Mysql Upgrade on WHM (Mysql 5.1 to 5.5)

heusdens

Active Member
Oct 1, 2013
25
0
1
cPanel Access Level
Root Administrator
Currently on Centos 6.4 VPS, Apache 2.2.25, PHP 5.3.27. WHM 11.38.2 (Build 7).

Last night I decided to upgrade Mysql from version 5.1 to 5.5 using the Mysql Upgrade under Software section in WHM.

I selected the unattended upgrade and rebuild php and apache. After doing this all sites showed Internal Server Error 500.

MySQL is not running and I can't get it to start either via WHM of SSH.

PhpMyAdmin shows:
Code:
#2002 - Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)
The server is not responding (or the local server's socket is not correctly configured).
I also get these notifications:

Code:
Problems were detected with cPanel-provided files which are RPM controlled. If you did not make these changes intentionally, you can correct them by running:

/usr/local/cpanel/scripts/check_cpanel_rpms --fix

The following RPMs are missing from your system: MySQL55-server.5.5.32-1.cp1136
Running /usr/local/cpanel/scripts/check_cpanel_rpms --fix did not yield any results.

Any help will be appreciated.
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,913
2,202
363
Hello :)

Please try reinstalling the MySQL RPMs with the following commands:

Code:
/scripts/update_local_rpm_versions --edit target_settings.MySQL55 uninstalled
/scripts/check_cpanel_rpms --fix
/scripts/update_local_rpm_versions --edit target_settings.MySQL55 installed
/scripts/check_cpanel_rpms --fix
Thank you.
 

heusdens

Active Member
Oct 1, 2013
25
0
1
cPanel Access Level
Root Administrator
Hi

Thank you I've run the commands and received the following output:

Code:
[email protected] [~]# /scripts/update_local_rpm_versions --edit target_settings.MySQ                                                                                                                                L55 uninstalled
[email protected] [~]# /scripts/check_cpanel_rpms --fix
[20131001.160154]
[20131001.160154]   The following RPMs are unneeded on your system and should be                                                                                                                                 uninstalled:
[20131001.160154]   MySQL55-client.5.5.32-1.cp1136
[20131001.160154]   MySQL55-devel.5.5.32-1.cp1136
[20131001.160154]   MySQL55-shared.5.5.32-1.cp1136
[20131001.160154]   MySQL55-test.5.5.32-1.cp1136
[20131001.160242]   Removing 0 broken rpms:
[20131001.160242]   rpm: no packages given for erase
[20131001.160243]   No new RPMS needed for install
[20131001.160244]   Uninstalling unneeded rpms: MySQL55-test MySQL55-client MySQL55-share                                                                                                                       [email protected] [~]# /scripts/update_local_rpm_versions --edit target_settings.MySQL55 installed
[email protected] [~]# /scripts/check_cpanel_rpms --fix
[20131001.160342]
[20131001.160342]   Problems were detected with cPanel-provided files which are RPM controlled.
[20131001.160342]   If you did not make these changes intentionally, you can correct them by running:
[20131001.160342]
[20131001.160342]   > /usr/local/cpanel/scripts/check_cpanel_rpms --fix
[20131001.160342]   The following RPMs are missing from your system:
[20131001.160342]   MySQL55-client.5.5.32-1.cp1136
[20131001.160342]   MySQL55-devel.5.5.32-1.cp1136
[20131001.160342]   MySQL55-server.5.5.32-1.cp1136
[20131001.160342]   MySQL55-shared.5.5.32-1.cp1136
[20131001.160342]   MySQL55-test.5.5.32-1.cp1136
[20131001.160351]   Removing 0 broken rpms:
[20131001.160351]   rpm: no packages given for erase
[20131001.160352]   Downloading [url]http://httpupdate.cpanel.net/RPM/11.36/centos/6/x86_64/rpm.md5[/url]
[20131001.160353]   MySQL55-client-5.5.32-1.cp1136.x86_64.rpm already downloaded
[20131001.160353]   MySQL55-devel-5.5.32-1.cp1136.x86_64.rpm already downloaded
[20131001.160354]   MySQL55-server-5.5.32-1.cp1136.x86_64.rpm already downloaded
[20131001.160354]   MySQL55-shared-5.5.32-1.cp1136.x86_64.rpm already downloaded
[20131001.160355]   MySQL55-test-5.5.32-1.cp1136.x86_64.rpm already downloaded
[20131001.160356]   Hooks system enabled
[20131001.160356]   Checking for and running RPM::Versions 'pre' hooks for any RPMs about to be installed
warn [check_cpanel_rpms] program "/scripts/premysqlup" is not executable
[20131001.160356]   All required 'pre' hooks have been run
[20131001.160356]   No RPMS need to be uninstalled
[20131001.160356]   Installing new rpms: MySQL55-client-5.5.32-1.cp1136.x86_64.rpm MySQL55-devel-5.5.32-1.cp1136.x                                                                                              86_64.rpm MySQL55-server-5.5.32-1.cp1136.x86_64.rpm MySQL55-shared-5.5.32-1.cp1136.x86_64.rpm MySQL55-test-5.5.32-                                                                                              1.cp1136.x86_64.rpm
[20131001.160356]   Preparing packages for installation...
[20131001.160357]   MySQL55-client-5.5.32-1.cp1136
[20131001.160358]   You have more than one PID file:
[20131001.160358]   -rw-rw----. 1 mysql mysql 5 Sep  9 08:12 /var/lib/mysql/DJFG001.pid
[20131001.160358]   -rw-rw----. 1 mysql mysql 5 Sep 10 04:11 /var/lib/mysql/server1.pid
[20131001.160358]   Please check which one (if any) corresponds to a running server
[20131001.160358]   and delete all others before repeating the MySQL upgrade.
[20131001.160358]   error: %pre(MySQL55-server-5.5.32-1.cp1136.x86_64) scriptlet failed, exit status 1
[20131001.160358]   error:   install: %pre scriptlet failed (2), skipping MySQL55-server-5.5.32-1.cp1136
[20131001.160358]   MySQL55-test-5.5.32-1.cp1136
[20131001.160411]   MySQL55-shared-5.5.32-1.cp1136
[20131001.160412]   MySQL55-devel-5.5.32-1.cp1136
[20131001.160412] W Error Code: 5
[20131001.160412] E The following possible errors were detected while installing RPMs:
[20131001.160412] E %pre(MySQL55-server-5.5.32-1.cp1136.x86_64) scriptlet failed, exit status 1 install
[20131001.160412]   The Administrator will be notified to review this output when this script completes
[20131001.160412]   Checking for and running RPM::Versions 'post' hooks for any RPMs just installed
warn [check_cpanel_rpms] program "/scripts/postmysqlinstall" is not executable
warn [check_cpanel_rpms] program "/scripts/postmysqlup" is not executable
[20131001.160412]   All required 'post' hooks have been run
Does this have to do with PIDs files?
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,913
2,202
363
Hello :)

The following error is relevant here:

[20131001.160356] Preparing packages for installation...
[20131001.160357] MySQL55-client-5.5.32-1.cp1136
[20131001.160358] You have more than one PID file:
[20131001.160358] -rw-rw----. 1 mysql mysql 5 Sep 9 08:12 /var/lib/mysql/DJFG001.pid
[20131001.160358] -rw-rw----. 1 mysql mysql 5 Sep 10 04:11 /var/lib/mysql/server1.pid
[20131001.160358] Please check which one (if any) corresponds to a running server
[20131001.160358] and delete all others before repeating the MySQL upgrade.
Delete those PID files in /var/lib/mysql if you do not have any MySQL processes running on your system. Then, attempt to reinstall MySQL again via:

Code:
/scripts/check_cpanel_rpms --fix
Thank you.
 

heusdens

Active Member
Oct 1, 2013
25
0
1
cPanel Access Level
Root Administrator
hi

Thank you I deleted the PID files and executed the command and this is what came out:

Code:
[email protected] [~]# /scripts/check_cpanel_rpms --fix
[20131001.174858]
[20131001.174858]   Problems were detected with cPanel-provided files which are                                                                                  RPM controlled.
[20131001.174858]   If you did not make these changes intentionally, you can cor                                                                                 rect them by running:
[20131001.174858]
[20131001.174858]   > /usr/local/cpanel/scripts/check_cpanel_rpms --fix
[20131001.174858]   The following RPMs are missing from your system:
[20131001.174858]   MySQL55-server.5.5.32-1.cp1136
[20131001.174908]   Removing 0 broken rpms:
[20131001.174908]   rpm: no packages given for erase
[20131001.174910]   Downloading [url]http://httpupdate.cpanel.net/RPM/11.36/centos/6/x86_64/rpm.md5[/url]
[20131001.174911]   MySQL55-server-5.5.32-1.cp1136.x86_64.rpm already downloaded
[20131001.174911]   Hooks system enabled
[20131001.174911]   Checking for and running RPM::Versions 'pre' hooks for any RPMs about to be installed
warn [check_cpanel_rpms] program "/scripts/premysqlup" is not executable
[20131001.174911]   All required 'pre' hooks have been run
[20131001.174911]   No RPMS need to be uninstalled
[20131001.174911]   Installing new rpms: MySQL55-server-5.5.32-1.cp1136.x86_64.rpm
[20131001.174912]   Preparing packages for installation...
[20131001.174912]   MySQL55-server-5.5.32-1.cp1136
[20131001.174915]   131001 17:49:15 [Warning] The syntax '--log-slow-queries' is deprecated and will be removed in a future release. Please use '--slow-query-log'/'--slow-query-log-file' instead.
[20131001.174916]   ERROR: 1136  Column count doesn't match value count at row 1
[20131001.174916]   131001 17:49:16 [ERROR] Aborting
[20131001.174916]
[20131001.174916]   131001 17:49:16 [Note] /usr/sbin/mysqld: Shutdown complete
[20131001.174916]
[20131001.174916]
[20131001.174916]   Installation of system tables failed!  Examine the logs in
[20131001.174916]   /var/lib/mysql for more information.
[20131001.174916]
[20131001.174916]   You can try to start the mysqld daemon with:
[20131001.174916]
[20131001.174916]       shell> /usr/sbin/mysqld --skip-grant &
[20131001.174916]
[20131001.174916]   and use the command line tool /usr/bin/mysql
[20131001.174916]   to connect to the mysql database and look at the grant tables:
[20131001.174916]
[20131001.174916]       shell> /usr/bin/mysql -u root mysql
[20131001.174916]       mysql> show tables
[20131001.174916]
[20131001.174916]   Try 'mysqld --help' if you have problems with paths.  Using --log
[20131001.174916]   gives you a log in /var/lib/mysql that may be helpful.
[20131001.174916]
[20131001.174916]   Please consult the MySQL manual section
[20131001.174916]   'Problems running mysql_install_db', and the manual section that
[20131001.174916]   describes problems on your OS.  Another information source are the
[20131001.174916]   MySQL email archives available at [url=http://lists.mysql.com/]MySQL Lists[/url].
[20131001.174916]
[20131001.174916]   Please check all of the above before mailing us!  And remember, if
[20131001.174916]   you do mail us, you MUST use the /usr/bin/mysqlbug script!
[20131001.174916]
[20131001.174920]   Looking for 'mysql' as: /usr/bin/mysql
[20131001.174920]   Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck
[20131001.174920]   FATAL ERROR: Upgrade failed
[20131001.174940]   /usr/bin/mysqladmin: connect to server at 'localhost' failed
[20131001.174940]   error: 'Access denied for user 'root'@'localhost' (using password: YES)'
[20131001.174940]   Starting MySQL[  OK  ]
[20131001.174940] E The following possible errors were detected while installing RPMs:
[20131001.174940] E 'Access denied for user 'root'@'localhost' (using password
[20131001.174940]   The Administrator will be notified to review this output when this script completes
[20131001.174940]   Checking for and running RPM::Versions 'post' hooks for any RPMs just installed
warn [check_cpanel_rpms] program "/scripts/postmysqlinstall" is not executable
warn [check_cpanel_rpms] program "/scripts/postmysqlup" is not executable
[20131001.174940]   All required 'post' hooks have been run
[/QUOTE]

Mysql is now running in Services 
[QUOTE]mysql	5.5.32-cll	up[/QUOTE]
My websites are now up and running.  This is good news for me.

Thank you very much for your help I really appreciate it and I've learnt a lot from this so far.

Just in terms of the output above it appears some issues were picked up, what would I need to address there? e.g. 
[QUOTE][20131001.174940]   /usr/bin/mysqladmin: connect to server at 'localhost' failed
[20131001.174940]   error: 'Access denied for user 'root'@'localhost' (using password: YES)'
 

heusdens

Active Member
Oct 1, 2013
25
0
1
cPanel Access Level
Root Administrator
Apologies I didn't quote the post correctly.

Mysql is now running in Services

mysql 5.5.32-cll up
My websites are now up and running. This is good news for me.

Thank you very much for your help I really appreciate it and I've learnt a lot from this so far.

Just in terms of the output above it appears some issues were picked up, what would I need to address there? e.g.
[20131001.174940] /usr/bin/mysqladmin: connect to server at 'localhost' failed
[20131001.174940] error: 'Access denied for user 'root'@'localhost' (using password: YES)'
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,913
2,202
363
I recommend running the following command while logged in as "root":

Code:
mysql_upgrade
If you continue to see "Access Denied" errors, check to ensure your MySQL root password is setup correctly. You can use the following option for this:

"WHM Home » SQL Services » MySQL Root Password"

Thank you.
 

heusdens

Active Member
Oct 1, 2013
25
0
1
cPanel Access Level
Root Administrator
Hi

Thanks I ran mysql_upgrade and all is in order. No Access Denied errors. MySQL root password is set up correctly.

Thank you again for all your help.