mysqld fails to start after upgrade: performance_schema definition errors

[Roger Chui]

Upgrading from 14.04 to 16.04, installer reported this bug.

Just need to access the uploaded logs to see if the issue is the same as #1567884

ProblemType: Package
DistroRelease: Ubuntu 16.04
Package: mysql-server-5.7 5.7.11-0ubuntu6
ProcVersionSignature: Ubuntu 3.13.0-85.129-generic 3.13.11-ckt36
Uname: Linux 3.13.0-85-generic x86_64
ApportVersion: 2.20.1-0ubuntu2
Architecture: amd64
Date: Mon Apr 18 11:18:53 2016
ErrorMessage: subprocess installed post-installation script returned error exit status 1
Logs.var.log.daemon.log:

MySQLConf.etc.mysql.conf.d.mysql.cnf: [mysql]
MySQLConf.etc.mysql.conf.d.mysqld_safe_syslog.cnf:
 [mysqld_safe]
 syslog
MySQLConf.etc.mysql.conf.d.mysqldump.cnf:
 [mysqldump]
 quick
 quote-names
 max_allowed_packet = 16M
MySQLConf.etc.mysql.mysql.conf.d.mysqld_safe_syslog.cnf:
 [mysqld_safe]
 syslog
MySQLVarLibDirListing: ['sys', 'auto.cnf', 'ibdata1', 'ibtmp1', 'ib_logfile0', 'mysql_upgrade_info', 'ib_logfile1', 'performance_schema', 'debian-5.5.flag', 'mysql', 'debian-5.7.flag']
ProcCmdline: BOOT_IMAGE=/boot/vmlinuz-3.13.0-85-generic root=UUID=49345884-23c0-4734-b4aa-e82106f7c3c2 ro splash quiet vt.handoff=7
RelatedPackageVersions:
 dpkg 1.18.4ubuntu1
 apt 1.2.10ubuntu1
SourcePackage: mysql-5.7
Title: package mysql-server-5.7 5.7.11-0ubuntu6 failed to install/upgrade: subprocess installed post-installation script returned error exit status 1
UpgradeStatus: Upgraded to xenial on 2016-04-18 (0 days ago)

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[Roger Chui (chui101)]

I am unable to reproduce this error further.

This happened twice on separate VMs when upgrading to 16.04 from clean installs of 14.04.4.

It has stopped happening on further upgrade attempts, so I would tend to think that it has been fixed, maybe as a side effect of some other update?

[Robie Basak (racb)]

You reported version 5.7.11-0ubuntu6 and that hasn't changed. Let's mark this Incomplete until someone can give us a reproducer.

[Jean-Max Reymond (jmreymond-free)]

Is your /var/lib/mysql a soft link ?
I have the bug #1474212 related to soft links

[Marcin Juszkiewicz (hrw)]

17:19 root@malenstwo:etc# dpkg --configure -a
Setting up mysql-server-5.7 (5.7.11-0ubuntu6) ...
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 1813: Tablespace '`mysql`.`innodb_table_stats`' exists.
mysql_upgrade failed with exit status 5
dpkg: error processing package mysql-server-5.7 (--configure):
 subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on mysql-server-5.7; however:
  Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 mysql-server-5.7
 mysql-server
17:20 root@malenstwo:etc# ll /var/log/|grep mysql$
drwxr-s--- 2 mysql adm 4096 Apr 22 06:41 mysql

Mysql 5.7 is working but unable to finish configuration.

[Roger Chui (chui101)]

Maybe there is something wrong with the mysql_update program, since Marcin got

mysql_upgrade: [ERROR] 1813: Tablespace '`mysql`.`innodb_table_stats`' exists.

and I got

mysql_upgrade: [ERROR] 1007: Can't create database 'performance_schema'; database exists

@Marcin does manually running mysql-upgrade work?

[Marcin Juszkiewicz (hrw)]

After removing /var/lib/mysql/mysql/innodb_table_stats.ibd I got:

00:18 root@malenstwo:~# mysql_upgrade
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 1030: Got error 168 from storage engine

MySQL works and all services I have (which uses mysql) work too.

[Robie Basak (racb)]

I've found three other bug reports that follow this pattern. Duping them in.

[Caysho (caysho)]

I get the following error:
mysql_upgrade: [ERROR] 1049: Unknown database 'performance_schema'

I am doing an upgrade from Mythbuntu 14.04 LTS to Mythbuntu 16.04 LTS and the error occurs very near the end of the upgrade.

When I ran
ubuntu-bug mysql
I get told the package is not installed

When I ran
ubuntu-bug mysql-server
I got directed to this bug.

[Caysho (caysho)]

Adding error logs in case they are useful.

[Ben Kietzman (ben-kietzman)]

I looked into the /var/log/mysql/error.log and saw a couple ERROR messages:

2016-05-11T16:44:29.464074Z 0 [ERROR] unknown variable 'key_buffer=16M'
2016-05-11T16:46:47.683724Z 0 [ERROR] unknown variable 'myisam-recover=BACKUP'

I removed the 'key_buffer=16M' and 'myisam-recover=BACKUP' entries from the /etc/mysql/my.cnf and /etc/mysql/mysql.conf.d/mysqld.cnf files.

Then I reran the 'dpkg --configure -a' command. It worked and finished the MySQL configuration.

[Prafulkr (prafulkr)]

Thanks Ben,

But I am not getting that error. BTW I fixed the issue. Thanks a lot

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On Wed, May 11, 2016 at 10:45 PM, Ben Kietzman <email address hidden> wrote:

> I looked into the /var/log/mysql/error.log and saw a couple ERROR
> messages:
>
> 2016-05-11T16:44:29.464074Z 0 [ERROR] unknown variable 'key_buffer=16M'
> 2016-05-11T16:46:47.683724Z 0 [ERROR] unknown variable
> 'myisam-recover=BACKUP'
>
> I removed the 'key_buffer=16M' and 'myisam-recover=BACKUP' entries from
> the /etc/mysql/my.cnf and /etc/mysql/mysql.conf.d/mysqld.cnf files.
>
> Then I reran the 'dpkg --configure -a' command. It worked and finished
> the MySQL configuration.
>
> --
> You received this bug notification because you are subscribed to a
> duplicate bug report (1575088).
> https://bugs.launchpad.net/bugs/1571764
>
> Title:
> mysqld fails to start after upgrade: performance_schema definition
> errors
>
> Status in mysql-5.7 package in Ubuntu:
> Triaged
>
> Bug description:
> Upgrading from 14.04 to 16.04, installer reported this bug.
>
> Just need to access the uploaded logs to see if the issue is the same
> as #1567884
>
> ProblemType: Package
> DistroRelease: Ubuntu 16.04
> Package: mysql-server-5.7 5.7.11-0ubuntu6
> ProcVersionSignature: Ubuntu 3.13.0-85.129-generic 3.13.11-ckt36
> Uname: Linux 3.13.0-85-generic x86_64
> ApportVersion: 2.20.1-0ubuntu2
> Architecture: amd64
> Date: Mon Apr 18 11:18:53 2016
> ErrorMessage: subprocess installed post-installation script returned
> error exit status 1
> Logs.var.log.daemon.log:
>
> MySQLConf.etc.mysql.conf.d.mysql.cnf: [mysql]
> MySQLConf.etc.mysql.conf.d.mysqld_safe_syslog.cnf:
> [mysqld_safe]
> syslog
> MySQLConf.etc.mysql....

[Lars Tangvald (lars-tangvald)]

@ben-kietzman:

Those two options have been renamed to key_buffer_size and myisam_recover_options, so you could do that instead of removing them (since they were not set to the server default values of 8M and OFF).

[shivaraj naidu (shivarajnaidu)]

I got following error while installing updates on ubuntu 16.04
mysql_upgrade: Got error: 2002: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) while connecting to the MySQL server
Upgrade process encountered error and will not continue.
mysql_upgrade failed with exit status 11
dpkg: error processing package mysql-server-5.7 (--configure):
 subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on mysql-server-5.7; however:
  Package mysql-server-5.7 is not configured yet.

dpkg: error processing package mysql-server (--configure):
 dependency problems - leaving unconfigured
No apport report written because the error message indicates its a followup error from a previous failure.
                                                                                                          Errors were encountered while processing:
 mysql-server-5.7
 mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)

[shivaraj naidu (shivarajnaidu)]

I refer this answer http://askubuntu.com/questions/760724/16-04-upgrade-broke-mysql-server/762775#762775

Works for me..

disabled status is the reason...

If you enable and start mysql server with following commands

sudo systemctl enable mysql.service && sudo systemctl start mysql.service

Then upgrading works fine without any issue ... we had previously

[Robie Basak (racb)]

I believe that the root cause of this bug was actually bug 1577712 that we fixed in June (Yakkety) and July (Xenial, 16.04), so am marking this bug as a duplicate of that one. See bug 1577712 for details.

For others subscribed to this bug, or otherwise believe they're affected by this issue: I see many comments above that I think are clearly due to unrelated issues, so this bug is probably not the one you want.

[Dac Chartrand (conner-bw)]

@shivarajnaidu: Thanks for the tip!

`sudo systemctl enable mysql.service && sudo apt upgrade` worked for me.

Even though it works now, I would like to hightlight that I, like many users, disable mysql auto start. My computer is a desktop not a server. I expect to control over these kinds of app. I expect upgrade to work with mysql.service disabled.

Thanks.

[Robie Basak (racb)]

Upgrades failing when the service is disabled is bug 1592669, not this bug. If you are affected, please mark yourself as affected on that bug.