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I currently have a hard drive that I backup using RSync. I do weekly; monthly snapshots. I would like to compress some of my hard drive using NTFS compression. How would that affect my future snapshots? I am not clear if my future snapshots would use hard links the same way or it will create an entire new backup.

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Do you really need to use NTFS compression?

Maybe will be better to compress with .tar.tgz using --rsyncable option. It will only send the differences of .tar.gz and will save network bandwidth.

If you really need more compress level, you can use gzip -9. And if you really need save more space, you can use rdiff-backupt to save only the differences (you have to preserve original file to recover). I do not recommend rdiff-backup because if you lose original file you will be in trouble.

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When a filesystem provides compression it is usually intended to be transparent, so that there should be no difference between the original file and a compressed version, apart from some meta-data such as the actual number of physical blocks used. This would seem to be the case with Linux NTFS-3g.

By default rsync only compares timestamps and sizes of files to decide if they are unchanged. Note, only new (i.e. different) files will be compressed.

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