[Bug 1512178] [NEW] after upgrade to mysql-5.6 database stopped working

m.hataj m.hataj at gmail.com
Sun Nov 1 22:59:57 UTC 2015 

Public bug reported:

my former running mysql-5.5 database stopped working after the upgrade.
what can I do?

root at server:~# service mysql start
start: Job failed to start

root at server:~# lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 14.04.3 LTS
Release:	14.04
Codename:	trusty

root at server:~# apt-cache policy mysql-server-5.6
mysql-server-5.6:
  Installiert:           5.6.27-0ubuntu0.14.04.1
  Installationskandidat: 5.6.27-0ubuntu0.14.04.1
  Versionstabelle:
 *** 5.6.27-0ubuntu0.14.04.1 0
        500 http://de.archive.ubuntu.com/ubuntu/ trusty-updates/universe amd64 Packages
        500 http://security.ubuntu.com/ubuntu/ trusty-security/universe amd64 Packages
        100 /var/lib/dpkg/status
     5.6.16-1~exp1 0
        500 http://de.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages

tail -f /var/log/mysql/mysql.log /var/log/mysql/error.log
==> /var/log/mysql/mysql.log <==

==> /var/log/mysql/error.log <==
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'CSV'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'MEMORY'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'MRG_MYISAM'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'MyISAM'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'sha256_password'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'mysql_old_password'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'mysql_native_password'
2015-11-01 23:51:04 1457 [Note] Shutting down plugin 'binlog'
2015-11-01 23:51:04 1457 [Note] /usr/sbin/mysqld: Shutdown complete

2015-11-01 23:54:49 2827 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
2015-11-01 23:54:49 2827 [Note] Plugin 'FEDERATED' is disabled.
/usr/sbin/mysqld: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2015-11-01 23:54:49 2827 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2015-11-01 23:54:49 2827 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-11-01 23:54:49 2827 [Note] InnoDB: The InnoDB memory heap is disabled
2015-11-01 23:54:49 2827 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-11-01 23:54:49 2827 [Note] InnoDB: Memory barrier is not used
2015-11-01 23:54:49 2827 [Note] InnoDB: Compressed tables use zlib 1.2.8
2015-11-01 23:54:49 2827 [Note] InnoDB: Using Linux native AIO
2015-11-01 23:54:49 2827 [Note] InnoDB: Not using CPU crc32 instructions
2015-11-01 23:54:49 2827 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2015-11-01 23:54:49 2827 [Note] InnoDB: Completed initialization of buffer pool
2015-11-01 23:54:49 2827 [ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
2015-11-01 23:54:49 2827 [ERROR] InnoDB: The system tablespace must be writable!
2015-11-01 23:54:49 2827 [ERROR] Plugin 'InnoDB' init function returned error.
2015-11-01 23:54:49 2827 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2015-11-01 23:54:49 2827 [ERROR] Unknown/unsupported storage engine: InnoDB
2015-11-01 23:54:49 2827 [ERROR] Aborting

2015-11-01 23:54:49 2827 [Note] Binlog end
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'partition'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'BLACKHOLE'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'ARCHIVE'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_METRICS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_CMPMEM'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_CMP'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_LOCKS'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'INNODB_TRX'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'CSV'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'MEMORY'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'MRG_MYISAM'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'MyISAM'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'sha256_password'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'mysql_old_password'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'mysql_native_password'
2015-11-01 23:54:49 2827 [Note] Shutting down plugin 'binlog'
2015-11-01 23:54:49 2827 [Note] /usr/sbin/mysqld: Shutdown complete

2015-11-01 23:54:50 2871 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
2015-11-01 23:54:50 2871 [Note] Plugin 'FEDERATED' is disabled.
/usr/sbin/mysqld: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2015-11-01 23:54:50 2871 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2015-11-01 23:54:50 2871 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-11-01 23:54:50 2871 [Note] InnoDB: The InnoDB memory heap is disabled
2015-11-01 23:54:50 2871 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-11-01 23:54:50 2871 [Note] InnoDB: Memory barrier is not used
2015-11-01 23:54:50 2871 [Note] InnoDB: Compressed tables use zlib 1.2.8
2015-11-01 23:54:50 2871 [Note] InnoDB: Using Linux native AIO
2015-11-01 23:54:50 2871 [Note] InnoDB: Not using CPU crc32 instructions
2015-11-01 23:54:50 2871 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2015-11-01 23:54:50 2871 [Note] InnoDB: Completed initialization of buffer pool
2015-11-01 23:54:50 2871 [ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
2015-11-01 23:54:50 2871 [ERROR] InnoDB: The system tablespace must be writable!
2015-11-01 23:54:50 2871 [ERROR] Plugin 'InnoDB' init function returned error.
2015-11-01 23:54:50 2871 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2015-11-01 23:54:50 2871 [ERROR] Unknown/unsupported storage engine: InnoDB
2015-11-01 23:54:50 2871 [ERROR] Aborting

2015-11-01 23:54:50 2871 [Note] Binlog end
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'partition'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'BLACKHOLE'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'ARCHIVE'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_METRICS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_CMPMEM'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_CMP'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_LOCKS'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'INNODB_TRX'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'CSV'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'MEMORY'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'MRG_MYISAM'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'MyISAM'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'sha256_password'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'mysql_old_password'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'mysql_native_password'
2015-11-01 23:54:50 2871 [Note] Shutting down plugin 'binlog'
2015-11-01 23:54:50 2871 [Note] /usr/sbin/mysqld: Shutdown complete

2015-11-01 23:54:51 2917 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
2015-11-01 23:54:51 2917 [Note] Plugin 'FEDERATED' is disabled.
/usr/sbin/mysqld: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2015-11-01 23:54:51 2917 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2015-11-01 23:54:51 2917 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-11-01 23:54:51 2917 [Note] InnoDB: The InnoDB memory heap is disabled
2015-11-01 23:54:51 2917 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-11-01 23:54:51 2917 [Note] InnoDB: Memory barrier is not used
2015-11-01 23:54:51 2917 [Note] InnoDB: Compressed tables use zlib 1.2.8
2015-11-01 23:54:51 2917 [Note] InnoDB: Using Linux native AIO
2015-11-01 23:54:51 2917 [Note] InnoDB: Not using CPU crc32 instructions
2015-11-01 23:54:51 2917 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2015-11-01 23:54:51 2917 [Note] InnoDB: Completed initialization of buffer pool
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

2015-11-01 23:54:51 2917 [Note] Binlog end
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'partition'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'BLACKHOLE'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'ARCHIVE'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_METRICS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_CMPMEM'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_CMP'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_LOCKS'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'INNODB_TRX'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'CSV'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'MEMORY'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'MRG_MYISAM'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'MyISAM'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'sha256_password'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'mysql_old_password'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'mysql_native_password'
2015-11-01 23:54:51 2917 [Note] Shutting down plugin 'binlog'
2015-11-01 23:54:52 2917 [Note] /usr/sbin/mysqld: Shutdown complete

** Affects: mysql-5.6 (Ubuntu)
     Importance: Undecided
         Status: New

-- 
You received this bug notification because you are a member of Ubuntu
Server Team, which is subscribed to mysql-5.6 in Ubuntu.
https://bugs.launchpad.net/bugs/1512178

Title:
  after upgrade to mysql-5.6 database stopped working

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/mysql-5.6/+bug/1512178/+subscriptions

More information about the Ubuntu-server-bugs mailing list