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Thread: [SOLVED] Upgrade 5.0.19 > 6.0.6 hangs on "starting mysql..."

  1. #1
    Jay2k1 is offline Intermediate Member
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    Default [SOLVED] Upgrade 5.0.19 > 6.0.6 hangs on "starting mysql..."

    Hello.

    So I started the upgrade grom 5.0.19 to 6.0.6 Network Edition on CentOS 5 x64. Everything ran smoothly so far, but now it hangs at "starting mysql...".

    I had a look into /opt/zimbra/log/mysql-error.log:
    Code:
    100424 16:57:48 [Note] /opt/zimbra/mysql/libexec/mysqld: Normal shutdown
    
    100424 16:57:49  InnoDB: Starting shutdown...
    100424 16:57:55  InnoDB: Shutdown completed; log sequence number 4 1415862554
    100424 16:57:55 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete
    
    100424 16:57:55  mysqld ended
    
    100424 17:20:46  mysqld started
    100424 17:20:51  InnoDB: Started; log sequence number 4 1415862554
    100424 17:20:51 [Note] /opt/zimbra/mysql/libexec/mysqld: ready for connections.
    Version: '5.0.51a-log'  socket: '/opt/zimbra/db/mysql.sock'  port: 7306  Source distribution
    100424 17:44:40 [Note] /opt/zimbra/mysql/libexec/mysqld: Normal shutdown
    
    100424 17:44:40  InnoDB: Starting shutdown...
    100424 17:44:42  InnoDB: Shutdown completed; log sequence number 4 1416207138
    100424 17:44:42 [Note] /opt/zimbra/mysql/libexec/mysqld: Shutdown complete
    
    100424 17:44:42  mysqld ended
    
    100424 17:46:46  mysqld started
    InnoDB: The first specified data file ./ibdata1 did not exist:
    InnoDB: a new database to be created!
    100424 17:46:46  InnoDB: Setting file ./ibdata1 size to 10 MB
    InnoDB: Database physically writes the file full: wait...
    100424 17:46:46  InnoDB: Log file ./ib_logfile0 did not exist: new to be created
    InnoDB: Setting log file ./ib_logfile0 size to 100 MB
    InnoDB: Database physically writes the file full: wait...
    InnoDB: Progress in MB: 100
    100424 17:46:49  InnoDB: Log file ./ib_logfile1 did not exist: new to be created
    InnoDB: Setting log file ./ib_logfile1 size to 100 MB
    InnoDB: Database physically writes the file full: wait...
    InnoDB: Progress in MB: 100
    InnoDB: Doublewrite buffer not found: creating new
    InnoDB: Doublewrite buffer created
    InnoDB: Creating foreign key constraint system tables
    InnoDB: Foreign key constraint system tables created
    100424 17:46:52  InnoDB: Started; log sequence number 0 0
    100424 17:46:52 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
    100424 17:46:52  mysqld ended
    
    100424 17:46:56  mysqld started
    InnoDB: Log scan progressed past the checkpoint lsn 0 36808
    100424 17:46:57  InnoDB: Database was not shut down normally!
    InnoDB: Starting crash recovery.
    InnoDB: Reading tablespace information from the .ibd files...
    InnoDB: Restoring possible half-written data pages from the doublewrite
    InnoDB: buffer...
    InnoDB: Doing recovery: scanned up to log sequence number 0 43655
    100424 17:46:57  InnoDB: Starting an apply batch of log records to the database...
    InnoDB: Progress in percents: 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
    InnoDB: Apply batch completed
    100424 17:46:58  InnoDB: Started; log sequence number 0 43655
    100424 17:46:58 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
    100424 17:46:58  mysqld ended
    
    100424 17:47:07  mysqld started
    InnoDB: Log scan progressed past the checkpoint lsn 0 36808
    100424 17:47:12  InnoDB: Database was not shut down normally!
    InnoDB: Starting crash recovery.
    InnoDB: Reading tablespace information from the .ibd files...
    InnoDB: Restoring possible half-written data pages from the doublewrite
    InnoDB: buffer...
    InnoDB: Doing recovery: scanned up to log sequence number 0 43655
    100424 17:47:14  InnoDB: Starting an apply batch of log records to the database...
    InnoDB: Progress in percents: 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
    InnoDB: Apply batch completed
    100424 17:47:14  InnoDB: Started; log sequence number 0 43655
    100424 17:47:14 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
    100424 17:47:14  mysqld ended
    
    100424 17:47:18  mysqld started
    InnoDB: Log scan progressed past the checkpoint lsn 0 36808
    100424 17:47:18  InnoDB: Database was not shut down normally!
    InnoDB: Starting crash recovery.
    InnoDB: Reading tablespace information from the .ibd files...
    InnoDB: Restoring possible half-written data pages from the doublewrite
    InnoDB: buffer...
    InnoDB: Doing recovery: scanned up to log sequence number 0 43655
    100424 17:47:18  InnoDB: Starting an apply batch of log records to the database...
    InnoDB: Progress in percents: 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 
    InnoDB: Apply batch completed
    100424 17:47:19  InnoDB: Started; log sequence number 0 43655
    100424 17:47:19 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
    100424 17:47:19  mysqld ended
    Here I cut it because the last parts keep repeating.

    This makes me kind of nervous... any suggestions?

    Edit: Now the install script added a "done" after "starting mysql" and then said "UPGRADE FAILED - exiting". :S
    Last edited by Jay2k1; 04-24-2010 at 09:20 AM.

  2. #2
    Jay2k1 is offline Intermediate Member
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    Default

    So it turns out this problem is bigger than I thought. I opened a support ticket and was helped only a few minutes after.

    Thanks Rick from Zimbra Support for your great help!

  3. #3
    phoenix is offline Zimbra Consultant & Moderator
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    Default

    Quote Originally Posted by Jay2k1 View Post
    So it turns out this problem is bigger than I thought. I opened a support ticket and was helped only a few minutes after
    How about posting the solution for other members to see?
    Regards


    Bill


    Acompli: A new adventure for Co-Founder KevinH.

  4. #4
    Jay2k1 is offline Intermediate Member
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    Default

    I don't really know what was wrong. He said somehow there was no LDAP data, and that he imported it manually, re-running the install.sh afterwards. But I have absolutely no clue what he did in detail.

  5. #5
    StefanFN is offline Intermediate Member
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    Default Same problem updating 6.0.4 to 6.0.7

    Hi,

    having the solution or at least a hint in this thread, would have been great as I just ran into the very same issue with our FOSS on Ubuntu 8.04.
    We are basically suffering a Production Down and I'm trying to resolve it now. I figured out that there's something not quite right with LDAP, since nothing authenticates as the ldap_root_password is not accepted anymore ..even for a simple ldapsearch -x -h ldapi:/// .

    /Stefan

  6. #6
    Jay2k1 is offline Intermediate Member
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    Sorry for the late reply, it was 3:39 am here, I was asleep.

    Thing is, I don't really have a clue about LDAP. We're just using Zimbra for mail and for the ability to have calendar and contacts in sync. Also, I didn't get a detailed report or log about what the support guy did (he ssh'ed into the server). All I can do is quote his mail:
    The first thing I noticed was that ldap had NO data in it. I managed to import ldap data, and copied the mysql data direct from the /zimbra directory; probably a good thing you copied that data. After the data was copied, I reran the installer.
    It took him two and a half hours from logging in the first time until he fixed it. After telling me that he's done and that I should try if things work, I asked him for what was wrong, and he replied with the quoted text above.

    I'm afraid this is all I can do to help here

    Hope this helps,

    Jay

  7. #7
    StefanFN is offline Intermediate Member
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    Default resolved - symlinks restored with mount --bind

    Hi Jay2k1,

    well, now that I managed to get our services back up and running, I'd like to bring up the solution here:
    We have /opt/zimbra/db and /opt/zimbra/data symlinked to a faster drive (RAID10).
    The update process apparently exports /opt/zimbra/data (or parts of it) and then deletes it (don't know why, but it's the case). I guess this happens because it is symlinked.

    I figured that out after running the installer a second time.

    Somewhere in the script it then recreates the directory with a new/or empty ldap database. Now of couse none of the services can retrieve their settings from LDAP and therefore fail to start.

    Solution in my case was to
    Code:
    root@host#mount --bind /path/to/zimbra/data /opt/zimbra/data
    which leads in /etc/fstab to
    Code:
    /path/to/zimbra/data    /opt/zimbra/data    none    rw,bind    0    0
    I did the same for the symlinked /opt/zimbra/db directory.

    Now our store has all its data in it and the mailboxes are current.

    The time consuming thing was learning why it failed and not the solution itself.
    Afterall it's been quite frustrating but I'm glad we didn't lose any data.

    /Stefan

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