MySQL 9.5 Reference Manual Including MySQL NDB Cluster 9.5
Installing a new version of MySQL may require upgrading these parts of the existing installation:
          The mysql system schema, which contains
          tables that store information required by the MySQL server as
          it runs (see Section 7.3, “The mysql System Schema”).
          mysql schema tables fall into two broad
          categories:
        
Data dictionary tables, which store database object metadata.
System tables (that is, the remaining non-data dictionary tables), which are used for other operational purposes.
Other schemas, some of which are built in and may be considered “owned” by the server, and others which are not:
              The performance_schema,
              INFORMATION_SCHEMA,
              ndbinfo, and
              sys schemas.
            
User schemas.
Two distinct version numbers are associated with parts of the installation that may require upgrading:
The data dictionary version. This applies to the data dictionary tables.
The server version, also known as the MySQL version. This applies to the system tables and objects in other schemas.
In both cases, the actual version applicable to the existing MySQL installation is stored in the data dictionary, and the current expected version is compiled into the new version of MySQL. When an actual version is lower than the current expected version, those parts of the installation associated with that version must be upgraded to the current version. If both versions indicate an upgrade is needed, the data dictionary upgrade must occur first.
As a reflection of the two distinct versions just mentioned, the upgrade occurs in two steps:
Step 1: Data dictionary upgrade.
This step upgrades:
              The data dictionary tables in the mysql
              schema. If the actual data dictionary version is lower
              than the current expected version, the server creates data
              dictionary tables with updated definitions, copies
              persisted metadata to the new tables, atomically replaces
              the old tables with the new ones, and reinitializes the
              data dictionary.
            
              The Performance Schema,
              INFORMATION_SCHEMA, and
              ndbinfo.
            
Step 2: Server upgrade.
This step comprises all other upgrade tasks. If the server version of the existing MySQL installation is lower than that of the new installed MySQL version, everything else must be upgraded:
              The system tables in the mysql schema
              (the remaining non-data dictionary tables).
            
              The sys schema.
            
User schemas.
      The data dictionary upgrade (step 1) is the responsibility of the
      server, which performs this task as necessary at startup unless
      invoked with an option that prevents it from doing so. The option
      is --upgrade=NONE.
    
If the data dictionary is out of date but the server is prevented from upgrading it, the server does not run, and exits with an error instead. For example:
[ERROR] [MY-013381] [Server] Server shutting down because upgrade is required, yet prohibited by the command line option '--upgrade=NONE'. [ERROR] [MY-010334] [Server] Failed to initialize DD Storage Engine [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
      The --upgrade server option
      controls whether and how the server performs an automatic upgrade
      at startup:
    
          With no option or with
          --upgrade=AUTO, the server
          upgrades anything it determines to be out of date (steps 1 and
          2).
        
          With --upgrade=NONE, the server
          upgrades nothing (skips steps 1 and 2), but also exits with an
          error if the data dictionary must be upgraded. It is not
          possible to run the server with an out-of-date data
          dictionary; the server insists on either upgrading it or
          exiting.
        
          With --upgrade=MINIMAL, the
          server upgrades the data dictionary, the Performance Schema,
          and the INFORMATION_SCHEMA, if necessary
          (step 1). Note that following an upgrade with this option,
          Group Replication cannot be started, because system tables on
          which the replication internals depend are not updated, and
          reduced functionality might also be apparent in other areas.
        
          With --upgrade=FORCE, the
          server upgrades the data dictionary, the Performance Schema,
          and the INFORMATION_SCHEMA, if necessary
          (step 1), and forces an upgrade of everything else (step 2).
          Expect server startup to take longer with this option because
          the server checks all objects in all schemas.
        
      FORCE is useful to force step 2 actions to be
      performed if the server thinks they are not necessary. One way
      that FORCE differs from AUTO
      is that with FORCE, the server re-creates
      system tables such as help tables or time zone tables if they are
      missing.
    
Additional notes about what occurs during upgrade step 2:
          Step 2 installs the sys schema if it is not
          installed, and upgrades it to the current version otherwise.
          An error occurs if a sys schema exists but
          has no version view, on the assumption that
          its absence indicates a user-created schema:
        
A sys schema exists with no sys.version view. If you have a user created sys schema, this must be renamed for the upgrade to succeed.
          To upgrade in this case, remove or rename the existing
          sys schema first. Then perform the upgrade
          procedure again. (It may be necessary to force step 2.)
        
          To prevent the sys schema check, start the
          server with the --upgrade=NONE or
          --upgrade=MINIMAL option.
        
Step 2 upgrades the system tables to ensure that they have the current structure, and this includes the help tables but not the time zone tables. The procedure for loading time zone tables is platform dependent and requires decision making by the DBA, so it cannot be done automatically.
          When Step 2 is upgrading the system tables in the
          mysql schema, the column order in the
          primary key of the mysql.db,
          mysql.tables_priv,
          mysql.columns_priv and
          mysql.procs_priv tables is changed to place
          the host name and user name columns together. Placing the host
          name and user name together means that index lookup can be
          used, which improves performance for
          CREATE USER,
          DROP USER, and
          RENAME USER statements, and for
          ACL checks for multiple users with multiple privileges.
          Dropping and re-creating the index is necessary and might take
          some time if the system has a large number of users and
          privileges.
        
          Step 2 processes all tables in all user schemas as necessary.
          Table checking might take a long time to complete. Each table
          is locked and therefore unavailable to other sessions while it
          is being processed. Check and repair operations can be
          time-consuming, particularly for large tables. Table checking
          uses the FOR UPGRADE option of the
          CHECK TABLE statement. For
          details about what this option entails, see
          Section 15.7.3.2, “CHECK TABLE Statement”.
        
          To prevent table checking, start the server with the
          --upgrade=NONE or
          --upgrade=MINIMAL option.
        
          To force table checking, start the server with the
          --upgrade=FORCE option.
        
Step 2 marks all checked and repaired tables with the current MySQL version number. This ensures that the next time upgrade checking occurs with the same version of the server, it can be determined whether there is any need to check or repair a given table again.