Did my upgrade from mySQL 5.1 to 5.5 work?

63bus

Active Member
Mar 31, 2007
35
0
156
Last night I ran the upgrade from mySQL 5.1 to 5.5 through the WHM interface.
I am not 100% sure it actually upgraded.
The upgrade ran, Apache was rebuilt afterward, and my server came back up fine.
phpMyAdmin on my server says the mySQL version is 5.5.30-cll

Here is my log file:
Code:
[20130316.005645]
[20130316.005645]   Problems were detected with cPanel-provided files which are RPM controlled.
[20130316.005645]   If you did not make these changes intentionally, you can correct them by running:
[20130316.005645]
[20130316.005645]   > /usr/local/cpanel/scripts/check_cpanel_rpms --fix
[20130316.005645]   The following RPMs are missing from your system:
[20130316.005645]   MySQL55-test.5.5.30-1.cp1136
[20130316.005645]   MySQL55-server.5.5.30-1.cp1136
[20130316.005645]   MySQL55-client.5.5.30-1.cp1136
[20130316.005645]   MySQL55-shared.5.5.30-1.cp1136
[20130316.005645]   MySQL55-devel.5.5.30-1.cp1136
[20130316.005646]
[20130316.005646]   The following RPMs are unneeded on your system and should be uninstalled:
[20130316.005646]   MySQL51-devel.5.1.68-1.cp1136
[20130316.005646]   MySQL51-test.5.1.68-1.cp1136
[20130316.005646]   MySQL51-shared.5.1.68-1.cp1136
[20130316.005646]   MySQL51-client.5.1.68-1.cp1136
[20130316.005646]   MySQL51-server.5.1.68-1.cp1136
[20130316.005646]   Removing 0 broken rpms:
[20130316.005646]   rpm: no packages given for erase
[20130316.005647]   Downloading [url]http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/rpm.md5[/url]
[20130316.005647]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-client-5.5.30-1.cp113$
[20130316.005649]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-shared-5.5.30-1.cp113$
[20130316.005649]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-server-5.5.30-1.cp113$
[20130316.005655]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-test-5.5.30-1.cp1136.$
[20130316.005656]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-devel-5.5.30-1.cp1136$
[20130316.005657]   Hooks system enabled
[20130316.005657]   Checking for and running RPM::Versions 'pre' hooks for any RPMs about to be installed
[20130316.005657]   All required 'pre' hooks have been run
[20130316.005657]   Uninstalling unneeded rpms: MySQL51-devel MySQL51-test MySQL51-shared MySQL51-client MySQL51-ser$
[20130316.005709]   Shutting down MySQL...... SUCCESS!
[20130316.005724]   Installing new rpms: MySQL55-client-5.5.30-1.cp1136.x86_64.rpm MySQL55-shared-5.5.30-1.cp1136.x8$
[20130316.005724]   Preparing packages for installation...
[20130316.005725]   MySQL55-client-5.5.30-1.cp1136
[20130316.005727]   MySQL55-shared-5.5.30-1.cp1136
[20130316.005728]   MySQL55-server-5.5.30-1.cp1136
[20130316.005733]   ERROR: 1136  Column count doesn't match value count at row 1
[20130316.005733]   130316  0:57:33 [ERROR] Aborting
[20130316.005733]
[20130316.005733]   130316  0:57:33 [Note] /usr/sbin/mysqld: Shutdown complete
[20130316.005733]
[20130316.005733]
[20130316.005733]   Installation of system tables failed!  Examine the logs in
[20130316.005733]   /var/lib/mysql for more information.
[20130316.005733]
[20130316.005733]   You can try to start the mysqld daemon with:
[20130316.005733]
[20130316.005733]       shell> /usr/sbin/mysqld --skip-grant &
[20130316.005733]
[20130316.005733]   and use the command line tool /usr/bin/mysql
[20130316.005733]   to connect to the mysql database and look at the grant tables:
[20130316.005733]
[20130316.005733]       shell> /usr/bin/mysql -u root mysql
[20130316.005733]       mysql> show tables
[20130316.005733]
[20130316.005733]   Try 'mysqld --help' if you have problems with paths.  Using --log
[20130316.005733]   gives you a log in /var/lib/mysql that may be helpful.
[20130316.005733]
[20130316.005733]   Please consult the MySQL manual section
[20130316.005733]   'Problems running mysql_install_db', and the manual section that
[20130316.005733]   describes problems on your OS.  Another information source are the
[20130316.005733]   MySQL email archives available at [url=http://lists.mysql.com/]MySQL Lists[/url].
[20130316.005733]
[20130316.005733]   Please check all of the above before mailing us!  And remember, if
[20130316.005733]   you do mail us, you MUST use the /usr/bin/mysqlbug script!
[20130316.005733]
[20130316.005849]   Failed to locate MySQL socket. Please check the mysql configuration.
[20130316.005849]   -- Startup Output --
[20130316.005849]   Starting MySQL. ERROR! The server quit without updating PID file (/var/lib/mysql/samba.thesamba.$
[20130316.005849]   130316 00:57:34 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
[20130316.005849]   130316  0:57:34 [Note] Plugin 'FEDERATED' is disabled.
[20130316.005849]   130316  0:57:34 InnoDB: The InnoDB memory heap is disabled
[20130316.005849]   130316  0:57:34 InnoDB: Mutexes and rw_locks use GCC atomic builtins
[20130316.005849]   130316  0:57:34 InnoDB: Compressed tables use zlib 1.2.3
[20130316.005849]   130316  0:57:34 InnoDB: Using Linux native AIO
[20130316.005849]   130316  0:57:34 InnoDB: Initializing buffer pool, size = 128.0M
[20130316.005849]   130316  0:57:34 InnoDB: Completed initialization of buffer pool
[20130316.005849]   InnoDB: Error: log file ./ib_logfile0 is of different size 0 157286400 bytes
[20130316.005849]   InnoDB: than specified in the .cnf file 0 5242880 bytes!
[20130316.005849]   130316  0:57:34 [ERROR] Plugin 'InnoDB' init function returned error.
[20130316.005849]   130316  0:57:34 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
[20130316.005849]   130316  0:57:34 [ERROR] Unknown/unsupported storage engine: InnoDB
[20130316.005849]   130316  0:57:34 [ERROR] Aborting
[20130316.005849]
[20130316.005849]   130316  0:57:34 [Note] /usr/sbin/mysqld: Shutdown complete
[20130316.005849]
[20130316.005849]   130316 00:57:34 mysqld_safe mysqld from pid file /var/lib/mysql/samba.thesamba.com.pid ended
[20130316.005849]   -- End Startup Output --
[20130316.005849]   Looking for 'mysql' as: /usr/bin/mysql
[20130316.005849]   Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck
[20130316.005849]   Running 'mysqlcheck with default connection arguments
[20130316.005849]   /usr/bin/mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/var/l$
[20130316.005849]   FATAL ERROR: Upgrade failed
[20130316.005850]   ^G/usr/bin/mysqladmin: connect to server at 'localhost' failed
[20130316.005850]   error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
[20130316.005850]   Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
[20130316.005850]   DBI connect('mysql:localhost','root',...) failed: Can't connect to local MySQL server through so$
[20130316.005850]   Unable to reset root MySQL password. at /usr/local/cpanel/scripts/securemysql line 151.
[20130316.005851]   Starting MySQL. ERROR! The server quit without updating PID file (/var/lib/mysql/samba.thesamba.$
[20130316.005851]   error: %post(MySQL55-server-5.5.30-1.cp1136.x86_64) scriptlet failed, exit status 1
[20130316.005851]   MySQL55-test-5.5.30-1.cp1136
[20130316.005856]   MySQL55-devel-5.5.30-1.cp1136
[20130316.005857] W Error Code: 5
[20130316.005857] E The following possible errors were detected while installing RPMs:
[20130316.005857] E 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)' %post(MySQL$
[20130316.005857]   The Administrator will be notified to review this output when this script completes
[20130316.005857]   Checking for and running RPM::Versions 'post' hooks for any RPMs just installed
[20130316.005857]   All required 'post' hooks have been run
Did it actually upgrade?

I use mytop and I noticed mytop no longer worked after the upgrade.
I ran
Code:
/scripts/perlinstaller --force DBD::mysql
and this fixed mytop.
mytop also says the version is 5.5.30-cll

I am wondering if I need to try again tonight with:
Code:
/scripts/mysqlup --force
Thank you.
 

63bus

Active Member
Mar 31, 2007
35
0
156
Last night I upgraded mySQL from 5.1 to 5.5.
Everything ran, Apache was recompiled, and my server came back up and is running.
phpMyAdmin shows version 5.5.30
But I am not 100% sure it worked.

Log file
Code:
[20130316.005645]
[20130316.005645]   Problems were detected with cPanel-provided files which are RPM controlled.
[20130316.005645]   If you did not make these changes intentionally, you can correct them by running:
[20130316.005645]
[20130316.005645]   > /usr/local/cpanel/scripts/check_cpanel_rpms --fix
[20130316.005645]   The following RPMs are missing from your system:
[20130316.005645]   MySQL55-test.5.5.30-1.cp1136
[20130316.005645]   MySQL55-server.5.5.30-1.cp1136
[20130316.005645]   MySQL55-client.5.5.30-1.cp1136
[20130316.005645]   MySQL55-shared.5.5.30-1.cp1136
[20130316.005645]   MySQL55-devel.5.5.30-1.cp1136
[20130316.005646]
[20130316.005646]   The following RPMs are unneeded on your system and should be uninstalled:
[20130316.005646]   MySQL51-devel.5.1.68-1.cp1136
[20130316.005646]   MySQL51-test.5.1.68-1.cp1136
[20130316.005646]   MySQL51-shared.5.1.68-1.cp1136
[20130316.005646]   MySQL51-client.5.1.68-1.cp1136
[20130316.005646]   MySQL51-server.5.1.68-1.cp1136
[20130316.005646]   Removing 0 broken rpms:
[20130316.005646]   rpm: no packages given for erase
[20130316.005647]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/rpm.md5
[20130316.005647]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-client-5.5.30-1.cp113$
[20130316.005649]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-shared-5.5.30-1.cp113$
[20130316.005649]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-server-5.5.30-1.cp113$
[20130316.005655]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-test-5.5.30-1.cp1136.$
[20130316.005656]   Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/x86_64/MySQL55-devel-5.5.30-1.cp1136$
[20130316.005657]   Hooks system enabled
[20130316.005657]   Checking for and running RPM::Versions 'pre' hooks for any RPMs about to be installed
[20130316.005657]   All required 'pre' hooks have been run
[20130316.005657]   Uninstalling unneeded rpms: MySQL51-devel MySQL51-test MySQL51-shared MySQL51-client MySQL51-ser$
[20130316.005709]   Shutting down MySQL...... SUCCESS!
[20130316.005724]   Installing new rpms: MySQL55-client-5.5.30-1.cp1136.x86_64.rpm MySQL55-shared-5.5.30-1.cp1136.x8$
[20130316.005724]   Preparing packages for installation...
[20130316.005725]   MySQL55-client-5.5.30-1.cp1136
[20130316.005727]   MySQL55-shared-5.5.30-1.cp1136
[20130316.005728]   MySQL55-server-5.5.30-1.cp1136
[20130316.005733]   ERROR: 1136  Column count doesn't match value count at row 1
[20130316.005733]   130316  0:57:33 [ERROR] Aborting
[20130316.005733]
[20130316.005733]   130316  0:57:33 [Note] /usr/sbin/mysqld: Shutdown complete
[20130316.005733]
[20130316.005733]
[20130316.005733]   Installation of system tables failed!  Examine the logs in
[20130316.005733]   /var/lib/mysql for more information.
[20130316.005733]
[20130316.005733]   You can try to start the mysqld daemon with:
[20130316.005733]
[20130316.005733]       shell> /usr/sbin/mysqld --skip-grant &
[20130316.005733]
[20130316.005733]   and use the command line tool /usr/bin/mysql
[20130316.005733]   to connect to the mysql database and look at the grant tables:
[20130316.005733]
[20130316.005733]       shell> /usr/bin/mysql -u root mysql
[20130316.005733]       mysql> show tables
[20130316.005733]
[20130316.005733]   Try 'mysqld --help' if you have problems with paths.  Using --log
[20130316.005733]   gives you a log in /var/lib/mysql that may be helpful.
[20130316.005733]
[20130316.005733]   Please consult the MySQL manual section
[20130316.005733]   'Problems running mysql_install_db', and the manual section that
[20130316.005733]   describes problems on your OS.  Another information source are the
[20130316.005733]   MySQL email archives available at http://lists.mysql.com/.
[20130316.005733]
[20130316.005733]   Please check all of the above before mailing us!  And remember, if
[20130316.005733]   you do mail us, you MUST use the /usr/bin/mysqlbug script!
[20130316.005733]
[20130316.005849]   Failed to locate MySQL socket. Please check the mysql configuration.
[20130316.005849]   -- Startup Output --
[20130316.005849]   Starting MySQL. ERROR! The server quit without updating PID file (/var/lib/mysql/samba.thesamba.$
[20130316.005849]   130316 00:57:34 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
[20130316.005849]   130316  0:57:34 [Note] Plugin 'FEDERATED' is disabled.
[20130316.005849]   130316  0:57:34 InnoDB: The InnoDB memory heap is disabled
[20130316.005849]   130316  0:57:34 InnoDB: Mutexes and rw_locks use GCC atomic builtins
[20130316.005849]   130316  0:57:34 InnoDB: Compressed tables use zlib 1.2.3
[20130316.005849]   130316  0:57:34 InnoDB: Using Linux native AIO
[20130316.005849]   130316  0:57:34 InnoDB: Initializing buffer pool, size = 128.0M
[20130316.005849]   130316  0:57:34 InnoDB: Completed initialization of buffer pool
[20130316.005849]   InnoDB: Error: log file ./ib_logfile0 is of different size 0 157286400 bytes
[20130316.005849]   InnoDB: than specified in the .cnf file 0 5242880 bytes!
[20130316.005849]   130316  0:57:34 [ERROR] Plugin 'InnoDB' init function returned error.
[20130316.005849]   130316  0:57:34 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
[20130316.005849]   130316  0:57:34 [ERROR] Unknown/unsupported storage engine: InnoDB
[20130316.005849]   130316  0:57:34 [ERROR] Aborting
[20130316.005849]
[20130316.005849]   130316  0:57:34 [Note] /usr/sbin/mysqld: Shutdown complete
[20130316.005849]
[20130316.005849]   130316 00:57:34 mysqld_safe mysqld from pid file /var/lib/mysql/samba.thesamba.com.pid ended
[20130316.005849]   -- End Startup Output --
[20130316.005849]   Looking for 'mysql' as: /usr/bin/mysql
[20130316.005849]   Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck
[20130316.005849]   Running 'mysqlcheck with default connection arguments
[20130316.005849]   /usr/bin/mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/var/l$
[20130316.005849]   FATAL ERROR: Upgrade failed
[20130316.005850]   ^G/usr/bin/mysqladmin: connect to server at 'localhost' failed
[20130316.005850]   error: 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)'
[20130316.005850]   Check that mysqld is running and that the socket: '/var/lib/mysql/mysql.sock' exists!
[20130316.005850]   DBI connect('mysql:localhost','root',...) failed: Can't connect to local MySQL server through so$
[20130316.005850]   Unable to reset root MySQL password. at /usr/local/cpanel/scripts/securemysql line 151.
[20130316.005851]   Starting MySQL. ERROR! The server quit without updating PID file (/var/lib/mysql/samba.thesamba.$
[20130316.005851]   error: %post(MySQL55-server-5.5.30-1.cp1136.x86_64) scriptlet failed, exit status 1
[20130316.005851]   MySQL55-test-5.5.30-1.cp1136
[20130316.005856]   MySQL55-devel-5.5.30-1.cp1136
[20130316.005857] W Error Code: 5
[20130316.005857] E The following possible errors were detected while installing RPMs:
[20130316.005857] E 'Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)' %post(MySQL$
[20130316.005857]   The Administrator will be notified to review this output when this script completes
[20130316.005857]   Checking for and running RPM::Versions 'post' hooks for any RPMs just installed
[20130316.005857]   All required 'post' hooks have been run
I use mytop and mytop did not work after the upgrade.
I did this
Code:
/scripts/perlinstaller --force DBD::mysql
and mytop was fixed.

Do I need to run the mySQL upgrade again using
Code:
/scripts/mysqlup --force
?

Thank you.
 

InterServed

Well-Known Member
Jul 10, 2007
268
14
68
cPanel Access Level
DataCenter Provider
You might want to try the following:
1) run this in order to ensure required table changes were perfromed : mysql_upgrade
2) run this in order to optimize and validate that you don't have any crashed tables: mysqlcheck --optimize --all-databases
 

63bus

Active Member
Mar 31, 2007
35
0
156
Thanks for the response.
I finally had enough downtime to run those commands tonight and everything went fine.
There were no error messages.

Is there something I can look at in regards to a particular table to verify it is marked as being version 5.5 instead of 5.1?
SHOW TABLE STATUS shows a version of 10 on the tables but I couldn't find anything via a Google search that states what 10 actually means.