Unable to run update_mysql in MySQL 5.5 I have recently taken over managing a MySQL database running on Windows Server 2008 R2. It is running 5.5.37 Community Edition. When it is started, it includes the following lines:

Thread, Type, Details
Column count of mysql.events_waits_current is wrong. Expected 16, found 19. The table is probably corrupted
Column count of mysql.events_waits_history is wrong. Expected 16, found 19. The table is probably corrupted
Column count of mysql.events_waits_history_long is wrong. Expected 16, found 19. The table is probably corrupted
Native table 'performance_schema'.'threads' has the wrong structure
Incorrect definition of table performance_schema.events_waits_summary_by_thread_by_event_name: expected column 'THREAD_ID' at position 0 to have type int(11), found type bigint(20) unsigned.
Column count of mysql.file_summary_by_event_name is wrong. Expected 5, found 23. The table is probably corrupted
Column count of mysql.file_summary_by_instance is wrong. Expected 6, found 25. The table is probably corrupted
Incorrect definition of table performance_schema.mutex_instances: expected column 'LOCKED_BY_THREAD_ID' at position 2 to have type int(11), found type bigint(20) unsigned.
Incorrect definition of table performance_schema.rwlock_instances: expected column 'WRITE_LOCKED_BY_THREAD_ID' at position 2 to have type int(11), found type bigint(20) unsigned.


I tried running mysql_upgrade, but get the following result:

Looking for 'mysql.exe' as: C:\Program Files\MySQL\MySQL Server 5.5\bin\mysql.exe
Looking for 'mysqlcheck.exe' as: C:\Program Files\MySQL\MySQL Server 5.5\bin\mysqlcheck.exe
The system cannot find the file specified.
FATAL ERROR: Upgrade failed


The paths point to the correct locations. I can run mysql.exe and mysqlcheck.exe from those locations. I am running from an Administrator-level command prompt.

I have tried running mysqlcheck.exe with the parameter --all-databases, and everything checks out as OK. But those errors still remain when I restart MySQL.

Any ideas how to get rid of these errors?
As you  mentioned you are tying to run mysql_upgrade and it's looking for 'mysql.exe' and  'mysqlcheck.exe'.

Try this To make it easier to invoke MySQL programs, you can add the path name of the MySQL bin directory to your Windows system PATH environment variable:

Here is the link to set Mysql environment variable in Windows system path.

Hope this will help you.