>From log:

2015-11-01 23:54:51 2917 [ERROR] InnoDB: ./ibdata1 can't be opened in 
read-write mode
2015-11-01 23:54:51 2917 [ERROR] InnoDB: The system tablespace must be writable!
2015-11-01 23:54:51 2917 [ERROR] Plugin 'InnoDB' init function returned error.
2015-11-01 23:54:51 2917 [ERROR] Plugin 'InnoDB' registration as a STORAGE 
ENGINE failed.
2015-11-01 23:54:51 2917 [ERROR] Unknown/unsupported storage engine: InnoDB
2015-11-01 23:54:51 2917 [ERROR] Aborting

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https://bugs.launchpad.net/bugs/1512178

Title:
  after upgrade to mysql-5.6 database stopped working

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