The solution is simple but strange, if you copy your /var/lib/mysql directory to another server and think it will work, be sure to check if you have /var/log/mysql and binary log files. If you do, the server will not work and will give you errors like below and crash without the proper log files.
UPDATE user SET password=password("newpass") WHERE user='root';
ERROR 2013 (HY000): Lost connection to MySQL server durin........
mysql errors even though these files do exist:
110405 13:21:37 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means mysqld does not have the access rights to
InnoDB: the directory.
InnoDB: File name ./ibdata1
InnoDB: File operation call: 'open'.
InnoDB: Cannot continue operation.
110405 13:26:15 InnoDB: Operating system error number 13 in a file operation.
InnoDB: The error means my........
don't delete /var/lib/mysql/ib_logfile0 or ibdata1 or mysql won't restart
I didn't realize they were internal and not part of replication like the relay files!
/usr/libexec/mysqld: ready for connections.
Version: '4.1.22-log' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source distribution
110127 16:31:00 [Note] /usr/libexec/mysqld: Normal shutdown
110127 16:31:00 InnoDB: Starting shutdown...........