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I am using the Amazon S3 backup, and it works great.
My only question is, is there a way to make it so I somehow only upload the changes made to the server and not the entire contents of each virtual server?
I know there's a program called rsync that does something along these lines.
Any thoughts?
It doesnt work that great if you cant make incremental backups :)
What kind of access does Amazon offer? FTP? SFTP? DAV?
See now FUSE over Amazon, which can manage rsync, as it mounts an S3 bucket as a local device:
http://code.google.com/p/s3fs/wiki/FuseOverAmazon
rsync won't work on S3 storage (at least not without some intermediary software), as it is neither a filesystem or an ssh accessible filesystem. It uses it's own XML-based protocol and it's own mechanisms for accessing files, and rsync can't talk those protocols. There are some projects underway to do rsync-like behavior on S3, but right now it isn't possible as far as I know.
We'll also probably add an incremental backup mode in the future...
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