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If you regularly plan on creating a backup for a certain database, use the Backup and Restore nodes in the Enterprise Manager. These will use backup and restore projects, saved to a file, so you can re-use them at a later time.
For a quick backup, simply use the Backup Database node in the Database Navigator or from the context menu for a database in the Enterprise Manager via Administration & Maintenance | Backup Database. Both options will show the dialog below:
•Database Workbench does not perform the backup, it instructs MySQL to create a backup and waits for the result. This means the "backup folder" needs to be as seen locally to the server.
The Backup Database Dialog
Click OK to start the backup, this might take a while and Database Workbench will be unavailable while waiting for MySQL to finish the backup.
An explanation of the options: