Ubuntu – Some files are not transferred by using rsync between 2 servers

Actually you do NOT need to allow root athentication via SSH to run rsync as Antoine suggests. The transport and system authentication can be done entirely over user accounts as long as you can run rsync with sudo on both ends for reading and writing the files.

As a user on your destination server you can suck the data from your source server like this:

sudo rsync -aPe ssh --rsync-path='sudo rsync' boron:/home/fred /home/

The user you run as on both servers will need passwordless* sudo access to the rsync binary, but you do NOT need to enable ssh login as root anywhere. If the user you are using doesn't match on the other end, you can add user@boron: to specify a different remote user.

Good luck.

*or you will need to have entered the password manually inside the timeout window.

rsync is a powerful tool, but it is, unfortunately, strangely picky about some of its pathnames.

If $DATA is an absolute path (i.e. it begins with a /), then the correct command-line to use is:

rsync -a --link-dest=$DATA $DATA/ $DATA/../upgrade_tmp

[Now, just a brief aside about rsync's strangeness. Note the trailing / added to the source argument. This tells rsync to work with the contents of the source directory, rather than with the source directory itself. (I'm assuming that $DATA doesn't already contain a trailing /.) In this case, we want to work with the contents, so we add the trailing /.]

If, on the other hand, $DATA is a relative path (i.e. it does not begin with a /), then Sean R's comment about --link-dest is bang on: The link-dest path is interpreted relative to the destination path, so you would use the following:

rsync -a --link-dest=../`basename $DATA` $DATA/ $DATA/../upgrade_tmp

EDIT

One final note, it turns out that the second rsync command-line I gave should work regardless of whether $DATA is an absolute path, since basename doesn't care whether a path is absolute or relative.