Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

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nitrogenetics
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Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby nitrogenetics » Fri Sep 14, 2012 4:59 am

Hi all, after upgrading from Zimbra 7.2.1 to 8.0.0 on Ubuntu 10.04 I noticed the following errors in /opt/zimbra/log/mysql_error.log
120914 11:22:38 mysqld_safe Starting mysqld daemon with databases from /opt/zimbra/db/data

120914 11:22:38 InnoDB: The InnoDB memory heap is disabled

120914 11:22:38 InnoDB: Mutexes and rw_locks use GCC atomic builtins

120914 11:22:38 InnoDB: Compressed tables use zlib 1.2.3.3

120914 11:22:38 InnoDB: Initializing buffer pool, size = 602.0M

120914 11:22:38 InnoDB: Completed initialization of buffer pool

120914 11:22:38 InnoDB: highest supported file format is Barracuda.

120914 11:22:38 InnoDB: Waiting for the background threads to start

120914 11:22:39 InnoDB: 1.1.8 started; log sequence number 1682054

120914 11:22:39 [Note] Server hostname (bind-address): 'localhost'; port: 7306

120914 11:22:39 [Note] - 'localhost' resolves to '::1';

120914 11:22:39 [Note] - 'localhost' resolves to '127.0.0.1';

120914 11:22:39 [Note] Server socket created on IP: '127.0.0.1'.

120914 11:22:39 [ERROR] Missing system table mysql.proxies_priv; please run mysql_upgrade to create it

120914 11:22:39 [ERROR] Native table 'performance_schema'.'events_waits_current' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'events_waits_history' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'events_waits_history_long' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'setup_consumers' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'setup_instruments' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'setup_timers' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'performance_timers' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'threads' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_thread_by_event_name' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_instance' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'events_waits_summary_global_by_event_name' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'file_summary_by_event_name' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'file_summary_by_instance' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'mutex_instances' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'rwlock_instances' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'cond_instances' has the wrong structure

120914 11:22:39 [ERROR] Native table 'performance_schema'.'file_instances' has the wrong structure

120914 11:22:39 [Note] Event Scheduler: Loaded 0 events

120914 11:22:39 [Note] /opt/zimbra/mysql/bin/mysqld: ready for connections.


Running a mysql_upgrade apparently got rid of them

/opt/zimbra/mysql/bin/mysql_upgrade -S /opt/zimbra/db/mysql.sock  -u root --password=yourpassword

(You can get your zimbra mysql root password by running zmlocalconfig -s | grep mysql_root_password )
I also tried to upgrade a clean installation on a vm with the same results.

Apparently zimbra installation is not calling mysql_upgrade, which seems to be recommended when upgrading to a major Mysql engine version (5.1 to 5.5).

Is this the expected behavior? Are there any other steps that need to be addressed manually (not mentioned in the release notes)?
Thanks


1542brian
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Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby 1542brian » Fri Sep 14, 2012 2:27 pm

This is recommended and covered on page 25 of the release notes.

http://files.zimbra.com/website/docs/8.0/Zimbra_NE_Release_Notes_8.0.0.pdf
nitrogenetics
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Joined: Sat Sep 13, 2014 2:38 am

Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby nitrogenetics » Sat Sep 15, 2012 6:32 am

Thanks for your feedback brian, of course I read that, but the manual states that running the upgrade script is only required when upgrading from 6.X.

The errors in the logfile refer explicitly to performance_schema database, so I suppose a zimbra table upgrade is really not needed.
phoenix
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Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby phoenix » Sat Sep 15, 2012 6:36 am

[quote user="nitrogenetics"]Thanks for your feedback brian, of course I read that, but the manual states that running the upgrade script is only required when upgrading from 6.X.

The errors in the logfile refer explicitly to performance_schema database, so I suppose a zimbra table upgrade is really not needed.[/QUOTE]Did you ever have ZCS 6.x installed and upgrade to ZCS 7.x? If you did then you would (should) have seen the same warning, in any case as you've now got the warning you will need to run upgrade the script.
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nitrogenetics
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Joined: Sat Sep 13, 2014 2:38 am

Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby nitrogenetics » Sat Sep 15, 2012 8:15 am

Never had ZCS 6.X installed, it was a fresh 7.2.0 installation.
However, as I said on my first post, you can see the errors even on a clean install:

-Install a new lucid server

-Install ZCS 7.2.1

-Upgrade to ZCS 8.0.0

and you'll get the errors in mysql_error.log.

Run mysql_upgrade and they are gone.
From mysql documentation MySQL :: MySQL 5.5 Reference Manual :: 4.4.7 mysql_upgrade

mysql_upgrade should be executed each time you upgrade MySQL
which seems to be the case, as we are upgrading from Mysql 5.1 on ZCS 7.2.1 to Mysql 5.5 on ZCS 8.0.0 ;)
phoenix
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Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby phoenix » Sat Sep 15, 2012 10:37 am

[quote user="nitrogenetics"]which seems to be the case, as we are upgrading from Mysql 5.1 on ZCS 7.2.1 to Mysql 5.5 on ZCS 8.0.0 ;)[/QUOTE]I suggest you run the upgrade and file a bug report.
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phoenix
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Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby phoenix » Mon Sep 17, 2012 4:47 am

[quote user="nitrogenetics"]Bug report filed:

Thanks for filing that report. :)
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humblemumble
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Errors in mysql_error.log after upgrading to Zimbra 8.0.0 GA

Postby humblemumble » Sat Nov 17, 2012 3:49 pm

hello,
just did and upgrade from 10.04 to 12.04 and afterwards from ZCS OSE from 7.1.4 to 8.0.1. Same error appeared and running the mysql_upgrade didn't help directly. I had to create /etc/mysql/conf.d after it complained, which it was looking for. Without it it failed to perform anything.
hth

br/h

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