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Duplicity & rsnapshot helps me backup my files to remote FTPs server. I can recover file if my server harddisk failed. But if someone hacking my local server and he can get all remote server access info from cron scripts, so hacker can remove the remote FTPs server files. How can I backup it properly. (prevent harddisk failed & hacker)

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A simple approach is to have a "pull" backup - a separate backup server has credentials to log into the main server to pull the data required for the backup, e.g. using rsnapshot logging in via SSH to the main server.

This stops the most obvious attacks where a malicious hacker deletes files on the main and backup server - I've seen people who have reported this on various security forums, so you are right to be concerned for a web server.

The pull backup is still vulnerable to an attacker who compromises the main server (e.g. installing a compromised SSH server that then exploits a hole in the SSH client on the backup server), but that's a much more determined and skillful attack, verging on a targetted attack. Having an offline copy of your backups will address that type of attack as well.

For more details including use with other tools for encrypted backups, see this answer.

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The easy answer would be offline backups, where the data (or access key) is protected by an air gap (and quite possibly steel and concrete)

There are specialized backup systems (usually client + server + custom protocol) that do not support "wipe this file AND every trace in history of it". I belive boxbackup falls into this category (and is open source and reliable), as do some vendors products.

Protection from accidental deletion is a basic function, but the threat of a determined hacker looking to delete your files sounds ... maybe excessive for home use. For me it falls in the same category as having you files in two different cities, in case a meteor strikes.

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I get what you're saying here, and obviously "air gap" backups re the most secure. But I've wondered about this myself and I think it's still a valid concern. For instance, I have a small web app with customers' data and files, which I backup regularly to S3 storage. A determined hacker that gets access to the server does indeed have full access to wipe out the backup history if he/she wanted to do real damage. My solution has been a scripted process from another server that pulls the backups. Access to the application's server therefore doesn't provide any access to the backups. – Yardboy Feb 9 '11 at 20:34

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