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Thread: zypper dup breaks root/sudo and reboot fails at switching root

  1. #1
    Join Date
    Apr 2014
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    Colorado Springs, CO
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    Default zypper dup breaks root/sudo and reboot fails at switching root

    I posted about this over on the openSUSE Reddit but I tried again today and getting similar results. I'll outline what happened (so far) and then update this as I go from my phone because I know once I reboot, the only way to get back into a working system is to go to Maintenance Mode and use snapper to undo the update.


    1. Perform a zypper dup - nothing out of the ordinary.
    2. Wait a few minutes, attempt to use sudo for something, password will fail.
    3. Try opening YaST and it'll complain user 'root' not found.
    4. Reboot.
    5. Startup will commence but fail at switch root (as far as I can tell).


    To recover:


    1. Boot into Maintenance Mode.
    2. snapper list (get the numbers)
    3. snapper -v undochange xx..xx
    4. Reboot
      1. The default option will no longer work, must go to advanced and select the previous kernel.


    System Information:
    Memory: 8GB
    Processor: Intel Core i7-3687U
    Graphics: Intel Ivybridge Mobile

    If there's any other information I can provide, please let me know. I thank anybody in advance for your help.

  2. #2
    Join Date
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    Location
    Glasgow, Scotland
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    Some details please.
    What version of Tumbleweed are you running (/etc/os-release), what version (or date) was your unsuccessful 'zypper dup'. what versions of 'ucode-intel' and 'kernel-firmware' are installed and what repositories do you have enabled, also what is the make and model of the machine?
    Code:
     >  zypper lr -d -E
     >  cat /etc/os-release
     >  rpm -q ucode-intel
     >  rpm -qa kernel-*
    --
    slàinte mhath,
    rayH

    ~ knowing the right answer is easier than knowing the right question.

  3. #3
    Join Date
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    Colorado Springs, CO
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    No problem. Thanks for helping me dig in to what I've got going on here.

    Repos:
    Code:
    ~> zypper lr -d -E
    Repository priorities are without effect. All enabled repositories share the same priority.
    
    # | Alias              | Name                        | Enabled | GPG Check | Refresh | Priority | Type   | URI                                                   | Service
    --+--------------------+-----------------------------+---------+-----------+---------+----------+--------+-------------------------------------------------------+--------
    1 | Visual Studio Code | Visual Studio Code          | Yes     | (r ) Yes  | No      |   99     | rpm-md | https://packages.microsoft.com/yumrepos/vscode        |        
    4 | repo-non-oss       | openSUSE-Tumbleweed-Non-Oss | Yes     | (r ) Yes  | Yes     |   99     | yast2  | http://download.opensuse.org/tumbleweed/repo/non-oss/ |        
    5 | repo-oss           | openSUSE-Tumbleweed-Oss     | Yes     | (r ) Yes  | Yes     |   99     | yast2  | http://download.opensuse.org/tumbleweed/repo/oss/     |        
    7 | repo-update        | openSUSE-Tumbleweed-Update  | Yes     | (r ) Yes  | Yes     |   99     | rpm-md | http://download.opensuse.org/update/tumbleweed/       |
    OS Version:
    This is trickier. I use TW as my daily driver and since I can easily backout this change, I've rolled back via Snapper and am on my last known working state. Right now, my os-release reads as below, but the problem was reproducible on 20180127 and is still reproducible on 20180128:
    Code:
    ~> cat /etc/os-release 
    NAME="openSUSE Tumbleweed"
    # VERSION="20180125 "
    ID=opensuse
    ID_LIKE="suse"
    VERSION_ID="20180125"
    PRETTY_NAME="openSUSE Tumbleweed"
    ANSI_COLOR="0;32"
    CPE_NAME="cpe:/o:opensuse:tumbleweed:20180125"
    BUG_REPORT_URL="https://bugs.opensuse.org"
    HOME_URL="https://www.opensuse.org/"
    Intel:
    Again, the output below is current system. 20180128 has a ucode-intel upgrade to 20171117-4.1.
    Code:
    ~> rpm -q ucode-intel
    ucode-intel-20171117-3.1.x86_64
    Kernel:
    Again, on my current system. Upgrading to 20180128 has kernel-default of 4.14.15-1.6 available for me.
    Code:
    ~> rpm -qa kernel-*
    kernel-default-4.14.14-1.7.x86_64
    kernel-default-4.14.12-1.5.x86_64
    kernel-firmware-20180104-1.2.noarch
    Hardware:
    Dell XPS13 (L321X), 8GB, Intel Core i7-3687U, Intel Ivybridge Mobile graphics

    If at any point you need me to return to full broken state to get information, just give me about 10-30 minutes (depending on if I'm at home or work; vastly different internet connections).

    Thank you!

  4. #4
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    I just tried upgrading again now that TW has the 20180129 snapshot in there and the behavior is the same.

  5. #5
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    I locked ucode-intel to its current version and upgraded and still fails.

  6. #6

    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    Do you maybe have installation of recommended packages disabled?
    Though I don't think that's the problem, otherwise there would have been a few more reports of this problem (judging from the Mesa-dri "issue").

    Btw, "switching root" has nothing to do with "user root", the former is when the system is switched to the installed / partition from the initrd.

    If switching to root fails, somehow the "driver" for the / partition may be missing in the initrd.
    So, any special partion setup, like LVM or the like?

    Wouldn't explain the missing "user root" though...

    Grasping at straws, do you have a separate /boot partition that might be full?
    But then you shouldn't even be able to use snapshots/revert to a previous snapshot, unless that has changed recently...
    Maybe your / partition is too full?

  7. #7

    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    I belive I am possibly suffering from the same. After a recent update in Tumbleweed, the system boots to Grub, then loads the initramdisk, but just after kernel spits out 'switching root' it hangs, then it tries to mount root and all other btrfs subvolumes but times out and offers rescue mode. In journalctl there is a line that initializing according to udev database failed. Trying to manually mount the subvolumes hangs the system forever.

    I can, however, boot a live disk and mount the subvolumes from there. They report no errors in the logs, scrub turns out fine and everything is fine. No hardware failure according to SMART. To me it looks like the automounting of the partition/subvolume just fails after Grub. And Grub, I believe, gets the location of root from the parameters that it hold in its own config or from the kernel when it is compiled in there. But I don't know what happens after that. Is it that systemd automounts the devices with the help of udev"?

    Sorry if this isn't the same issue.

    EDIT here is another person reporting it and the screen shots look exactly like what I have now.
    https://forums.opensuse.org/showthre...system-on-boot

  8. #8
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    Quote Originally Posted by wolfi323 View Post
    Do you maybe have installation of recommended packages disabled?
    I have not explicitly defined that in {zypp,zypper}.conf so it is using Zypper defaults, which I believe is to install recommended packages.

    Quote Originally Posted by wolfi323 View Post
    If switching to root fails, somehow the "driver" for the / partition may be missing in the initrd. So, any special partion setup, like LVM or the like?
    It is an encrypted installation (LVM+LUKS) with btrfs, set up through the Tumbleweed installer.

    Quote Originally Posted by wolfi323 View Post
    Wouldn't explain the missing "user root" though...
    Yeah, that one is really weird to me. Never seen that happen before.

    Quote Originally Posted by wolfi323 View Post
    Grasping at straws, do you have a separate /boot partition that might be full?
    The /boot is separate but it isn't close to being full, at least not looking at it through df.

    Code:
    ~> df -h /boot
    Filesystem      Size  Used Avail Use% Mounted on
    /dev/sda2       403M   96M  264M  27% /boot
    Quote Originally Posted by wolfi323 View Post
    Maybe your / partition is too full?
    Only 50% showing but that's because df is only seeing 40GB even though I extended the lv to the rest of the disk and Partitioner shows the rest of the disk. I'm guessing there's some btrfs magic I need to do to expand to the rest of the LV, though. Just haven't go around to it.
    Code:
    ~> df -h /
    Filesystem               Size  Used Avail Use% Mounted on
    /dev/mapper/system-root   40G   25G   16G  62% /
    
    ~> sudo lvdisplay
    [sudo] password for root: 
      --- Logical volume ---
      LV Path                /dev/system/root
      LV Name                root
      VG Name                system
      LV UUID                xcoUgu-CkZp-z1QB-HICy-0QSZ-BQMc-uFeXRZ
      LV Write Access        read/write
      LV Creation host, time voyager, 2017-12-27 14:23:38 -0700
      LV Status              available
      # open                 1
      LV Size                468.34 GiB
      Current LE             119896
      Segments               2
      Allocation             inherit
      Read ahead sectors     auto
      - currently set to     1024
      Block device           254:1
    Thanks for hopping on, wolfi. I've read enough on here to be worried when you throw out things like "grasping at straws" and the confusion on missing root bit. I just assume you've seen everything.

  9. #9
    Join Date
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    Just making LVM bigger does not expand the file system you have to tell the FS to expand.

    man BTRFS-filesystem

    for details

  10. #10
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    Default Re: zypper dup breaks root/sudo and reboot fails at switching root

    Quote Originally Posted by gogalthorp View Post
    Just making LVM bigger does not expand the file system you have to tell the FS to expand.

    man BTRFS-filesystem

    for details
    I did immediately after I posted. I tried to update my post but was past my 10 minute limit. Just a stupid step I forgot, that's all. Now it's all good.

    Code:
    ~> df -h /
    Filesystem               Size  Used Avail Use% Mounted on
    /dev/mapper/system-root  469G   27G  442G   6% /

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