Would it be possible for you to describe your rdiff process a bit more? Do you dump the database periodically and backup that data or do you run rdiff on the binary data directory of your DB? Also, where is the rdiff backup data stored? I am guessing you would need another server for this and cannot be just Amazon S3? Thanks!
On a local server at home, it's a low powered ARM box (QNAP TS-219 running Debian) with RAID1. The same thing could probably be done with a Raspberry Pi for lower costs if I was doing it now.
For database backups, you need a consistent snapshot of the data - something which might not happen if you attempt to access the data directly. Add a script to your daily crontab directory, such as:
Into a directory which rdiff-backup will download.
I always prefer to pull my backups from a local server I can trust instead of running a process on the server to push backups - if someone gains access to the server they could potentially destroy the backups if all the credentials are left on the server.
