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I've got a webserver on Debian 6. The system is also always running some processes sensitive to CPU usage. When I am using some of tools like rsync or tar, they are using CPU too much and my sensitive processes are experiencing trouble.

When I've tried to use CPU-Limit tool it was terrible experience when server went down.

I am looking for any lightweight backup tool that can create incremental backups.

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Is your server multi-core? If so, have you tried running taskset -pc 0 [rsync-pid] after executing rsync, to limit it to the first (#0) core? (or is this the cpu-limit tool you mention?) Also try setting rsync's niceness. –  zmode Oct 15 '12 at 10:14
    
Thank you! But, sure, we understand that backup is running by cron. Well, using taskset once will save this preference for further runs? –  Semyon Vyskubov Oct 22 '12 at 10:27
    
No; taskset runs once on that single process ID. You will have to add it in cron or in your script. (Possibly (1)background the rsync process, (2) run taskset and then (3) wait for the backgrounded rsync process to finish). –  zmode Oct 22 '12 at 12:15

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