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We used to have mostly MyISAM tables (only 1 InnoDB). Our backup solution uses mysqldump. However we noticed that sometimes the backup "broke" the site for a couple of minutes.

So we've switched to InnoDB, to have more reliable backups and remove the table locks that MyISAM uses.

Now I was wondering whether there are better ways to handle daily backups.

Note: Since we're using Amazon RDS, we can't use programs that need to run on the DB machine itself.

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Typical way to backup MySQL is to setup a slave MySQL instance and take backups from there instead of the master MySQL instance.

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Amazon RDS has an extra slave (we use the Multi AZ deployment). But at the moment, we can't access it. – Gert Aug 26 '10 at 8:50

Xtrabackup is the definitive Open Source backup utility for InnoDB. InnoDB hot backup is the commercial counterpart, which was developed by InnoDB developers.

The slave replicant for nightly snapshots is a good recommendation as part of a full backup strategy. This topic is covered well on Server Fault, I suggest you search.

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I would recommend that you look into Zmanda which doesn't require that you run on the same host as the MySQL server.

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