How to Fix “FATAL ERROR: Upgrade failed” When Running mysql_upgrade from MySQL 5.1 to 5.5

The error occurs because critical system tables in the mysql database are either missing or corrupted. The key error messages indicate:

Table 'mysql.plugin' doesn't exist
Table 'mysql.host' doesn't exist
Table 'mysql.servers' doesn't exist
performance_schema tables have wrong structure

1. Stop MySQL Service

sudo service mysql stop
# Or if using systemd:
sudo systemctl stop mysql

2. Start MySQL in Recovery Mode

Run mysqld with --skip-grant-tables to bypass privilege checks:

mysqld_safe --skip-grant-tables &

3. Reinitialize System Tables

Create a temporary SQL file (reinit.sql) with these commands:

CREATE DATABASE IF NOT EXISTS mysql;
USE mysql;

SOURCE /usr/share/mysql/mysql_system_tables.sql;
SOURCE /usr/share/mysql/mysql_system_tables_data.sql;

# For MySQL 5.5 specific additions
SOURCE /usr/share/mysql/fill_help_tables.sql;

Then execute it:

mysql -uroot < reinit.sql

4. Repair Performance Schema

For MySQL 5.5, you'll need to rebuild the performance_schema:

mysql -uroot -e "DROP DATABASE IF EXISTS performance_schema;"
mysql -uroot -e "CREATE DATABASE performance_schema;"
mysql -uroot performance_schema < /usr/share/mysql/performance_schema.sql

If the standard files aren't available, you can manually create essential tables. Here's the minimal host table structure:

CREATE TABLE host (
  Host char(60) COLLATE utf8_bin NOT NULL DEFAULT '',
  Db char(64) COLLATE utf8_bin NOT NULL DEFAULT '',
  Select_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Insert_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Update_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Delete_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Create_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Drop_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Grant_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  References_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Index_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Alter_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Create_tmp_table_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Lock_tables_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Create_view_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Show_view_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Create_routine_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Alter_routine_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Execute_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  Trigger_priv enum('N','Y') COLLATE utf8_bin NOT NULL DEFAULT 'N',
  PRIMARY KEY (Host,Db)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_bin COMMENT='Host privileges';

After reconstructing the system tables:

mysql_upgrade --force
sudo service mysql restart

Check the error log for any remaining issues:

tail -f /var/log/mysql/error.log

Always back up the mysql database before upgrades
Consider using mysql_upgrade --force if standard upgrade fails
Verify the existence of system table SQL files in /usr/share/mysql/

When upgrading from MySQL 5.1 to 5.5, the mysql_upgrade utility fails with a generic "FATAL ERROR: Upgrade failed" message. The error log reveals deeper issues with missing system tables (mysql.plugin, mysql.host, etc.) and performance_schema table structure mismatches.

Key error patterns appearing in loops:

ERROR: Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
ERROR: Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
ERROR: Native table 'performance_schema'.'events_waits_current' has the wrong structure

Try running mysql_upgrade with the MySQL server in safe mode:

# Stop MySQL normally
sudo service mysql stop

# Start in safe mode with grant tables disabled
mysqld_safe --skip-grant-tables --skip-networking &

# Run upgrade with force option
mysql_upgrade --force

If the above fails, we need to manually rebuild system tables. First create a backup:

# Backup existing mysql database
mysqldump --all-databases --routines --events > full_backup.sql
cp -r /var/lib/mysql /var/lib/mysql_backup

For severe corruption, we must recreate the system database:

# Stop MySQL
sudo service mysql stop

# Move old mysql database
mv /var/lib/mysql/mysql /var/lib/mysql/mysql_old

# Reinitialize data directory
mysqld --initialize-insecure --user=mysql

# Restart and secure installation
sudo service mysql start
mysql_secure_installation

After successful recovery:

Import your user databases from backup
Recreate users and permissions
Verify all application functionality

For performance_schema issues, run:

mysql_upgrade --upgrade-system-tables --force
mysqlcheck --all-databases --repair --use-frm

Always:

Create full backups before major version upgrades
Test upgrades in staging environments
Review MySQL upgrade documentation for version-specific notes