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I have the following in RPM_UPGRADE_HISTORY in /var/lib/mysql

MySQL RPM upgrade to version 5.6.10-1.linux_glibc2.5
'pre' step running at Fri Mar 15 15:41:26 EDT 2013

ERR file(s):
-rw-r----- 1 mysql root 1725 2013-03-15 13:45 /var/lib/mysql/mysql.err

I checked the error file to find this information:

2013-03-15 15:43:22 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2013-03-15 15:43:22 11993 [Note] Plugin 'FEDERATED' is disabled.
2013-03-15 15:43:22 11993 [Note] InnoDB: The InnoDB memory heap is disabled
2013-03-15 15:43:22 11993 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2013-03-15 15:43:22 11993 [Note] InnoDB: Compressed tables use zlib 1.2.3
2013-03-15 15:43:22 11993 [Note] InnoDB: CPU does not support crc32 instructions
2013-03-15 15:43:22 11993 [Note] InnoDB: Using Linux native AIO
2013-03-15 15:43:22 11993 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2013-03-15 15:43:22 11993 [Note] InnoDB: Completed initialization of buffer pool
2013-03-15 15:43:22 11993 [ERROR] InnoDB: auto-extending data file ./ibdata1 is of a different size 640 pages (rounded down to MB) than specified in the .cnf file: initial 768 pages, max 0 (relevant if non-zero) pages!
2013-03-15 15:43:22 11993 [ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_data_file_path in my.cnf back to what it was, and remove the new ibdata files InnoDB created in this failed attempt. InnoDB only wrote those files full of zeros, but did not yet use them in any way. But be careful: do not remove old data files which contain your precious data!
2013-03-15 15:43:22 11993 [ERROR] Plugin 'InnoDB' init function returned error.
2013-03-15 15:43:22 11993 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2013-03-15 15:43:22 11993 [ERROR] Unknown/unsupported storage engine: InnoDB
2013-03-15 15:43:22 11993 [ERROR] Aborting

2013-03-15 15:43:22 11993 [Note] Binlog end
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'partition'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'BLACKHOLE'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'ARCHIVE'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_INSERTED'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_METRICS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_CMPMEM'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_CMP'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_LOCKS'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'INNODB_TRX'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'MRG_MYISAM'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'MEMORY'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'CSV'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'MyISAM'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'sha256_password'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'mysql_old_password'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'mysql_native_password'
2013-03-15 15:43:22 11993 [Note] Shutting down plugin 'binlog'
2013-03-15 15:43:22 11993 [Note] /usr/sbin/mysqld: Shutdown complete

130315 15:43:22 mysqld_safe mysqld from pid file /var/lib/mysql/mysql.pid ended

I installed using rpm package on MySQL web site. What went wrong?

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2
  • What version did you upgrade from ???
    – RolandoMySQLDBA
    Mar 15, 2013 at 20:29
  • Well technically none since I used yast to remove the old version and then used rpm -i, but it was at 5.1.
    – thatidiotguy
    Mar 15, 2013 at 20:36

7 Answers 7

Reset to default
7

DISCLAIMER : Not a Full Expert on MySQL 5.6

Looks like the InnoDB Plugin is complaining about the present ibdata1 file.

If data and index pages exist inside ibdata1, it's probably using Antelope as the innodb_file_format.

There are four(4) things you can try:

SUGGESTION #1 : UNINSTALL AND REINSTALL MySQL 5.6

  • Uninstall MySQL
  • mv /var/lib/mysql /var/lib/mysql_old
  • Reinstall MySQL

SUGGESTION #2 : Using a cleaned-up datadir

mv /var/lib/mysql /var/lib/mysql_old
mkdir /var/lib/mysql
mkdir /var/lib/mysql/mysql
cp /var/lib/mysql_old /var/lib/mysql/mysql
chown -R mysql:mysql /var/lib/mysql/mysql
service mysql start

This will construct brand spanking new InnoDB Files

  • /var/lib/mysql/ibdata1
  • /var/lib/mysql/ib_logfile0
  • /var/lib/mysql/ib_logfile1

SUGGESTION #3 : Switch innodb_file_format (May be risky)

This may be a little risky but add this to my.cnf

[mysqld]
innodb_file_format=Barracuda
innodb_file_format_max=Barracuda

and restart mysql

SUGGESTION #4 : GIVE IT A TRY !!!

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0
3

Even though I'm quite late to the question, I recently had this issue and it was a rather simple fix... After I found it.

I was upgrading from 5.1 to 5.6 and had the same exact errors in my mysqld.log file.

Put this in your my.cnf under [mysqld]:

innodb_data_file_path = ibdata1:10M:autoextend
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1
  • 1
    this worked for me as well while upgrading 5.1 to 5.6
    – sherpaurgen
    Mar 22, 2017 at 9:19
1

Deleting ibdata1 is risky.

I could fix this issue by adding,

innodb_data_file_path = ibdata1:10M:autoextend

to my.cnf file.

Then restart the server.

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0

SUGGESTION #1 helped to me with the modification

first rename data dir from /var/lib/mysql to /var/lib/mysql2
apt-get remove mysql-server-5.6
apt-get autoremove
apt-get install mysql-server-5.6
service mysql stop
rename /var/lib/mysql to /var/lib/mysql.clean
rename /var/lib/mysql2 to /var/lib/mysql
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0

I know that it was already solved, but I just had the same issue, and the solution in my case was to free up some disk space.

I recommend to run df -h to make sure that we have available disk space.

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-1

If you have upgraded from MySQL 5.x to 5.y and you have below error in the MySQL logs (/var/log/mysqld.log):

error=[ERROR] InnoDB: auto-extending data file ./ibdata1 is of a
different size 640 pages (rounded down to MB) than specified in the
.cnf file: initial 768 pages, max 0 (relevant if non-zero) pages!

... then you have to add a line in /etc/my.cnf under the section [mysqld]: 

innodb_data_file_path = ibdata1:10M:autoextend

...and restart mysqld by issuing the following command in your shell:

service mysqld restart

This will solve the above error.

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1
  • How does this answer differ from other answers already given?
    – John K. N.
    Apr 26, 2018 at 9:00
-4

i just removed the below files:

  • /var/lib/mysql/ibdata1
  • /var/lib/mysql/ib_logfile0
  • /var/lib/mysql/ib_logfile1

then start mysqld service and it works successfully ...

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2
  • 3
    And you still have all of your data?
    – Colin 't Hart
    Mar 4, 2015 at 15:07
  • Yes just have to repair a table but really not sure if it is related to the above action.
    – Mazen Ora
    Mar 5, 2015 at 10:10

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