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Its always good to keep your MySQL server backed up regularly.

However if you need to backup the entire server with all databases at once here is what you do

$ mysqldump --all-databases -p | bzip2 -c > databasebackup.sql.bz2
Enter password:

This will save a bz2 file with all the databases.

To restore the databases back use the following (take care not to restore it to a server with the same table names – it may corrupt your data)

$ mysql -p < databasebackup.sql
Enter password: