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Thread: Upgrade from 5.0.13 NE hangs

  1. #11
    tonster is offline Zimbra Employee
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    Quote Originally Posted by SageMajor View Post
    The following commands are before any upgrade

    Code:
    before upgrade
     zmlocalconfig -s zimbra_mysql_password mysql_root_password
    zimbra_mysql_password = zimbrapwd
    mysql_root_password = zimbrapwd
    zimbra@mail2:/tmp$ source bin/zmshutil
    bash: bin/zmshutil: No such file or directory
    zimbra@mail2:/tmp$ cd /opt/zimbra
    You have new mail in /var/mail/zimbra
    zimbra@mail2:~$ !s
    source bin/zmshutil
    zimbra@mail2:~$ zmsetvars
    zimbra@mail2:~$ mysql -u root --password=zimbrapwd
    ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/opt/zimbra/db/mysql.sock' (2)
    zimbra@mail2:~$ mysql
    ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/opt/zimbra/db/mysql.sock' (2)
    zimbra@mail2:/tmp$ which mysql
    /opt/zimbra/bin/mysql
    Also the rc command returned 8 as expected

    Note that my current 5.0.13 install is currently running fine with now errors, I have about 50 users and about 30gb of mail. I had similar issues both times in the past when I tried upgraded from the 5.0.2 and 4.x years ago.
    Well, the first command (source bin/zmshutil) didn't work because you weren't in the zimbra home directory, but why mysql wasn't running is a big question. If you run 'mysql.server start' does it hang attempting to start? Are there any errors in /opt/zimbra/log/mysql_error.log? You may need to check /opt/zimbra/log for what that file was called in 5.x, because I don't remember and I think it was something different. If there's no mysql-related file there, you might need to look in /opt/zimbra/conf/my.cnf to see where it was stored. I know it changed at some point, but I don't recall exactly when.

    If you're a NE customer, this might be something we look at in more depth in a ticket. I could help if I could gain access to the system, but not until next week unfortunately as I'll be traveling. Let me know if you want to do that.

  2. #12
    SageMajor is offline Senior Member
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    weird
    I just ran the commands and they all worked.

    Code:
    root@mail2:~# su zimbra
    zimbra@mail2:/root$ cd /opt/zimbra/
    zimbra@mail2:~$ zmlocalconfig -s zimbra_mysql_password mysql_root_password
    zimbra_mysql_password = zimbrapwd
    mysql_root_password = zimbrapwd
    zimbra@mail2:~$ source bin/zmshutil
    zimbra@mail2:~$ zmsetvars
    zimbra@mail2:~$ mysql.server start
    mysqld_safe already running with pid 18195
    zimbra@mail2:~$ mysql -u root --password=zimbrapwd
    Welcome to the MySQL monitor.  Commands end with ; or \g.
    Your MySQL connection id is 2068
    Server version: 5.0.67-log Source distribution
    
    Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
    
    mysql>
    Yes I am a NE customer however my support contract is not current.

    I will try again tonight, this is interesting.

  3. #13
    tonster is offline Zimbra Employee
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    Quote Originally Posted by SageMajor View Post
    weird
    I just ran the commands and they all worked.

    Code:
    root@mail2:~# su zimbra
    zimbra@mail2:/root$ cd /opt/zimbra/
    zimbra@mail2:~$ zmlocalconfig -s zimbra_mysql_password mysql_root_password
    zimbra_mysql_password = zimbrapwd
    mysql_root_password = zimbrapwd
    zimbra@mail2:~$ source bin/zmshutil
    zimbra@mail2:~$ zmsetvars
    zimbra@mail2:~$ mysql.server start
    mysqld_safe already running with pid 18195
    zimbra@mail2:~$ mysql -u root --password=zimbrapwd
    Welcome to the MySQL monitor.  Commands end with ; or \g.
    Your MySQL connection id is 2068
    Server version: 5.0.67-log Source distribution
    
    Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
    
    mysql>
    Yes I am a NE customer however my support contract is not current.

    I will try again tonight, this is interesting.
    It's possible it just took awhile for mysql to come up. I can't be certain right now, but it's also possible that there's some corruption in your tables. You may consider running through Mysql Crash Recovery - Zimbra :: Wiki and exporting/importing your mysql databases.

    In any event, if the upgrade fails and you run these commands and find that mysql is working again, run /opt/zimbra/libexec/zmsetup.pl to continue the upgrade, don't attempt running install.sh again.

    Good luck!

  4. #14
    SageMajor is offline Senior Member
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    I did the change in the tables, so it definately is a mysql problem. I ran the upgrade with the command in the mysql.server file.
    I then ran upgrade to 5.0.x and it worked. I ran the upgrade to 6.0.16 and it failed in the same place. I put the --skip-grant-tables in mysql.server and ran the
    /opt/zimbra/libexec/zmsetup.pl and I now have 6.0.13 running.


    Now attempting to upgrade to 7.0.14

    In this case the mysql does not start evenn with /opt/zimbra/libexec/zmsetup.pl edited as follows

    Code:
    case "$1" in
      'start')
        checkInitLock
        if [ "x$pid" != "x" ]; then
          kill -0 $pid 2> /dev/null
          if [ $? = 0 ]; then
            echo "mysqld_safe already running with pid $pid"
            quit 0
          fi
        fi
        # --defaults-file must be first argument
        echo -n "Starting mysqld..."
        cd ${mysql_directory}; \
          ${mysql_directory}/bin/mysqld_safe \
          --defaults-file=${mysql_mycnf} \
          --external-locking \
          --skip-grant-tables \
          --log-error=${mysql_errlogfile} \
          --ledir=${mysql_directory}/libexec < /dev/null > /dev/null 2>&1 &
        SQLSTARTED=0
    Code:
    zimbra@mail2:/root$ mysql.server start
    Starting mysqld...failed.
    You have new mail in /var/mail/zimbra
    zimbra@mail2:/root$
    The results of the upgrade attempt
    Code:
    Do you agree with the terms of the software license agreement? [N] y
    
    Checking for prerequisites...
         FOUND: NPTL
         FOUND: netcat-traditional-1.10-36
         FOUND: sudo-1.6.9p10-1ubuntu3.4
         FOUND: libidn11-1.1-1
         FOUND: libpcre3-7.4-1ubuntu2.1
         FOUND: libgmp3c2-2:4.2.2+dfsg-1ubuntu2
         FOUND: libexpat1-2.0.1-0ubuntu1
         FOUND: libstdc++6-4.2.4-1ubuntu4
         FOUND: libperl5.8-5.8.8-12ubuntu0.4
    Checking for suggested prerequisites...
         FOUND: perl-5.8.8
         MISSING: sysstat does not appear to be installed.
         MISSING: sqlite3 does not appear to be installed.
    
    ###WARNING###
    
    The suggested version of one or more packages is not installed.
    This could cause problems with the operation of Zimbra.
    
    Do you wish to continue? [N] n
    
    Exit? [N] n
    
    Do you wish to continue? [N] y
    Prerequisite check complete.
    Checking current number of databases...
    Checking for a recent backup
    
    Do you want to verify message store database integrity? [Y] y
    Verifying integrity of message store databases.  This may take a while.
    mysqld is alive
    No errors found
    
    Checking for installable packages
    
    Found zimbra-core
    Found zimbra-ldap
    Found zimbra-logger
    Found zimbra-mta
    Found zimbra-snmp
    Found zimbra-store
    Found zimbra-apache
    Found zimbra-spell
    Found zimbra-convertd
    Found zimbra-memcached
    Found zimbra-proxy
    Found zimbra-archiving
    
    
    The Zimbra Collaboration Suite appears already to be installed.
    It can be upgraded with no effect on existing accounts,
    or the current installation can be completely removed prior
    to installation for a clean install.
    
    Do you wish to upgrade? [Y] y
    
    Select the packages to install
        Upgrading zimbra-core
        Upgrading zimbra-ldap
        Upgrading zimbra-logger
        Upgrading zimbra-mta
        Upgrading zimbra-snmp
        Upgrading zimbra-store
        Upgrading zimbra-apache
        Upgrading zimbra-spell
        Upgrading zimbra-convertd
    
    Install zimbra-memcached [N] n
    
    Install zimbra-proxy [N] n
        Upgrading zimbra-archiving
    Checking required space for zimbra-core
    checking space for zimbra-store
    
    Installing:
        zimbra-core
        zimbra-ldap
        zimbra-logger
        zimbra-mta
        zimbra-snmp
        zimbra-store
        zimbra-apache
        zimbra-spell
        zimbra-convertd
        zimbra-archiving
    
    The system will be modified.  Continue? [N] y
    
    Shutting down zimbra mail
    
    Backing up the ldap database...done.
    
    Removing existing packages
    
       zimbra-ldap...done
       zimbra-logger...done
       zimbra-mta...done
       zimbra-snmp...done
       zimbra-store...done
       zimbra-spell...done
       zimbra-convertd...done
       zimbra-archiving...done
       zimbra-apache...done
       zimbra-core...done
    
    Removing deployed webapp directories
    Installing packages
    
        zimbra-core......zimbra-core_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-ldap......zimbra-ldap_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-logger......zimbra-logger_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-mta......zimbra-mta_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-snmp......zimbra-snmp_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-store......zimbra-store_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-apache......zimbra-apache_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-spell......zimbra-spell_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-convertd......zimbra-convertd_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
        zimbra-archiving......zimbra-archiving_7.1.4_GA_2555.UBUNTU8_64_amd64.deb...done
    
    Setting defaults from saved config in /opt/zimbra/.saveconfig/config.save
       HOSTNAME=mail2.dmrcom.com
       LDAPHOST=mail2.dmrcom.com
       LDAPPORT=389
       SNMPTRAPHOST=mail2.dmrcom.com
       SMTPSOURCE=admin@poboxdmr.com
       SMTPDEST=admin@poboxdmr.com
       SNMPNOTIFY=yes
       SMTPNOTIFY=yes
       LDAPROOTPW=zimbra
       LDAPZIMBRAPW=zimbra
       LDAPPOSTPW=zimbra
       LDAPREPPW=6kN8JFmF
       LDAPAMAVISPW=z1mbr4
       LDAPNGINXPW=6kN8JFmF
    Restoring existing configuration file from /opt/zimbra/.saveconfig/localconfig.xml...done
    Operations logged to /tmp/zmsetup.09222013-231052.log
    Upgrading from 6.0.16_GA_2998 to 7.1.4_GA_2555
    Stopping zimbra services...done.
    Verifying /opt/zimbra/conf/my.cnf
    Starting mysql...
    root@mail2:/tmp/zcs-NETWORK-7.1.4_GA_2555.UBUNTU8_64.20120105094735# vim /opt/zimbra/bin/mysql.server
    root@mail2:/tmp/zcs-NETWORK-7.1.4_GA_2555.UBUNTU8_64.20120105094735# /opt/zimbra/libexec/zmsetup.pl
    Operations logged to /tmp/zmsetup.09222013-232033.log
    Upgrading from 6.0.16_GA_2998 to 7.1.4_GA_2555
    Stopping zimbra services...done.
    Verifying /opt/zimbra/conf/my.cnf
    Starting mysql...
    everything is working except mysqld
    Code:
    zimbra@mail2:~/mysql/bin$ zmcontrol status
    Host mail2.dmrcom.com
            antispam                Running
            antivirus               Running
            convertd                Running
            ldap                    Running
            logger                  Running
            mailbox                 Stopped
                    mysql.server is not running.
            mta                     Stopped
                    postfix is not running
            snmp                    Running
            spell                   Running
            stats                   Running
            zmconfigd               Running
    zimbra@mail2:~/mysql/bin$
    attempting to start mysqld manually
    Code:
    imbra@mail2:~/mysql/bin$ ./mysqld_safe --defaults-file=/opt/zimbra/conf/my.cnf  --external-locking --skip-grant-tables
    130922 23:39:24 mysqld_safe Logging to '/opt/zimbra/db/data/mail2.poboxdmr.com.err'.
    130922 23:39:24 mysqld_safe Starting mysqld daemon with databases from /opt/zimbra/db/data
    130922 23:39:24 mysqld_safe mysqld from pid file /opt/zimbra/db/mysql.pid ended
    error log
    Code:
    130922 21:44:23  mysqld started
    nohup: ignoring input
    130922 21:44:24  InnoDB: Started; log sequence number 3 4089418735
    130922 21:44:24 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.87-log'  socket: '/opt/zimbra/db/mysql.sock'  port: 7306  Source distribution
    130922 23:38:28 mysqld_safe Starting mysqld daemon with databases from /opt/zimbra/db/data
    130922 23:38:28 [Warning] '--log_slow_queries' is deprecated and will be removed in a future release. Please use ''--slow_query_log'/'--slow_query_log_file'' instead.
    130922 23:38:28 [Warning] '--log-long-format' is deprecated and will be removed in a future release. Please use '--log-short-format' instead.
    /opt/zimbra/mysql-standard-5.1.58-pc-linux-gnu-i686-glibc23/libexec/mysqld: Table 'mysql.plugin' doesn't exist
    130922 23:38:28 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
    130922 23:38:28 [ERROR] /opt/zimbra/mysql-standard-5.1.58-pc-linux-gnu-i686-glibc23/libexec/mysqld: unknown variable 'innodb_flush_log_at_trx_commit=0'
    130922 23:38:28 [ERROR] Aborting
    
    130922 23:38:28 [Note] /opt/zimbra/mysql-standard-5.1.58-pc-linux-gnu-i686-glibc23/libexec/mysqld: Shutdown complete
    
    130922 23:38:28 mysqld_safe mysqld from pid file /opt/zimbra/db/mysql.pid ended
    130922 23:39:24 mysqld_safe Starting mysqld daemon with databases from /opt/zimbra/db/data
    130922 23:39:24 [Warning] '--log_slow_queries' is deprecated and will be removed in a future release. Please use ''--slow_query_log'/'--slow_query_log_file'' instead.
    130922 23:39:24 [Warning] '--log-long-format' is deprecated and will be removed in a future release. Please use '--log-short-format' instead.
    130922 23:39:24 [ERROR] /opt/zimbra/mysql-standard-5.1.58-pc-linux-gnu-i686-glibc23/libexec/mysqld: unknown variable 'innodb_flush_log_at_trx_commit=0'
    130922 23:39:24 [ERROR] Aborting
    
    130922 23:39:24 [Note] /opt/zimbra/mysql-standard-5.1.58-pc-linux-gnu-i686-glibc23/libexec/mysqld: Shutdown complete
    
    130922 23:39:24 mysqld_safe mysqld from pid file /opt/zimbra/db/mysql.pid ended
    output from the mysql_upgrade
    Code:
    zimbra@mail2:~/mysql/bin$ ./mysql_upgrade
    Looking for 'mysql' as: ./mysql
    Looking for 'mysqlcheck' as: ./mysqlcheck
    Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock'
    ./mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) when trying to connect
    FATAL ERROR: Upgrade failed
    So I have moved up 1 major version, 2 more to go. Any suggestions would be good.
    Last edited by SageMajor; 09-22-2013 at 11:45 PM.

  5. #15
    SageMajor is offline Senior Member
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    I called in to zimbra today to get support to work on this issue, anyone know how long it takes them to get back to a customer?

  6. #16
    tonster is offline Zimbra Employee
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    Quote Originally Posted by SageMajor View Post
    I called in to zimbra today to get support to work on this issue, anyone know how long it takes them to get back to a customer?
    It depends on several factors, depending on your support level (Advantage vs. Premium), as well as the severity of the issue reported (Sev-1 to Sev-4). Generally we'll reply within a couple of hours, but if it's low severity and you've got Advantage support then your SLA could be 12-24 hours.

  7. #17
    SageMajor is offline Senior Member
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    I attempted to engage your sales team to renew my support but they want me to pay 4 years of back support and the current one would end in 3 months. This seems unacceptable to us as we no loner host customers on zimbra and just use it for inhouse mail.

    Whit that being said can you suggest what my next step should be to resolve this issue.

    Sage

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