Last night I did a zypper dup update on my main machine, it completely broke
the system.
I had /, /usr, /opt and /var on separate ext4 partitions, and I think this
might be the reason.
It looks like the update was trying to create hard links from files in /usr to
/bin, which won't work since those are different partitions.
After this, the system was completely unusable, and I could not access any
coreutils such as ls and cp, not even the shell.
I ended up booting up a parted magic USB stick, chroot'ed the system, there I
tried to do the same update, and got the following error, which I remember as
identical to the one I got before:


Checking for file conflicts:
................................................................................................................................................................................[done]
(   1/6461) Installing: filesystem-15.5-40.2.x86_64
........................................................................................................................................................[error]
Installation of filesystem-15.5-40.2.x86_64 failed:
Error: Subprocess failed. Error: RPM failed: Make a copy of `/bin'.
cp: cannot create hard link '/usr/bin.usrmerge/ksh93' to '/bin/ksh93': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/rpcinfo' to '/bin/rpcinfo':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/ps' to '/bin/ps': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/fsync' to '/bin/fsync': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/usleep' to '/bin/usleep':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/login' to '/bin/login': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/pgrep' to '/bin/pgrep': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/pkill' to '/bin/pkill': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/[' to '/bin/[': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/b2sum' to '/bin/b2sum': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/base32' to '/bin/base32':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/base64' to '/bin/base64':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/basenc' to '/bin/basenc':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/chcon' to '/bin/chcon': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/chroot' to '/bin/chroot':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/cksum' to '/bin/cksum': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/comm' to '/bin/comm': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/csplit' to '/bin/csplit':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/cut' to '/bin/cut': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/dir' to '/bin/dir': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/dircolors' to '/bin/dircolors':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/dirname' to '/bin/dirname':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/du' to '/bin/du': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/env' to '/bin/env': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/expand' to '/bin/expand':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/expr' to '/bin/expr': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/factor' to '/bin/factor':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/fmt' to '/bin/fmt': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/fold' to '/bin/fold': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/groups' to '/bin/groups':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/head' to '/bin/head': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/hostid' to '/bin/hostid':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/id' to '/bin/id': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/install' to '/bin/install':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/join' to '/bin/join': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/link' to '/bin/link': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/logname' to '/bin/logname':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/mkfifo' to '/bin/mkfifo':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/nice' to '/bin/nice': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/nl' to '/bin/nl': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/nohup' to '/bin/nohup': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/nproc' to '/bin/nproc': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/numfmt' to '/bin/numfmt':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/od' to '/bin/od': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/paste' to '/bin/paste': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/pathchk' to '/bin/pathchk':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/pinky' to '/bin/pinky': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/pr' to '/bin/pr': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/printenv' to '/bin/printenv':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/printf' to '/bin/printf':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/ptx' to '/bin/ptx': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/realpath' to '/bin/realpath':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/runcon' to '/bin/runcon':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/seq' to '/bin/seq': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sha1sum' to '/bin/sha1sum':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sha224sum' to '/bin/sha224sum':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sha256sum' to '/bin/sha256sum':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sha384sum' to '/bin/sha384sum':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sha512sum' to '/bin/sha512sum':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/shred' to '/bin/shred': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/shuf' to '/bin/shuf': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/split' to '/bin/split': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/stdbuf' to '/bin/stdbuf':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sum' to '/bin/sum': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/tac' to '/bin/tac': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/tail' to '/bin/tail': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/tee' to '/bin/tee': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/test' to '/bin/test': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/timeout' to '/bin/timeout':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/tr' to '/bin/tr': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/truncate' to '/bin/truncate':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/tsort' to '/bin/tsort': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/tty' to '/bin/tty': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/unexpand' to '/bin/unexpand':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/uniq' to '/bin/uniq': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/unlink' to '/bin/unlink':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/uptime' to '/bin/uptime':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/users' to '/bin/users': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/vdir' to '/bin/vdir': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/wc' to '/bin/wc': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/who' to '/bin/who': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/whoami' to '/bin/whoami':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/yes' to '/bin/yes': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/arch' to '/bin/arch': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/basename' to '/bin/basename':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/cat' to '/bin/cat': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/chgrp' to '/bin/chgrp': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/chmod' to '/bin/chmod': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/chown' to '/bin/chown': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/cp' to '/bin/cp': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/date' to '/bin/date': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/dd' to '/bin/dd': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/df' to '/bin/df': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/echo' to '/bin/echo': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/false' to '/bin/false': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/ln' to '/bin/ln': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/ls' to '/bin/ls': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/md5sum' to '/bin/md5sum':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/mkdir' to '/bin/mkdir': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/mknod' to '/bin/mknod': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/mktemp' to '/bin/mktemp':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/mv' to '/bin/mv': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/pwd' to '/bin/pwd': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/readlink' to '/bin/readlink':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/rm' to '/bin/rm': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/rmdir' to '/bin/rmdir': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sleep' to '/bin/sleep': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sort' to '/bin/sort': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/stat' to '/bin/stat': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/stty' to '/bin/stty': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sync' to '/bin/sync': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/touch' to '/bin/touch': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/true' to '/bin/true': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/uname' to '/bin/uname': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/bash' to '/bin/bash': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/bashbug' to '/bin/bashbug':
Invalid cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/rbash' to '/bin/rbash': Invalid
cross-device link
cp: cannot create hard link '/usr/bin.usrmerge/sh' to '/bin/sh': Invalid
cross-device link
Something failed, cleaning up
error: lua script failed: [string "%pretrans(filesystem-15.5-40.2.x86_64)"]:37:
exit
error: filesystem-15.5-40.2.x86_64: install skipped
error: filesystem-15.5-40.1.x86_64: erase skipped

Abort, retry, ignore? [a/r/i] (a):  


From what I remember I managed to complete the update there by downloading and
copying coreutils and extracting it to /bin, I also created some symbolic links
from /usr/bin/sh to /bin/sh, etc.
However I managed to delete all the symbolic links in /sbin, although I could
boot the system I was missing stuff in /sbin, and I decided to just do a
reinstall instead.

I have a couple of other machines with the same partition setup, and I need to
know if I will run into the same issue there, and what I can do to fix it
without repartitioning the disk. And if this will also be an issue when
upgrading from LP 15.2 to 15.3.