In terms of features, the MySQL Enterprise Backup product is a superset of the InnoDB Hot Backup product that it supersedes:
The ibbackup command is available on all
platforms, with the same options as before plus some new
ones. In particular, the --incremental
option enables incremental backups of InnoDB tables.
The mysqlbackup command, a cross-platform
replacement for the innobackup command,
is now available on Windows. Windows users can back up
MyISAM tables and tables from other storage engines besides
InnoDB, without writing their own wrapper script for the
ibbackup command.
The mysqlbackup command is a C program
connecting to the server through the MySQL API, rather than
a Perl script that runs the mysql
command. Because it does not run the actual
mysql command, it does not support the
--mysql-extra-args option of
innobackup, but otherwise the syntax is
compatible.
This documentation refers to the
mysqlbackup command exclusively.
If this implementation change presents any issues for former
users of the InnoDB Hot Backup product (for example, if you customized
the innobackup script or relied on
specific mysqld options passed through
the --mysql-extra-args option), please
submit requirements against the new
mysqlbackup command.
Currently, the old innobackup Perl script
is still supplied on Linux and Unix systems, for
troubleshooting in case of upgrade issues as you transition
to the mysqlbackup command.
Backups produced by the InnoDB Hot Backup product can be restored by the MySQL Enterprise Backup product.
The incremental backup feature is new to MySQL Enterprise Backup.
Support for the Barracuda file format is new to MySQL Enterprise Backup.
The MySQL Enterprise Backup product includes some new performance
optimizations, such as the
posix_fadvise() system call.
A new logging capability records the progress of running backup jobs, and historical details for completed backup jobs. For details, see Section 9.3, “Using the MySQL Enterprise Backup Backup Logs”.
The mysqlbackup command has extra
flexibility for specifying the MySQL connection information.
It can read the user, password, port and socket options from
the [client] group of your default or
user-specified configuration file. If you supply the
--password option without an argument,
you are prompted to enter the password interactively.

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