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Thread: Upgrade 4.5.1 -> 4.5.2 Network Edition on RH Failed

  1. #1
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    Default Upgrade 4.5.1 -> 4.5.2 Network Edition on RH Failed

    Hi,

    tested two times to upgrade to 4.5.2 (from 4.5.1)

    But failed with following error:

    Fri Feb 23 20:43:03 2007: Starting mysql
    ERROR 1017 (HY000) at line 1: Can't find file: 'config' (errno: 2)
    Error while running '/opt/zimbra/bin/mysql --user=zimbra --password=[password here] --database=zimbra --batch --skip-column-names'. at /opt/zimbra/libexec/scripts/Migrate.pm line 220.

    Fortunately downgrade afterwards was OK

    Any idea ?

    Cheers
    Christian
    Last edited by jholder; 02-23-2007 at 01:01 PM.

  2. #2
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    Lets take a look at a couple things. Brian will have more info than I but what's your
    df -h look like?

    Also, try running the zmfixperms script located in the /opt/zimbra/libexec dir, and let me know how it works out.

    -john
    Last edited by jholder; 02-23-2007 at 01:05 PM.

  3. #3
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    Are you sure your 4.5.1 install is functioning correctly? That error indicates the zimbra db config table is missing or corrupt. Either way your install wouldn't really function without it.

    Make surethe config table is there.
    mysql -u zimbra -Dzimbra -e "show tables;"

    mysql HY000 1017 is file not found so make sure /opt/zimbra/db/data/zimbra/config.{frm,ibd} exists
    Bugzilla - Wiki - Downloads - Before posting... Search!

  4. #4
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    * Are you sure your 4.5.1 install is functioning correctly?

    Yes, using it daily for testing incl. mobile and Outlook

    zmcontrol status
    Host abcd
    antispam Running
    antivirus Running
    ldap Running
    logger Running
    mailbox Running
    mta Running
    snmp Running
    spell Running

    * what's your df -h look like?

    Easy ;-)

    Filesystem Size Used Avail Use% Mounted on
    /dev/mapper/VolGroup00-LogVol00
    536G 49G 460G 10% /
    /dev/sda1 99M 52M 43M 55% /boot
    none 4.0G 0 4.0G 0% /dev/shm

    * try running the zmfixperms script located in the /opt/zimbra/libexec dir, and let me know how it works out.

    /opt/zimbra/libexec/

    As zimbra
    zmfixperms (Operation not permitted)

    As root
    zmfixperms (No output at all)

    * Make sure the config table is there.
    mysql -u zimbra -Dzimbra -e "show tables;"

    su zimbra
    $ mysql -u zimbra -Dzimbra -e "show tables;"
    +-------------------+
    | Tables_in_zimbra |
    +-------------------+
    | config |
    | current_volumes |
    | mailbox |
    | mailbox_metadata |
    | out_of_office |
    | service_status |
    | table_maintenance |
    | volume |
    +-------------------+

    * mysql HY000 1017 is file not found so make sure /opt/zimbra/db/data/zimbra/config.{frm,ibd} exists

    cd /opt/zimbra/db/data/zimbra
    $ ll
    total 1124
    -rw-rw---- 1 zimbra zimbra 8674 Jul 12 2006 config.frm
    -rw-rw---- 1 zimbra zimbra 98304 Jan 17 07:38 config.ibd

    * OK - tried again :

    Did a fresh Download ....

    Install :

    :-( :-( :-( :-( No Change :-( :-( :-( :-(

    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]

    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

    Installing:
    zimbra-core
    zimbra-ldap
    zimbra-logger
    zimbra-mta
    zimbra-snmp
    zimbra-store
    zimbra-apache
    zimbra-spell

    The system will be modified. Continue? [N] y

    Shutting down zimbra mail

    Backing up ldap


    Removing existing packages

    zimbra-ldap...done
    zimbra-logger...done
    zimbra-mta...done
    zimbra-snmp...done
    zimbra-store...done
    zimbra-spell...done
    zimbra-apache...done
    zimbra-core...done

    Removing deployed webapp directories
    Installing packages

    zimbra-core......zimbra-core-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-ldap......zimbra-ldap-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-logger......zimbra-logger-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-mta......zimbra-mta-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-snmp......zimbra-snmp-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-store......zimbra-store-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-apache......zimbra-apache-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done
    zimbra-spell......zimbra-spell-4.5.2_GA_699.RHEL4-20070216151950.i386.rpm...done

    Setting defaults from saved config in /opt/zimbra/.saveconfig/config.save
    HOSTNAME=abcd
    LDAPHOST=abcd
    LDAPPORT=389
    SNMPTRAPHOST=abcd
    SMTPSOURCE=abcd
    SMTPDEST=abcd
    SNMPNOTIFY=yes
    SMTPNOTIFY=yes
    LDAPROOTPW=abcd
    LDAPZIMBRAPW=abcd

    =====>>>>>>>>>>

    Restoring existing configuration file from /opt/zimbra/.saveconfig/config.save...Restoring backup schedule...done
    Operations logged to /tmp/zmsetup.log.14032
    Setting defaults...Setting defaults from existing config...Done
    Upgrading from 4.5.1_GA_660 to 4.5.2_GA_699
    Sat Feb 24 16:48:57 2007: Stopping zimbra services
    Sat Feb 24 16:49:02 2007: Starting mysql
    ERROR 1017 (HY000) at line 1: Can't find file: 'config' (errno: 2)
    Error while running '/opt/zimbra/bin/mysql --user=zimbra --password=[Password Here] --database=zimbra --batch --skip-column-names'. at /opt/zimbra/libexec/scripts/Migrate.pm line 220.
    Last edited by jholder; 02-28-2007 at 08:56 PM. Reason: Took password out.

  5. #5
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    How much memory does your server have? Your buffer settings in /opt/zimbra/conf/my.cnf might be set too high, during the initial install. Check the output in /opt/zimbra/db/data/.err for malloc errors, on startup. We had another report of this same error and that was the cause.
    Bugzilla - Wiki - Downloads - Before posting... Search!

  6. #6
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    Quote Originally Posted by brian View Post
    How much memory does your server have? Your buffer settings in /opt/zimbra/conf/my.cnf might be set too high, during the initial install. Check the output in /opt/zimbra/db/data/.err for malloc errors, on startup. We had another report of this same error and that was the cause.
    Hi Brain

    8GB memory -> can be set to high ;-)
    Hope for your advise.

    cheers
    Christian


    * cat /proc/meminfo
    MemTotal: 8308584 kB
    MemFree: 5386764 kB
    Buffers: 100784 kB
    Cached: 1158656 kB
    SwapCached: 0 kB
    Active: 2032176 kB
    Inactive: 756248 kB
    HighTotal: 7470840 kB
    HighFree: 4771520 kB
    LowTotal: 837744 kB
    LowFree: 615244 kB
    SwapTotal: 2031608 kB
    SwapFree: 2031608 kB
    Dirty: 608 kB
    Writeback: 0 kB
    Mapped: 1518228 kB
    Slab: 109328 kB
    CommitLimit: 6185900 kB
    Committed_AS: 6350096 kB
    PageTables: 7888 kB
    VmallocTotal: 106488 kB
    VmallocUsed: 3000 kB
    VmallocChunk: 102984 kB
    HugePages_Total: 0
    HugePages_Free: 0
    Hugepagesize: 2048 kB

    * /opt/zimbra/conf/my.cnf

    [mysqld]

    basedir = /opt/zimbra/mysql
    datadir = /opt/zimbra/db/data
    socket = /opt/zimbra/db/mysql.sock
    pid-file = /opt/zimbra/db/mysql.pid
    bind-address = localhost
    port = 7306
    user = zmbra

    skip-external-locking

    log-slow-queries = /opt/zimbra/log/myslow.log
    long-query-time = 1
    log-long-format
    log-queries-not-using-indexes
    log-bin

    thread_cache = 71
    max_connections = 71

    # We do a lot of writes, query cache turns out to be not useful.
    query_cache_type = 0

    sort_buffer_size = 1048576
    read_buffer_size = 1048576

    # Increase the size of the table cache, since each mailbox has its
    # own set of tables
    table_cache = 500

    innodb_buffer_pool_size = 2552400690
    innodb_log_file_size = 104857600
    innodb_log_buffer_size = 8388608
    innodb_file_per_table

    [mysqld_safe]

    err-log = /opt/zimbra/log/mysqld.log

    __________________________________________________ ________

    * cat /opt/zimbra/db/data/.err

    Sorry couldn't give the upgrade a new try at the moment.

    Just attached the "gibberish" out of the error file. Will give it a clean try asap.

    ------------------------------------------------------
    InnoDB: Error in opening ./ibdata1
    070224 16:52:45 InnoDB: Operating system error number 11 in a file operation.
    InnoDB: Error number 11 means 'Resource temporarily unavailable'.
    InnoDB: Some operating system error numbers are described at
    InnoDB: http://dev.mysql.com/doc/refman/5.0/...ror-codes.html
    InnoDB: Could not open or create data files.
    InnoDB: If you tried to add new data files, and it failed here,
    InnoDB: you should now edit innodb_data_file_path in my.cnf back
    InnoDB: to what it was, and remove the new ibdata files InnoDB created
    InnoDB: in this failed attempt. InnoDB only wrote those files full of
    InnoDB: zeros, but did not yet use them in any way. But be careful: do not
    InnoDB: remove old data files which contain your precious data!
    070224 16:52:45 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.33-log' socket: '/opt/zimbra/db/mysql.sock' port: 7306 Source distribution
    InnoDB: Unable to lock ./ibdata1, error: 11
    InnoDB: Check that you do not already have another mysqld process
    InnoDB: using the same InnoDB data or log files.
    070224 16:52:46 InnoDB: Unable to open the first data file
    InnoDB: Error in opening ./ibdata1
    070224 16:52:46 InnoDB: Operating system error number 11 in a file operation.
    InnoDB: Error number 11 means 'Resource temporarily unavailable'.
    InnoDB: Some operating system error numbers are described at
    InnoDB: http://dev.mysql.com/doc/refman/5.0/...ror-codes.html
    InnoDB: Could not open or create data files.
    InnoDB: If you tried to add new data files, and it failed here,
    InnoDB: you should now edit innodb_data_file_path in my.cnf back
    InnoDB: to what it was, and remove the new ibdata files InnoDB created
    InnoDB: in this failed attempt. InnoDB only wrote those files full of
    InnoDB: zeros, but did not yet use them in any way. But be careful: do not
    InnoDB: remove old data files which contain your precious data!
    070224 16:52:46 [ERROR] Can't start server: Bind on TCP/IP port: Address already in use
    070224 16:52:46 [ERROR] Do you already have another mysqld server running on port: 7306 ?
    070224 16:52:46 [ERROR] Aborting

    070224 16:52:46 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    InnoDB: Unable to lock ./ibdata1, error: 11
    InnoDB: Check that you do not already have another mysqld process
    InnoDB: using the same InnoDB data or log files.
    070224 16:52:46 InnoDB: Unable to open the first data file
    InnoDB: Error in opening ./ibdata1
    070224 16:52:46 InnoDB: Operating system error number 11 in a file operation.
    InnoDB: Error number 11 means 'Resource temporarily unavailable'.
    InnoDB: Some operating system error numbers are described at
    InnoDB: http://dev.mysql.com/doc/refman/5.0/...ror-codes.html
    InnoDB: Could not open or create data files.
    InnoDB: If you tried to add new data files, and it failed here,
    InnoDB: you should now edit innodb_data_file_path in my.cnf back
    InnoDB: to what it was, and remove the new ibdata files InnoDB created
    InnoDB: in this failed attempt. InnoDB only wrote those files full of
    InnoDB: zeros, but did not yet use them in any way. But be careful: do not
    InnoDB: remove old data files which contain your precious data!
    070224 16:52:46 [ERROR] Can't start server: Bind on TCP/IP port: Address already in use
    070224 16:52:46 [ERROR] Do you already have another mysqld server running on port: 7306 ?
    070224 16:52:46 [ERROR] Aborting

    070224 16:52:46 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    070224 16:52:46 mysqld ended

    070224 16:52:46 mysqld ended

    070224 16:53:05 InnoDB: We now intentionally generate a seg fault so that
    InnoDB: on Linux we get a stack trace.
    mysqld got signal 11;
    This could be because you hit a bug. It is also possible that this binary
    or one of the libraries it was linked against is corrupt, improperly built,
    or misconfigured. This error can also be caused by malfunctioning hardware.
    We will try our best to scrape up some info that will hopefully help diagnose
    the problem, but since we have already crashed, something is definitely wrong
    and this may fail.

    key_buffer_size=0
    read_buffer_size=1044480
    max_used_connections=0
    max_connections=71
    threads_connected=0
    It is possible that mysqld could use up to
    key_buffer_size + (read_buffer_size + sort_buffer_size)*max_connections = 145123 K
    bytes of memory
    Hope that's ok; if not, decrease some variables in the equation.

    thd=(nil)
    Attempting backtrace. You can use the following information to find out
    where mysqld died. If you see no messages after this, something went
    terribly wrong...
    Cannot determine thread, fp=0xbfe5988c, backtrace may not be correct.
    Stack range sanity check OK, backtrace follows:
    0x816df93
    0x8366ac9
    0x8366b9a
    0x8363e05
    0x8320e05
    0x832551a
    0x8292755
    0x822ab43
    0x8220a32
    0x816e30e
    0x8171f21
    0x1d8de3
    0x80e63f1
    New value of fp=(nil) failed sanity check, terminating stack trace!
    Please read http://dev.mysql.com/doc/mysql/en/us...ack-trace.html and follow instructions on how to resolve the stack trace. Resolved
    stack trace is much more helpful in diagnosing the problem, so please do
    resolve it
    The manual page at http://www.mysql.com/doc/en/Crashing.html contains
    information that should help you find out what is causing the crash.
    070224 16:53:05 mysqld ended

    070224 16:54:53 mysqld started
    070224 16:54:53 [Warning] One can only use the --user switch if running as root

    070224 16:54:53 [Warning] No argument was provided to --log-bin, and --log-bin-index was not used; so replication may break when this MySQL server acts as a master and has his hostname changed!! Please use '--log-bin=zmail-bin' to avoid this problem.
    070224 16:54:54 InnoDB: Error: cannot allocate 161631436 bytes of
    InnoDB: memory with malloc! Total allocated memory
    InnoDB: by InnoDB 2740576092 bytes. Operating system errno: 12
    InnoDB: Check if you should increase the swap file or
    InnoDB: ulimits of your operating system.
    InnoDB: On FreeBSD check you have compiled the OS with
    InnoDB: a big enough maximum process size.
    InnoDB: Note that in most 32-bit computers the process
    InnoDB: memory space is limited to 2 GB or 4 GB.
    InnoDB: We keep retrying the allocation for 60 seconds...
    070224 16:55:54 InnoDB: We now intentionally generate a seg fault so that
    InnoDB: on Linux we get a stack trace.
    mysqld got signal 11;
    This could be because you hit a bug. It is also possible that this binary
    or one of the libraries it was linked against is corrupt, improperly built,
    or misconfigured. This error can also be caused by malfunctioning hardware.
    We will try our best to scrape up some info that will hopefully help diagnose
    the problem, but since we have already crashed, something is definitely wrong
    and this may fail.

    key_buffer_size=0
    read_buffer_size=1044480
    max_used_connections=0
    max_connections=71
    threads_connected=0
    It is possible that mysqld could use up to
    key_buffer_size + (read_buffer_size + sort_buffer_size)*max_connections = 145123 K
    bytes of memory
    Hope that's ok; if not, decrease some variables in the equation.

    thd=(nil)
    Attempting backtrace. You can use the following information to find out
    where mysqld died. If you see no messages after this, something went
    terribly wrong...
    Cannot determine thread, fp=0xbfecb90c, backtrace may not be correct.
    Stack range sanity check OK, backtrace follows:
    0x816df93
    0x8366ac9
    0x8366b9a
    0x8363e05
    0x8320e05
    0x832551a
    0x8292755
    0x822ab43
    0x8220a32
    0x816e30e
    0x8171f21
    0x1d8de3
    0x80e63f1
    New value of fp=(nil) failed sanity check, terminating stack trace!
    Please read http://dev.mysql.com/doc/mysql/en/us...ack-trace.html and follow instructions on how to resolve the stack trace. Resolved
    stack trace is much more helpful in diagnosing the problem, so please do
    resolve it
    The manual page at http://www.mysql.com/doc/en/Crashing.html contains
    information that should help you find out what is causing the crash.
    070224 16:55:54 mysqld ended

    070224 17:00:26 mysqld started
    070224 17:00:26 [Warning] One can only use the --user switch if running as root

    070224 17:00:26 [Warning] No argument was provided to --log-bin, and --log-bin-index was not used; so replication may break when this MySQL server acts as a master and has his hostname changed!! Please use '--log-bin=zmail-bin' to avoid this problem.
    070224 17:00:28 InnoDB: Started; log sequence number 0 242054503
    070224 17:00:28 [ERROR] Can't start server: Bind on TCP/IP port: Address already in use
    070224 17:00:28 [ERROR] Do you already have another mysqld server running on port: 7306 ?
    070224 17:00:28 [ERROR] Aborting

    070224 17:00:28 InnoDB: Starting shutdown...
    070224 17:00:30 InnoDB: Shutdown completed; log sequence number 0 242054503
    070224 17:00:30 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    070224 17:00:30 mysqld ended

    070224 17:44:20 mysqld started
    070224 17:44:20 [Warning] One can only use the --user switch if running as root

    070224 17:44:20 [Warning] No argument was provided to --log-bin, and --log-bin-index was not used; so replication may break when this MySQL server acts as a master and has his hostname changed!! Please use '--log-bin=zmail-bin' to avoid this problem.
    070224 17:44:21 InnoDB: Started; log sequence number 0 242054503
    070224 17:44:21 [ERROR] Can't start server: Bind on TCP/IP port: Address already in use
    070224 17:44:21 [ERROR] Do you already have another mysqld server running on port: 7306 ?
    070224 17:44:21 [ERROR] Aborting

    070224 17:44:21 InnoDB: Starting shutdown...
    070224 17:44:24 InnoDB: Shutdown completed; log sequence number 0 242054503
    070224 17:44:24 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    070224 17:44:24 mysqld ended

    070224 17:47:55 [Note] /opt/zimbra/mysql/libexec/mysqld: Normal shutdown

    070224 17:47:55 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete

    070224 17:47:55 mysqld ended

    070224 17:52:53 mysqld started
    070224 17:52:53 [Warning] One can only use the --user switch if running as root

    070224 17:52:53 [Warning] No argument was provided to --log-bin, and --log-bin-index was not used; so replication may break when this MySQL server acts as a master and has his hostname changed!! Please use '--log-bin=zmail-bin' to avoid this problem.
    070224 17:52:55 InnoDB: Started; log sequence number 0 242054503
    070224 17:52:55 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.26-log' socket: '/opt/zimbra/db/mysql.sock' port: 7306 Source distribution
    A mysqld process already exists at Wed Feb 28 07:46:15 CET 2007

  7. #7
    phoenix is offline Zimbra Consultant & Moderator
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    Try reducing the "innodb_buffer_pool_size " to something less than 2GB, that should fix the problem.
    Regards


    Bill


    Acompli: A new adventure for Co-Founder KevinH.

  8. #8
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    Default >> RESOLVED << Upgrade 4.5.1 -> 4.5.2 Network Edition on RH Failed

    Quote Originally Posted by phoenix View Post
    Try reducing the "innodb_buffer_pool_size " to something less than 2GB, that should fix the problem.
    - RESOLVED -

    TA !

    => innodb_buffer_pool_size = 1992294400
    Did the trick

    :-)

    Cheers
    Christian

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