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Thread: MySQL 9.04. > 9.10 problem

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  1. #1
    Join Date
    Apr 2008
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    12

    MySQL 9.04. > 9.10 problem

    Functioning, fully updated 9.04 server running MySQL out of the box (presumably MySQL 5.0).

    Apparently painless upgrade to 9.10. Everything I've tested so far works perfectly, except for MySQL, which refuses to start. This seems to be because of a failed script during the conversion process -- see below for output from manual attempt to install MySQL 5.1.

    I've tried everything I can think of (back to 5.0 and back again, tweaking permissions on the socket directory, etc. Same result, and 5.0 doesn't work now either, so something important has been changed.

    Any ideas or suggestions? Inasmuch as this was a plain vanilla setup that was working perfectly, I assume this might be a problem I'm not alone in experiencing.

    ------------------

    $ sudo aptitude install mysql-server-5.1
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    Reading extended state information
    Initializing package states... Done
    The following NEW packages will be installed:
    libdbd-mysql-perl{a} libdbi-perl{a} libhtml-template-perl{a}
    libnet-daemon-perl{a} libplrpc-perl{a} mysql-client-5.1{a}
    mysql-server-5.1 mysql-server-core-5.1{a}
    0 packages upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
    Need to get 0B/20,3MB of archives. After unpacking 48,7MB will be used.
    Do you want to continue? [Y/n/?] y
    Writing extended state information... Done
    Preconfiguring packages ...
    Selecting previously deselected package libnet-daemon-perl.
    (Reading database ... 50271 files and directories currently installed.)
    Unpacking libnet-daemon-perl (from .../libnet-daemon-perl_0.43-1_all.deb) ...
    Selecting previously deselected package libplrpc-perl.
    Unpacking libplrpc-perl (from .../libplrpc-perl_0.2020-2_all.deb) ...
    Selecting previously deselected package libdbi-perl.
    Unpacking libdbi-perl (from .../libdbi-perl_1.609-1_i386.deb) ...
    Selecting previously deselected package libdbd-mysql-perl.
    Unpacking libdbd-mysql-perl (from .../libdbd-mysql-perl_4.011-1ubuntu1_i386.deb) ...
    Selecting previously deselected package mysql-client-5.1.
    Unpacking mysql-client-5.1 (from .../mysql-client-5.1_5.1.37-1ubuntu5_i386.deb) ...
    Selecting previously deselected package mysql-server-core-5.1.
    Unpacking mysql-server-core-5.1 (from .../mysql-server-core-5.1_5.1.37-1ubuntu5_ i386.deb) ...
    Selecting previously deselected package mysql-server-5.1.
    Unpacking mysql-server-5.1 (from .../mysql-server-5.1_5.1.37-1ubuntu5_i386.deb) ...
    * Stopping MySQL database server mysqld [ OK ]
    Selecting previously deselected package libhtml-template-perl.
    Unpacking libhtml-template-perl (from .../libhtml-template-perl_2.9-1_all.deb) . ..
    Processing triggers for man-db ...
    Setting up libnet-daemon-perl (0.43-1) ...
    Setting up libplrpc-perl (0.2020-2) ...
    Setting up libdbi-perl (1.609-1) ...
    Setting up libdbd-mysql-perl (4.011-1ubuntu1) ...
    Setting up mysql-client-5.1 (5.1.37-1ubuntu5) ...

    Setting up mysql-server-core-5.1 (5.1.37-1ubuntu5) ...
    Setting up mysql-server-5.1 (5.1.37-1ubuntu5) ...
    * Stopping MySQL database server mysqld [ OK ]
    091030 11:37:05 [Note] Plugin 'FEDERATED' is disabled.
    091030 11:37:05 InnoDB: Started; log sequence number 0 43655
    091030 11:37:05 [ERROR] /usr/sbin/mysqld: unknown option '--skip-bdb'
    091030 11:37:05 [ERROR] Aborting

    091030 11:37:05 InnoDB: Starting shutdown...
    091030 11:37:06 InnoDB: Shutdown completed; log sequence number 0 43655
    091030 11:37:06 [Warning] Forcing shutdown of 1 plugins
    091030 11:37:06 [Note] /usr/sbin/mysqld: Shutdown complete

    Warning: found usr.sbin.mysqld in /etc/apparmor.d/force-complain, forcing compla in mode
    * Starting MySQL database server mysqld [fail]
    invoke-rc.d: initscript mysql, action "start" failed.
    dpkg: error processing mysql-server-5.1 (--configure):
    subprocess installed post-installation script returned error exit status 1
    Setting up libhtml-template-perl (2.9-1) ...
    Errors were encountered while processing:
    mysql-server-5.1
    E: Sub-process /usr/bin/dpkg returned an error code (1)
    A package failed to install. Trying to recover:
    Setting up mysql-server-5.1 (5.1.37-1ubuntu5) ...
    * Stopping MySQL database server mysqld [ OK ]
    Warning: found usr.sbin.mysqld in /etc/apparmor.d/force-complain, forcing compla in mode
    * Starting MySQL database server mysqld [fail]
    invoke-rc.d: initscript mysql, action "start" failed.
    dpkg: error processing mysql-server-5.1 (--configure):
    subprocess installed post-installation script returned error exit status 1
    Errors were encountered while processing:
    mysql-server-5.1
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    Reading extended state information
    Initializing package states... Done
    Writing extended state information... Done

    >>> Syslog:

    Oct 30 11:41:09 nlhserver kernel: [ 6617.956712] __ratelimit: 6 callbacks suppressed
    Oct 30 11:41:09 nlhserver kernel: [ 6617.956716] type=1502 audit(1256899269.707:664): operation="open" pid=8494 parent=8493 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6617.956737] type=1502 audit(1256899269.707:665): operation="file_perm" pid=8494 parent=8493 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6617.956758] type=1502 audit(1256899269.707:666): operation="file_perm" pid=8494 parent=8493 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6617.986200] type=1502 audit(1256899269.735:667): operation="open" pid=8514 parent=8513 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6617.986222] type=1502 audit(1256899269.735:668): operation="file_perm" pid=8514 parent=8513 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6617.986243] type=1502 audit(1256899269.735:669): operation="file_perm" pid=8514 parent=8513 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver mysqld_safe: Starting mysqld daemon with databases from /var/lib/mysql
    Oct 30 11:41:09 nlhserver kernel: [ 6618.090559] type=1502 audit(1256899269.839:670): operation="open" pid=8634 parent=8520 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6618.090581] type=1502 audit(1256899269.839:671): operation="file_perm" pid=8634 parent=8520 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver kernel: [ 6618.090603] type=1502 audit(1256899269.839:672): operation="file_perm" pid=8634 parent=8520 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:09 nlhserver mysqld: 091030 11:41:09 [Note] Plugin 'FEDERATED' is disabled.
    Oct 30 11:41:09 nlhserver mysqld: /usr/sbin/mysqld: Table 'mysql.plugin' doesn't exist
    Oct 30 11:41:09 nlhserver mysqld: 091030 11:41:09 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
    Oct 30 11:41:09 nlhserver mysqld: 091030 11:41:09 InnoDB: Started; log sequence number 0 43655
    Oct 30 11:41:09 nlhserver mysqld: 091030 11:41:09 [ERROR] /usr/sbin/mysqld: unknown option '--skip-bdb'
    Oct 30 11:41:09 nlhserver mysqld: 091030 11:41:09 [ERROR] Aborting
    Oct 30 11:41:09 nlhserver mysqld:
    Oct 30 11:41:09 nlhserver mysqld: 091030 11:41:09 InnoDB: Starting shutdown...
    Oct 30 11:41:10 nlhserver kernel: [ 6619.002058] type=1502 audit(1256899270.751:673): operation="open" pid=8648 parent=8647 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:11 nlhserver mysqld: 091030 11:41:11 InnoDB: Shutdown completed; log sequence number 0 43655
    Oct 30 11:41:11 nlhserver mysqld: 091030 11:41:11 [Warning] Forcing shutdown of 1 plugins
    Oct 30 11:41:11 nlhserver mysqld: 091030 11:41:11 [Note] /usr/sbin/mysqld: Shutdown complete
    Oct 30 11:41:11 nlhserver mysqld:
    Oct 30 11:41:11 nlhserver mysqld_safe: mysqld from pid file /var/run/mysqld/mysqld.pid ended
    Oct 30 11:41:14 nlhserver kernel: [ 6623.064383] __ratelimit: 33 callbacks suppressed
    Oct 30 11:41:14 nlhserver kernel: [ 6623.064386] type=1502 audit(1256899274.815:685): operation="open" pid=8690 parent=8689 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:14 nlhserver kernel: [ 6623.064408] type=1502 audit(1256899274.815:686): operation="file_perm" pid=8690 parent=8689 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:14 nlhserver kernel: [ 6623.064430] type=1502 audit(1256899274.815:687): operation="file_perm" pid=8690 parent=8689 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:15 nlhserver kernel: [ 6624.081069] type=1502 audit(1256899275.831:688): operation="open" pid=8700 parent=8699 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:15 nlhserver kernel: [ 6624.081092] type=1502 audit(1256899275.831:689): operation="file_perm" pid=8700 parent=8699 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:15 nlhserver kernel: [ 6624.081114] type=1502 audit(1256899275.831:690): operation="file_perm" pid=8700 parent=8699 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:16 nlhserver kernel: [ 6625.096187] type=1502 audit(1256899276.847:691): operation="open" pid=8710 parent=8709 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:16 nlhserver kernel: [ 6625.096208] type=1502 audit(1256899276.847:692): operation="file_perm" pid=8710 parent=8709 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:16 nlhserver kernel: [ 6625.096228] type=1502 audit(1256899276.847:693): operation="file_perm" pid=8710 parent=8709 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:17 nlhserver kernel: [ 6626.110232] type=1502 audit(1256899277.859:694): operation="open" pid=8720 parent=8719 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:19 nlhserver kernel: [ 6628.140422] __ratelimit: 15 callbacks suppressed
    Oct 30 11:41:19 nlhserver kernel: [ 6628.140426] type=1502 audit(1256899279.891:700): operation="open" pid=8740 parent=8739 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:19 nlhserver kernel: [ 6628.140444] type=1502 audit(1256899279.891:701): operation="file_perm" pid=8740 parent=8739 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:19 nlhserver kernel: [ 6628.140464] type=1502 audit(1256899279.891:702): operation="file_perm" pid=8740 parent=8739 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:20 nlhserver kernel: [ 6629.154392] type=1502 audit(1256899280.903:703): operation="open" pid=8750 parent=8749 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:20 nlhserver kernel: [ 6629.154414] type=1502 audit(1256899280.903:704): operation="file_perm" pid=8750 parent=8749 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:20 nlhserver kernel: [ 6629.154436] type=1502 audit(1256899280.903:705): operation="file_perm" pid=8750 parent=8749 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:21 nlhserver kernel: [ 6630.169725] type=1502 audit(1256899281.919:706): operation="open" pid=8760 parent=8759 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:21 nlhserver kernel: [ 6630.169746] type=1502 audit(1256899281.919:707): operation="file_perm" pid=8760 parent=8759 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:21 nlhserver kernel: [ 6630.169767] type=1502 audit(1256899281.919:708): operation="file_perm" pid=8760 parent=8759 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:22 nlhserver kernel: [ 6631.185737] type=1502 audit(1256899282.935:709): operation="open" pid=8770 parent=8769 profile="/usr/sbin/mysqld" requested_mask="r::" denied_mask="r::" fsuid=0 ouid=0 name="/sys/devices/system/cpu/"
    Oct 30 11:41:23 nlhserver /etc/init.d/mysql[8796]: 0 processes alive and '/usr/bin/mysqladmin --defaults-file=/etc/mysql/debian.cnf ping' resulted in
    Oct 30 11:41:23 nlhserver /etc/init.d/mysql[8796]: #007/usr/bin/mysqladmin: connect to server at 'localhost' failed
    Oct 30 11:41:23 nlhserver /etc/init.d/mysql[8796]: error: 'Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)'
    Oct 30 11:41:23 nlhserver /etc/init.d/mysql[8796]: Check that mysqld is running and that the socket: '/var/run/mysqld/mysqld.sock' exists!
    Oct 30 11:41:23 nlhserver /etc/init.d/mysql[8796]:
    Last edited by pnmoslo; October 30th, 2009 at 12:04 PM.

  2. #2
    Join Date
    Apr 2005
    Beans
    105

    Re: MySQL 9.04. > 9.10 problem

    I am trying to upgrade from CD, and I also have mysql related upgrade issue (see attachment).
    Now, I don't mind restarting the upgrade if it can be done safely and if I don't have to download the packages again. I thought new packages are downloaded to /var/cache/apt, but they're not. Where are they?

    EDIT: I killed mysql process and upgrade continued...
    Attached Images Attached Images
    Last edited by mehaga; October 30th, 2009 at 12:30 PM.

  3. #3
    Join Date
    Apr 2008
    Beans
    12

    Re: MySQL 9.04. > 9.10 problem

    Fixed this by moving the database files (happily only one database that really mattered, and I had a good backup), removing all traces of MySQL (including mysql-common) and installing mysql again with aptitude. Then slowly and painfully reconstructing users and moving the database back in etc.

    It seems to have worked -- but whatever happened remains unsolved: the 9.04 to 9.10 upgrade zilched a functioning plain vanilla MySQL setup.

    Ah well -- back to what I should have been doing for the last 6 hours.

  4. #4
    Join Date
    Nov 2009
    Beans
    2

    Unhappy Re: MySQL 9.04. > 9.10 problem

    My existing MySQL installation was also effected after I upgraded to 9.10

    So far I think that was the only that effected. I did notice during the upgrade process that seemed to hang a while why trying to restart MySQL, although I did not see how it resolved itself, apparently it didn't.

    When I try to log into MySQL I get the following:

    ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (111)

    Is there any way to fix this (without having to reinstall MySQL???

    Thanks.

  5. #5
    Join Date
    Apr 2008
    Beans
    12

    Re: MySQL 9.04. > 9.10 problem

    My conclusion after a lot of trial and error is that either there was something in my.cnf that the new version didn't like, or that the update process did something to my.cnf and didn't complete the process.

    I found that moving my.cnf to eg. my.cnf.back and restarting MySQL worked (with an error message that my.cnf was missing, but the database came up, presumably in some sort of generic configuration). I then found a minimal my.cnf on the net and tried again - it worked. Next step should have been to systematically compare the new my.cnf and my.cnf.back, but time had run out.

    I also had to do an "aptitude reinstall mysql-server" several times before the installation scripts accepted that the programme was correctly installed.

  6. #6
    Join Date
    Sep 2007
    Location
    Cambs, UK
    Beans
    51
    Distro
    Ubuntu 11.04 Natty Narwhal

    Re: MySQL 9.04. > 9.10 problem

    The error message is not reflecting the primary problem for me.

    Code:
    grep mysqld /var/log/daemon.log
    Nov  4 13:42:16 desktop mysqld: 091104 13:42:16 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
    Nov  4 13:42:16 desktop mysqld: 091104 13:42:16  InnoDB: Started; log sequence number 0 209835
    Nov  4 13:42:16 desktop mysqld: 091104 13:42:16 [ERROR] /usr/sbin/mysqld: unknown option '--skip-bdb'
    Nov  4 13:42:16 desktop mysqld: 091104 13:42:16 [ERROR] Aborting
    So I remove the skip-bdb option in the config file
    Code:
    sudo sed -i 's/dkip-bdb/#skip-bdb/' /etc/mysqld/my.cnf
    It seems there is now some corrupted files,
    Code:
    sudo apt-get install mysql-server
    seems to allow me to get mysql up and running. Myth still won't connect at this point...
    If I use a host name of 'localhost' for myth, it works, 192.168.0.1 doesn't (despite me thinking thats what I set mysql for,) and 127.0.0.1 doesn't.
    Last edited by tsh; November 4th, 2009 at 03:12 PM. Reason: fixed myth part.

  7. #7
    Join Date
    Feb 2007
    Location
    Australia
    Beans
    1

    Re: MySQL 9.04. > 9.10 problem

    Quote Originally Posted by pnmoslo View Post
    My conclusion after a lot of trial and error is that either there was something in my.cnf that the new version didn't like, or that the update process did something to my.cnf and didn't complete the process.

    I found that moving my.cnf to eg. my.cnf.back and restarting MySQL worked (with an error message that my.cnf was missing, but the database came up, presumably in some sort of generic configuration). I then found a minimal my.cnf on the net and tried again - it worked. Next step should have been to systematically compare the new my.cnf and my.cnf.back, but time had run out.

    I also had to do an "aptitude reinstall mysql-server" several times before the installation scripts accepted that the programme was correctly installed.
    First Google post, this must be my lucky day!

    Thanks to pnmoslo, I was able to fix the problem without having to reinstall anything at all. My solution is below:

    Code:
    cd /etc/mysql
    sudo mv my.cnf my.cnf.9.04
    sudo cp my.cnf.dpkg-dist my.cnf
    After this MySQL should start alright as it did for me. I /think/ the culprit might be this:

    Code:
    # * Federated
    #
    # The FEDERATED storage engine is disabled since 5.0.67 by default in the .cnf files
    # shipped with MySQL distributions (my-huge.cnf, my-medium.cnf, and so forth).
    #
    skip-federated

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