Upgrade to Zimbra 7 - Table upgrade required

[n8bounds]

Saw this error:

zimbra@mail:~$ /opt/zimbra/libexec/zmdbintegrityreport
Database errors found.
/opt/zimbra/mysql/bin/mysqlcheck --defaults-file=/opt/zimbra/conf/my.cnf -S /opt/zimbra/db/mysql.sock -A -C -s -u root --password=vGon83gjgpoRky3HYvQW6qWUNU3ekaC1
mboxgroup1.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup1.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup1.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup1.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup1.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mboxgroup2.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup2.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup2.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup2.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup2.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mboxgroup3.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup3.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup3.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup3.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup3.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mboxgroup4.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup4.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup4.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup4.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup4.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mboxgroup5.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup5.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup5.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup5.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup5.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mboxgroup6.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup6.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup6.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup6.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup6.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mboxgroup7.appointment
 error    : Table upgrade required. Please do "REPAIR TABLE `appointment`" or dump/reload to fix it!
 mboxgroup7.data_source_item
 error    : Table upgrade required. Please do "REPAIR TABLE `data_source_item`" or dump/reload to fix it!
 mboxgroup7.imap_folder
 error    : Table upgrade required. Please do "REPAIR TABLE `imap_folder`" or dump/reload to fix it!
 mboxgroup7.mail_item
 error    : Table upgrade required. Please do "REPAIR TABLE `mail_item`" or dump/reload to fix it!
 mboxgroup7.pop3_message
 error    : Table upgrade required. Please do "REPAIR TABLE `pop3_message`" or dump/reload to fix it!
 mysql.general_log
 Error    : You can't use locks with log tables.
 mysql.slow_log
 Error    : You can't use locks with log tables.
 zimbra.config
 error    : Table upgrade required. Please do "REPAIR TABLE `config`" or dump/reload to fix it!
 zimbra.deleted_account
 error    : Table upgrade required. Please do "REPAIR TABLE `deleted_account`" or dump/reload to fix it!
 zimbra.mailbox
 error    : Table upgrade required. Please do "REPAIR TABLE `mailbox`" or dump/reload to fix it!
 zimbra.mailbox_metadata
 error    : Table upgrade required. Please do "REPAIR TABLE `mailbox_metadata`" or dump/reload to fix it!
 zimbra.mobile_devices
 error    : Table upgrade required. Please do "REPAIR TABLE `mobile_devices`" or dump/reload to fix it!
 zimbra.out_of_office
 error    : Table upgrade required. Please do "REPAIR TABLE `out_of_office`" or dump/reload to fix it!
 zimbra.scheduled_task
 error    : Table upgrade required. Please do "REPAIR TABLE `scheduled_task`" or dump/reload to fix it!
 zimbra.table_maintenance
 error    : Table upgrade required. Please do "REPAIR TABLE `table_maintenance`" or dump/reload to fix it!
 zimbra.volume
 error    : Table upgrade required. Please do "REPAIR TABLE `volume`" or dump/reload to fix it!

The release notes warned about this, so I ran the repair script:

zimbra@mail:~$ /opt/zimbra/libexec/scripts/migrate20100913-Mysql51.pl
Adding mboxgroup1.mail_item to be optimized
Adding mboxgroup1.appointment to be optimized
Adding mboxgroup1.imap_folder to be optimized
Adding mboxgroup1.imap_message to be optimized
Adding mboxgroup1.open_conversation to be optimized
Adding mboxgroup1.pop3_message to be optimized
Adding mboxgroup1.revision to be optimized
Adding mboxgroup1.tombstone to be optimized
Adding mboxgroup1.data_source_item to be optimized
Adding mboxgroup2.mail_item to be optimized
Adding mboxgroup2.appointment to be optimized
Adding mboxgroup2.imap_folder to be optimized
Adding mboxgroup2.imap_message to be optimized
Adding mboxgroup2.open_conversation to be optimized
Adding mboxgroup2.pop3_message to be optimized
Adding mboxgroup2.revision to be optimized
Adding mboxgroup2.tombstone to be optimized
Adding mboxgroup2.data_source_item to be optimized
Adding mboxgroup3.mail_item to be optimized
Adding mboxgroup3.appointment to be optimized
Adding mboxgroup3.imap_folder to be optimized
Adding mboxgroup3.imap_message to be optimized
Adding mboxgroup3.open_conversation to be optimized
Adding mboxgroup3.pop3_message to be optimized
Adding mboxgroup3.revision to be optimized
Adding mboxgroup3.tombstone to be optimized
Adding mboxgroup3.data_source_item to be optimized
Adding mboxgroup4.mail_item to be optimized
Adding mboxgroup4.appointment to be optimized
Adding mboxgroup4.imap_folder to be optimized
Adding mboxgroup4.imap_message to be optimized
Adding mboxgroup4.open_conversation to be optimized
Adding mboxgroup4.pop3_message to be optimized
Adding mboxgroup4.revision to be optimized
Adding mboxgroup4.tombstone to be optimized
Adding mboxgroup4.data_source_item to be optimized
Adding mboxgroup5.mail_item to be optimized
Adding mboxgroup5.appointment to be optimized
Adding mboxgroup5.imap_folder to be optimized
Adding mboxgroup5.imap_message to be optimized
Adding mboxgroup5.open_conversation to be optimized
Adding mboxgroup5.pop3_message to be optimized
Adding mboxgroup5.revision to be optimized
Adding mboxgroup5.tombstone to be optimized
Adding mboxgroup5.data_source_item to be optimized
Adding mboxgroup6.mail_item to be optimized
Adding mboxgroup6.appointment to be optimized
Adding mboxgroup6.imap_folder to be optimized
Adding mboxgroup6.imap_message to be optimized
Adding mboxgroup6.open_conversation to be optimized
Adding mboxgroup6.pop3_message to be optimized
Adding mboxgroup6.revision to be optimized
Adding mboxgroup6.tombstone to be optimized
Adding mboxgroup6.data_source_item to be optimized
Adding mboxgroup7.mail_item to be optimized
Adding mboxgroup7.appointment to be optimized
Adding mboxgroup7.imap_folder to be optimized
Adding mboxgroup7.imap_message to be optimized
Adding mboxgroup7.open_conversation to be optimized
Adding mboxgroup7.pop3_message to be optimized
Adding mboxgroup7.revision to be optimized
Adding mboxgroup7.tombstone to be optimized
Adding mboxgroup7.data_source_item to be optimized
Adding zimbra.volume to be optimized
Adding zimbra.current_volumes to be optimized
Adding zimbra.mailbox to be optimized
Adding zimbra.deleted_account to be optimized
Adding zimbra.mailbox_metadata to be optimized
Adding zimbra.out_of_office to be optimized
Adding zimbra.config to be optimized
Adding zimbra.table_maintenance to be optimized
Adding zimbra.scheduled_task to be optimized
Adding zimbra.mobile_devices to be optimized
...........

Altered 7 mailbox groups in 15 seconds

...but only received partial joy:

zimbra@mail:~$ /opt/zimbra/libexec/zmdbintegrityreport
Database errors found.
/opt/zimbra/mysql/bin/mysqlcheck --defaults-file=/opt/zimbra/conf/my.cnf -S /opt/zimbra/db/mysql.sock -A -C -s -u root --password=vGon83gjgpoRky3HYvQW6qWUNU3ekaC1
mysql.general_log
 Error    : You can't use locks with log tables.
 mysql.slow_log
 Error    : You can't use locks with log tables.

Restarting the server doesn't help:

zimbra@mail:~$ date; zmcontrol stop; zmcontrol start; date
Mon Feb 28 12:25:26 EST 2011
Host mail.n8.thruhere.net
	Stopping stats...Done.
	Stopping mta...Done.
	Stopping spell...Done.
	Stopping snmp...Done.
	Stopping cbpolicyd...Done.
	Stopping archiving...Done.
	Stopping antivirus...Done.
	Stopping antispam...Done.
	Stopping imapproxy...Done.
	Stopping memcached...Done.
	Stopping mailbox...Done.
	Stopping logger...Done.
	Stopping zmconfigd...Done.
	Stopping ldap...Done.
Host mail.n8.thruhere.net
	Starting ldap...Done.
	Starting zmconfigd...Done.
	Starting logger...Done.
	Starting mailbox...Done.
	Starting antispam...Done.
	Starting antivirus...Done.
	Starting snmp...Done.
	Starting spell...Done.
	Starting mta...Done.
	Starting stats...Done.
Mon Feb 28 12:28:23 EST 2011

zimbra@mail:~$ date; /opt/zimbra/libexec/scripts/migrate20100913-Mysql51.pl; /opt/zimbra/libexec/zmdbintegrityreport; date
Mon Feb 28 12:28:37 EST 2011
Adding mboxgroup1.mail_item to be optimized
Adding mboxgroup1.appointment to be optimized
Adding mboxgroup1.imap_folder to be optimized
Adding mboxgroup1.imap_message to be optimized
Adding mboxgroup1.open_conversation to be optimized
Adding mboxgroup1.pop3_message to be optimized
Adding mboxgroup1.revision to be optimized
Adding mboxgroup1.tombstone to be optimized
Adding mboxgroup1.data_source_item to be optimized
Adding mboxgroup2.mail_item to be optimized
Adding mboxgroup2.appointment to be optimized
Adding mboxgroup2.imap_folder to be optimized
Adding mboxgroup2.imap_message to be optimized
Adding mboxgroup2.open_conversation to be optimized
Adding mboxgroup2.pop3_message to be optimized
Adding mboxgroup2.revision to be optimized
Adding mboxgroup2.tombstone to be optimized
Adding mboxgroup2.data_source_item to be optimized
Adding mboxgroup3.mail_item to be optimized
Adding mboxgroup3.appointment to be optimized
Adding mboxgroup3.imap_folder to be optimized
Adding mboxgroup3.imap_message to be optimized
Adding mboxgroup3.open_conversation to be optimized
Adding mboxgroup3.pop3_message to be optimized
Adding mboxgroup3.revision to be optimized
Adding mboxgroup3.tombstone to be optimized
Adding mboxgroup3.data_source_item to be optimized
Adding mboxgroup4.mail_item to be optimized
Adding mboxgroup4.appointment to be optimized
Adding mboxgroup4.imap_folder to be optimized
Adding mboxgroup4.imap_message to be optimized
Adding mboxgroup4.open_conversation to be optimized
Adding mboxgroup4.pop3_message to be optimized
Adding mboxgroup4.revision to be optimized
Adding mboxgroup4.tombstone to be optimized
Adding mboxgroup4.data_source_item to be optimized
Adding mboxgroup5.mail_item to be optimized
Adding mboxgroup5.appointment to be optimized
Adding mboxgroup5.imap_folder to be optimized
Adding mboxgroup5.imap_message to be optimized
Adding mboxgroup5.open_conversation to be optimized
Adding mboxgroup5.pop3_message to be optimized
Adding mboxgroup5.revision to be optimized
Adding mboxgroup5.tombstone to be optimized
Adding mboxgroup5.data_source_item to be optimized
Adding mboxgroup6.mail_item to be optimized
Adding mboxgroup6.appointment to be optimized
Adding mboxgroup6.imap_folder to be optimized
Adding mboxgroup6.imap_message to be optimized
Adding mboxgroup6.open_conversation to be optimized
Adding mboxgroup6.pop3_message to be optimized
Adding mboxgroup6.revision to be optimized
Adding mboxgroup6.tombstone to be optimized
Adding mboxgroup6.data_source_item to be optimized
Adding mboxgroup7.mail_item to be optimized
Adding mboxgroup7.appointment to be optimized
Adding mboxgroup7.imap_folder to be optimized
Adding mboxgroup7.imap_message to be optimized
Adding mboxgroup7.open_conversation to be optimized
Adding mboxgroup7.pop3_message to be optimized
Adding mboxgroup7.revision to be optimized
Adding mboxgroup7.tombstone to be optimized
Adding mboxgroup7.data_source_item to be optimized
Adding zimbra.volume to be optimized
Adding zimbra.current_volumes to be optimized
Adding zimbra.mailbox to be optimized
Adding zimbra.deleted_account to be optimized
Adding zimbra.mailbox_metadata to be optimized
Adding zimbra.out_of_office to be optimized
Adding zimbra.config to be optimized
Adding zimbra.table_maintenance to be optimized
Adding zimbra.scheduled_task to be optimized
Adding zimbra.mobile_devices to be optimized
...........

Altered 7 mailbox groups in 13 seconds
Database errors found.
/opt/zimbra/mysql/bin/mysqlcheck --defaults-file=/opt/zimbra/conf/my.cnf -S /opt/zimbra/db/mysql.sock -A -C -s -u root --password=vGon83gjgpoRky3HYvQW6qWUNU3ekaC1
mysql.general_log
 Error    : You can't use locks with log tables.
 mysql.slow_log
 Error    : You can't use locks with log tables.
Mon Feb 28 12:28:53 EST 2011

does anyone have a cluebat they can swing my way?

[phoenix]

Originally Posted by n8bounds

does anyone have a cluebat they can swing my way?

They are warnings not an error, you can ignore them.

[albgdy]

When you run the script I see that you did with the zimbra user and was the server zimbra up?
Should be done in this way or as root?

[n8bounds]

Originally Posted by albgdy

When you run the script I see that you did with the zimbra user and was the server zimbra up?
Should be done in this way or as root?

It won't work with the server down. It did all the other changes as $notroot, so I assumed they intended for you to run it as zimbra, like most of their scripts. I'll try it as root today.

[phoenix]

Originally Posted by n8bounds

It won't work with the server down. It did all the other changes as $notroot, so I assumed they intended for you to run it as zimbra, like most of their scripts. I'll try it as root today.

You do not run Zimbra scripts as root unless you're told to do that. You also don't need to run this script again, I've already told you that the messages you've seen are warnings not errors and can be ignored.

[aswen]

@Phoenix: I don't understand why one has integrity check scripts and then should ignore the error that are the result of them. WHenever you receive an error you have to act.
so, in this case you should stop zimbra, remove slow_log.frm and general_log.frm (i moved them to /tmp after making a complete backup) from /opt/zimbra/db/data/mysql and then start zimbra again. /opt/zimbra/libexec/zmdbintegrityreport works then again.
So, in the future, any message from this report will be taken seriously instead of ignored because it fails every day.

[jrefl5]

I hit this on First Database Integrity check after 6.0.9 -> 7.1 upgrade.

The "migrate20100913-Mysql51.pl" script took care of all but the log errors.

I now need to clean up the log messages,

@Phoenix the error message is a bug, if there is not a "Documented Fix" I want a clean report and not need to check that its the same error I've been seeing for X weeks.

I'm be heading to BugZilla for this one.

[jorge_s]

There are already bug reports about this issue, apparently they are MySQL bugs and not Zimbra bugs.

more info in this thread:
http://www.zimbra.com/forums/install...s-ose-7-a.html

You can find the MySQL bug reports there. This thread should be marked as [SOLVED] now.

And remeber, Google is your friend

[phoenix]

Originally Posted by jrefl5

@Phoenix the error message is a bug, if there is not a "Documented Fix" I want a clean report and not need to check that its the same error I've been seeing for X weeks.

You are correct but it's not a Zimbra bug - see the post above and a search would have told you that. You can still ignore the message as it's harmless.

[msheean]

So should the zimbra server be shut down and only have mysql.server running to do the migrate20100913-Mysql51.pl script or is it ok to run on a live server?