.
InnoDB: 2) If the table is not needed, or you can restore it from a backup,
InnoDB: then you can remove the .ibd file, and InnoDB will do a normal
InnoDB: crash recovery and ignore that table.
InnoDB: 3) If the file system or the disk is broken, and you cannot remove
InnoDB: the .ibd file, you can set innodb_force_recovery &gt; 0 in my.cnf
InnoDB: and force InnoDB to continue crash recovery here.
140923 05:23:08 mysqld_safe mysqld from pid file /var/lib/mysql/vps1.xxx.eu.pid ended


Now unfortunately because of this I have no acces to the mysql console. 

I did create user backups through Directadmin daily BUT if I delete all mysql content I assume DirectAdmin itself will no longer be functional. (Which I found out when fixing Roundcube :P).

So I really have no clue on how to fix this. Anyone out there some experience with these issues?
MySQL can not open file ./datumklok_web/wp3_postmeta.ibd . Check if it exists, but most probably it doesn't. It might have gone after file system check. If so, restore the database from backup. If you don't have them - mount MySQL partition read-only or take image from the partition.