Ubuntu – Why does ‘rysnc’ change file-system permissions

“Do not cross filesystem boundaries” means “do not look inside mount points”. A boundary between filesystems is a mount point. Effectively, this means “only act on the specified partition”, except that not all filesystems are on a partition. See What mount points exist on a typical Linux system?

When you make a backup, you should avoid a number of filesystems, in particular:

• remote filesystems (NFS, Samba, SSHFS, …);
• filesystems whose content is generated on the fly from runtime data (/proc, /sys, …);
• filesystems which are a view of another part of the directory tree (bindfs, avfs, …);
• in-memory filesystems containing data that is only valid until the next reboot (/tmp, /dev/shm, …);
• removable media which may or may not be present at any given time and aren't part of the system proper.

The filesystems to back up are only the ones that correspond to on-disk storage. Many systems have only a single such filesystem, mounted on the root directory /. You can tell which filesystems correspond to on-disk storage because their source (first column titled “Filesystem” of the df output, first column before on of the mount output) is a disk volume (a PC-style partition such as /dev/sda1, an LVM logical volume such as /dev/mapper/mygroup-mylogicalvolume, …).

There are a few subtleties that can make determining which filesystems to back up harder than just looking at the source to see if it's on-disk:

• Removable volumes shouldn't get backed up, even though they are on-disk.
• Linux allows the same filesystem (or parts thereof) to be mounted at multiple locations, with mount --bind; only one of them should be backed up.
• It can be difficult to enumerate all on-disk volumes: there are encrypted volumes, distributed storage volumes, etc.

On your system, the filesystems to back up are /dev/sda7 mounted on /, /dev/sda6 mounted on /boot and /dev/sda8 mounted on /home. So you should tell rsnapshot to back up those three directories. You should almost always use the -x option with rsnapshot.

There are 2 parts to this question. First, why is there a difference between "Number of files" and "Number of files transferred". This is explained in the rsync manpage:

Number of files: is the count of all "files" (in the generic sense), which includes directories, symlinks, etc.

Number of files transferred: is the count of normal files that were updated via rsync’s delta-transfer algorithm, which does not include created dirs, symlinks, etc.

The difference here should be equal to the total amount of directories, symnlinks, other special files. Those were not "transferred" but just re-created.

Now for the second part, why is there a size difference with du. du shows the amount of disk space used by a file, not the size of the file. The same file can take up a different amount of disk space, if for example the filesystems blocksizes differ.

If you are still worried about data integrity, a easy way to be sure is to created hashes for all your files and compare:

( cd /home/hholtmann && find . -type f -exec md5sum {} \; ) > /tmp/hholtmann.md5sum
( cd /media/wd750/c51/home/ && md5sum -c /tmp/hholtmann.md5sum )