10

I run MySQL 5.7.11 inside the official docker image.

When I want to upgrade I get the following error:

mysql_upgrade -uroot -p
password:
Error occurred: Cannot setup server variables.

I searched around, didn't find any hint. I tried to run with --verbose, but no luck.

For reference here are the logs when I start the db:

db_1  | 2016-02-17T11:23:10.453190Z 0 [ERROR] Incorrect definition of table performance_schema.events_waits_current: expected column 'NESTING_EVENT_TYPE' at position 15 to have type enum('TRANSACTION','STATEMENT','STAGE','WAIT', found type enum('STATEMENT','STAGE','WAIT').
db_1  | 2016-02-17T11:23:10.453233Z 0 [ERROR] Incorrect definition of table performance_schema.events_waits_history: expected column 'NESTING_EVENT_TYPE' at position 15 to have type enum('TRANSACTION','STATEMENT','STAGE','WAIT', found type enum('STATEMENT','STAGE','WAIT').
db_1  | 2016-02-17T11:23:10.453275Z 0 [ERROR] Incorrect definition of table performance_schema.events_waits_history_long: expected column 'NESTING_EVENT_TYPE' at position 15 to have type enum('TRANSACTION','STATEMENT','STAGE','WAIT', found type enum('STATEMENT','STAGE','WAIT').
db_1  | 2016-02-17T11:23:10.453411Z 0 [ERROR] Incorrect definition of table performance_schema.events_waits_summary_by_user_by_event_name: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.453451Z 0 [ERROR] Incorrect definition of table performance_schema.events_waits_summary_by_account_by_event_name: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.453799Z 0 [ERROR] Column count of performance_schema.setup_actors is wrong. Expected 5, found 3. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.453902Z 0 [ERROR] Incorrect definition of table performance_schema.setup_objects: expected column 'OBJECT_TYPE' at position 0 to have type enum('EVENT','FUNCTION','PROCEDURE','TABLE','TRIGGER', found type enum('TABLE').
db_1  | 2016-02-17T11:23:10.454171Z 0 [ERROR] Column count of performance_schema.table_lock_waits_summary_by_table is wrong. Expected 68, found 73. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454237Z 0 [ERROR] Column count of performance_schema.threads is wrong. Expected 17, found 14. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454316Z 0 [ERROR] Column count of performance_schema.events_stages_current is wrong. Expected 12, found 10. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454375Z 0 [ERROR] Column count of performance_schema.events_stages_history is wrong. Expected 12, found 10. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454429Z 0 [ERROR] Column count of performance_schema.events_stages_history_long is wrong. Expected 12, found 10. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454559Z 0 [ERROR] Incorrect definition of table performance_schema.events_stages_summary_by_account_by_event_name: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.454614Z 0 [ERROR] Incorrect definition of table performance_schema.events_stages_summary_by_user_by_event_name: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.454807Z 0 [ERROR] Column count of performance_schema.events_statements_current is wrong. Expected 41, found 40. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454908Z 0 [ERROR] Column count of performance_schema.events_statements_history is wrong. Expected 41, found 40. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.454983Z 0 [ERROR] Column count of performance_schema.events_statements_history_long is wrong. Expected 41, found 40. Created with MySQL 50626, now running 50711. Please use mysql_upgrade to fix this error.
db_1  | 2016-02-17T11:23:10.455093Z 0 [ERROR] Incorrect definition of table performance_schema.events_statements_summary_by_account_by_event_name: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.455151Z 0 [ERROR] Incorrect definition of table performance_schema.events_statements_summary_by_user_by_event_name: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.455347Z 0 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_program' has the wrong structure
db_1  | 2016-02-17T11:23:10.455367Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_current' has the wrong structure
db_1  | 2016-02-17T11:23:10.455383Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_history' has the wrong structure
db_1  | 2016-02-17T11:23:10.455400Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_history_long' has the wrong structure
db_1  | 2016-02-17T11:23:10.455419Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_summary_by_thread_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455437Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_summary_by_account_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455456Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_summary_by_user_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455474Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_summary_by_host_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455492Z 0 [ERROR] Native table 'performance_schema'.'events_transactions_summary_global_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455542Z 0 [ERROR] Incorrect definition of table performance_schema.users: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.455591Z 0 [ERROR] Incorrect definition of table performance_schema.accounts: expected column 'USER' at position 0 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.455916Z 0 [ERROR] Native table 'performance_schema'.'memory_summary_global_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455952Z 0 [ERROR] Native table 'performance_schema'.'memory_summary_by_account_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455974Z 0 [ERROR] Native table 'performance_schema'.'memory_summary_by_host_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.455995Z 0 [ERROR] Native table 'performance_schema'.'memory_summary_by_thread_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.456018Z 0 [ERROR] Native table 'performance_schema'.'memory_summary_by_user_by_event_name' has the wrong structure
db_1  | 2016-02-17T11:23:10.456046Z 0 [ERROR] Native table 'performance_schema'.'table_handles' has the wrong structure
db_1  | 2016-02-17T11:23:10.456075Z 0 [ERROR] Native table 'performance_schema'.'metadata_locks' has the wrong structure
db_1  | 2016-02-17T11:23:10.456095Z 0 [ERROR] Native table 'performance_schema'.'replication_connection_configuration' has the wrong structure
db_1  | 2016-02-17T11:23:10.456109Z 0 [ERROR] Native table 'performance_schema'.'replication_group_members' has the wrong structure
db_1  | 2016-02-17T11:23:10.456122Z 0 [ERROR] Native table 'performance_schema'.'replication_connection_status' has the wrong structure
db_1  | 2016-02-17T11:23:10.456136Z 0 [ERROR] Native table 'performance_schema'.'replication_applier_configuration' has the wrong structure
db_1  | 2016-02-17T11:23:10.456148Z 0 [ERROR] Native table 'performance_schema'.'replication_applier_status' has the wrong structure
db_1  | 2016-02-17T11:23:10.456163Z 0 [ERROR] Native table 'performance_schema'.'replication_applier_status_by_coordinator' has the wrong structure
db_1  | 2016-02-17T11:23:10.456176Z 0 [ERROR] Native table 'performance_schema'.'replication_applier_status_by_worker' has the wrong structure
db_1  | 2016-02-17T11:23:10.456190Z 0 [ERROR] Native table 'performance_schema'.'replication_group_member_stats' has the wrong structure
db_1  | 2016-02-17T11:23:10.456202Z 0 [ERROR] Native table 'performance_schema'.'prepared_statements_instances' has the wrong structure
db_1  | 2016-02-17T11:23:10.456217Z 0 [ERROR] Native table 'performance_schema'.'user_variables_by_thread' has the wrong structure
db_1  | 2016-02-17T11:23:10.456229Z 0 [ERROR] Native table 'performance_schema'.'status_by_account' has the wrong structure
db_1  | 2016-02-17T11:23:10.456244Z 0 [ERROR] Native table 'performance_schema'.'status_by_host' has the wrong structure
db_1  | 2016-02-17T11:23:10.456261Z 0 [ERROR] Native table 'performance_schema'.'status_by_thread' has the wrong structure
db_1  | 2016-02-17T11:23:10.456274Z 0 [ERROR] Native table 'performance_schema'.'status_by_user' has the wrong structure
db_1  | 2016-02-17T11:23:10.456287Z 0 [ERROR] Native table 'performance_schema'.'global_status' has the wrong structure
db_1  | 2016-02-17T11:23:10.456299Z 0 [ERROR] Native table 'performance_schema'.'session_status' has the wrong structure
db_1  | 2016-02-17T11:23:10.456311Z 0 [ERROR] Native table 'performance_schema'.'variables_by_thread' has the wrong structure
db_1  | 2016-02-17T11:23:10.456325Z 0 [ERROR] Native table 'performance_schema'.'global_variables' has the wrong structure
db_1  | 2016-02-17T11:23:10.456339Z 0 [ERROR] Native table 'performance_schema'.'session_variables' has the wrong structure
db_1  | 2016-02-17T11:23:10.456385Z 0 [ERROR] Incorrect definition of table mysql.db: expected column 'User' at position 2 to have type char(32), found type char(16).
db_1  | 2016-02-17T11:23:10.456395Z 0 [ERROR] mysql.user has no `Event_priv` column at position 28
db_1  | 2016-02-17T11:23:10.456488Z 0 [ERROR] Event Scheduler: An error occurred when initializing system tables. Disabling the Event Scheduler.
db_1  | 2016-02-17T11:23:10.456574Z 0 [Note] mysqld: ready for connections.
db_1  | Version: '5.7.11'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)
15

I found a workaround!

Stop your db. Then start it with:

mysqld --skip-grant-tables &

And then, I could finally do my upgrade:

mysql_upgrade
| improve this answer | |
  • I got Could not create unix socket lock file /var/run/mysqld/mysqld.sock.lock error first, created /var/run/mysqld then chown mysql:mysql /var/run/mysqld then started mysql and mysql_upgrade worked. – endo64 May 29 '18 at 12:31
0

I had a similar problem when upgrading from 5.7.x to 5.7.15 using apt-get but not within a Docker image, but on a basic Ubuntu 16.04 EC2 instance.

I managed to get past by setting up a .mylogin.cnf file for my Linux root user account, so that it was able to login without supplying the username and password, then running the mysql_upgrade command while logged in to the root account.

This managed to perform the required system table upgrades, and then I was able to complete the apt-get upgrade command without issue.

| improve this answer | |
0

On mine I had to

mv /var/lib/mysql /var/lib/mysql.bak

copy a fresh /var/lib/mysql folder over that has just a basic mysql database. I just happened to have one stored at /var/lib/mysql-new

mv /var/lib/mysql-new /var/lib/mysql
service mysql restart

apt-get install -f

It went through and upgraded the mysql database and then you can:

 mv /var/lib/mysql /var/lib/mysql-new
 mv /var/lib/mysql.bak /var/lib/mysql
 service mysql restart

Worked for me. I tried a ton of other suggestions including purging, deleting everything and starting over, playing with apparmor and so on, but this was the only way that worked for me.

| improve this answer | |
0

In my case, same issue, solved this way:

$ mysql_upgrade db_username@db_host -p
Enter password:
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
Checking system database.
| improve this answer | |
  • Welcome to the StackExchange site. Always try to write down some explanation along with code , for understanding to other professional. – Md Haidar Ali Khan Oct 24 '18 at 3:52

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