How do correct mysqld.log error messages on start up? [duplicate]

Question

I'm running Plesk and CentOS 6.7

Following is the excerpt of the log file mysqld.log when I restart mysqld service.

I normally don't check this log file, but I just noticed some errors messages. It could have been there for a long time already.

This is a live production server up and running for a couple of months, and I don't want to run anything destructive that can potentially jeopardize the stability and data integrity of the server.

170207 13:29:52 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
170207 13:29:52 [Note] libgovernor.so not found
170207 13:29:52 [Note] /usr/libexec/mysqld (mysqld 5.5.44-cll-lve) starting as process 20524 ...
170207 13:29:52 [Note] Plugin 'FEDERATED' is disabled.
170207 13:29:52 InnoDB: The InnoDB memory heap is disabled
170207 13:29:52 InnoDB: Mutexes and rw_locks use GCC atomic builtins
170207 13:29:52 InnoDB: Compressed tables use zlib 1.2.3
170207 13:29:52 InnoDB: Using Linux native AIO
170207 13:29:52 InnoDB: Initializing buffer pool, size = 16.0G
170207 13:29:53 InnoDB: Completed initialization of buffer pool
170207 13:29:53 InnoDB: highest supported file format is Barracuda.
170207 13:29:54  InnoDB: Waiting for the background threads to start
170207 13:29:55 InnoDB: 5.5.44 started; log sequence number 408971509487
170207 13:29:55 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
170207 13:29:55 [Note]   - '127.0.0.1' resolves to '127.0.0.1';
170207 13:29:55 [Note] Server socket created on IP: '127.0.0.1'.
170207 13:29:55 [ERROR] Missing system table mysql.proxies_priv; please run mysql_upgrade to create it
170207 13:29:55 [ERROR] Native table 'performance_schema'.'events_waits_current' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'events_waits_history' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'events_waits_history_long' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'setup_consumers' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'setup_instruments' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'setup_timers' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'performance_timers' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'threads' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_thread_by_event_name' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_instance' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'events_waits_summary_global_by_event_name' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'file_summary_by_event_name' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'file_summary_by_instance' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'mutex_instances' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'rwlock_instances' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'cond_instances' has the wrong structure
170207 13:29:55 [ERROR] Native table 'performance_schema'.'file_instances' has the wrong structure
170207 13:29:55 [Note] Event Scheduler: Loaded 0 events
170207 13:29:55 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.5.44-cll-lve'  socket: '/var/lib/mysql/mysql.sock'  port: 3306  MySQL Community Server (GPL) by Atomicorp

Questions:

1. Even with all these startup errors, MySQL is still up and running well. Is this going to cause any performance impact on current MySQL server performance?

2. Regarding to missing system table mysql.proxies_priv, is this critical? and can I safely run the suggested mysql_upgrade without damaging the existing database?

3. If I were to run mysql_upgrade, do I need to stop mysqld first?

4. How do I correct/repair all the performance_schema wrong structure error messages?

Answer 1

It looks like this may have been upgraded at some point and mysql_upgrade was not run afterwards as it should have been.

Have a look at the documentation for this and see if you can run it in your environment.

It's pretty safe to run this (not much risk of b0rking your data), but as with any tool that makes changes to anything, make sure you've got backups first.