I ran into what appeared to be an identical deadlock today when rsyncing a directory hierarchy between two local directories. I too had all three rsync processes all stuck inside a select system call with a sixty second timeout.
I was executing: rsync --delete-before --exclude 'pattern.*' -vat /source/ /destination/ with rsync 3.1.1-3 from Jessie. I noticed that the files and directories in destination hierarchy were owned by the wrong user and the permissions did not permit the user running rsync to write to them. Initially, during the delete-before phase, rsync complains about failing to unlink with Permission denied, but continues. Then it complains with: rsync: failed to set times on "/destination/.": Operation not permitted (1) for each directory as it comes to it. But it does not complain about individual files. It gets through about 580 files (with relatively long filenames) and then gets stuck seemingly indefinitely as described above. Fixing the destination ownership resolved the problem. This may not have been the same cause for the original bug reporter, however, it's possible that a more subtle problem could cause the same failure mode. Mike.
