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I am getting the following:

Native table 'performance_schema'.'file_instances' has the wrong structure
Native table 'performance_schema'.'cond_instances' has the wrong structure
Native table 'performance_schema'.'rwlock_instances' has the wrong structure
Native table 'performance_schema'.'mutex_instances' has the wrong structure
...

And on it goes These errors come up when I restart MySql. It seems to cause MySql Administrator to become unstable, I get a lot of:

"MySQL server has gone away"
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8 Answers 8

Reset to default
250

Try following command in shell (the root user here is the mysql root user, not the system root)

sudo mysql_upgrade -u root -p

sudo service mysql restart

Make sure to restart mysql after running this (All credit to @Mikepote in the comments.)

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8
  • Yeah, upgrade to the newer version without mysql_upgrade may cause the wrong structure error
    – Truong Hua
    Commented Mar 9, 2015 at 16:04
  • 87
    If anyone still has this error after running mysql_upgrade try restarting the mysql service. This fixed it for me.
    – Mikepote
    Commented Oct 29, 2015 at 13:08
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    Thanks, Mikepote, that's exactly the problem I had. I ran mysql_upgrade, then got this error, and realized after reading your comment that I hadn't restarted mysql.
    – Geoffrey Wiseman
    Commented Nov 25, 2015 at 20:00
  • I was upgrade to 5.7.10 on Ubuntu 15.04 and it required a restart of the machine for that error to disappear from MySQL Workbench.
    – Hatem Jaber
    Commented Jan 16, 2016 at 13:10
  • 2
    Worked for me as well on two debian based machines, though I had to use the --force switch as it was no mysql fault in my case.
    – Nicolas
    Commented Mar 9, 2016 at 22:22
24

Im my case it appeared when specific query was run on a table.

And log also contained:

Missing system table mysql.proxies_priv; please run mysql_upgrade to create it

I've run mysql_upgrade and after that problem has gone.

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1
  • 3
    As above, you have to restart the server after running mysql_upgrade. Until you do, you will continue to see these errors.
    – mostlydev
    Commented Jan 6, 2016 at 14:24
19

I had this problem, the answer was here by @Berend de Boer

Restart mysql after the upgrade.

[ERROR]Native table performance schema has the wrong structure

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8

This error is encountered when you installed MySQL over a previous installation that was configured without the Performance Schema or an older version of Performance schema that may not have all the current tables.

I also encountered this issue on . To resolve it, I have executed the following:

cd /Applications/MAMP/bin/
sudo ./upgradeMysql.sh

Remember to restart the mysql server.

You can read the Performance Schema Build Configuration for more details.

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2

If the database is a Akonadi (KDE) database the above won't be enough. You need to mirror the options given to your mysqld, check with

ps aux | grep mysql

Copy the options to the mysql_upgrade commands (I did not need '-u root -p' but you might)

mysql_upgrade --defaults-file=/home/USER/.local/share/akonadi/mysql.conf --datadir=/home/USER/.local/share/akonadi/db_data/ --socket=/tmp/akonadi-USER.x0Bvxr/mysql.socket

I really think the --socket option is the key.

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2
  • What is it? Never heard of it! @@
    – Scott Chu
    Commented Apr 15, 2016 at 6:39
  • It will be required only if running multiple mysql services on same machine.
    – Zafar Malik
    Commented Jun 2, 2017 at 5:38
0

Try mysql_upgrade and then restart mysql and its working back

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0

It seems this happens after you have done upgrade. Simply restart mysql:

Like run below command in CMD

sudo mysql_upgrade -u root -p

service mysql restart

and the error should now have disappeared.

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-3

Apparently MySQL schema storage is broken due to a reason. These reasons may be:

  • You have broken the database information_schema
  • File system corrupted or some bugs in the file system damaged the database.
  • MySQL internals broke the schema database due to a bug in MySQL (maybe nobody encountered it before).

If you don't have backups however you are still able to access your data, first backup your data then do the following:

If you have backups, then reinstall MySQL (before that completely clear all data of mysql) and then import your data.

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5
  • It was innodb tried a number of times to reinstall, didn't work. In the end I had to reinstall as a non-transactional database (disabling innodb I believe) and that fixed it. Thanks
    – CarbonMan
    Commented Jun 9, 2011 at 11:36
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    Instead of reinstallation first check this answer: stackoverflow.com/a/20262826/2166188 . @Musa's answer worked for me.
    – Michal_Szulc
    Commented Apr 18, 2016 at 0:33
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    This answer needs to be deleted.
    – Real Dreams
    Commented Sep 1, 2016 at 18:30
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    right solution is what @Musa updated in his post....this may be fine with small data size but what about if db size is more than 500 GB.
    – Zafar Malik
    Commented Jun 2, 2017 at 5:40
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    This answer is the extreme path, while Musa's answer proved effective for many (including me) and, being faster and easier to apply, should be tried before proceeding with a database replacement.
    – dubrox
    Commented Dec 19, 2017 at 17:53

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