Error when trying to update system

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1

Hello there,

When I run dnf update the update fails and the entire system becomes read only

example as below

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image1324×902 14.6 KB

after I run sudo dnf update

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image1325×489 55.3 KB

then I try to create a new file

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image1325×489 58.8 KB

System:
  Kernel: 6.8.11-300.fc40.x86_64 arch: x86_64 bits: 64 compiler: gcc
    v: 2.41-37.fc40
  Desktop: GNOME v: 46.2 tk: GTK v: 3.24.42 wm: gnome-shell dm: GDM
    Distro: Fedora Linux 40 (Workstation Edition)
Machine:
  Type: Laptop System: LENOVO product: 82Y4 v: Legion Slim 7 16APH8
    serial: <superuser required> Chassis: type: 10 v: Legion Slim 7 16APH8
    serial: <superuser required>
  Mobo: LENOVO model: LNVNB161216 v: No DPK serial: <superuser required>
    part-nu: LENOVO_MT_82Y4_BU_idea_FM_Legion Slim 7 16APH8 UEFI: LENOVO
    v: M1CN38WW date: 02/15/2024
Battery:
  ID-1: BAT1 charge: 71.6 Wh (79.5%) condition: 90.1/99.9 Wh (90.2%)
    volts: 16.6 min: 15.6 model: Sunwoda L22D4PC3 serial: <filter>
    status: not charging
CPU:
  Info: 8-core model: AMD Ryzen 7 7840HS w/ Radeon 780M Graphics bits: 64
    type: MT MCP arch: Zen 4 rev: 1 cache: L1: 512 KiB L2: 8 MiB L3: 16 MiB
  Speed (MHz): avg: 521 high: 1393
    min/max: 400/5608:6080:5924:5764:5449:5293:5137 cores: 1: 400 2: 400 3: 400
    4: 1353 5: 400 6: 400 7: 400 8: 400 9: 400 10: 400 11: 400 12: 400 13: 400
    14: 400 15: 400 16: 1393 bogomips: 121381
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3 svm
Graphics:
  Device-1: NVIDIA AD107M [GeForce RTX 4060 Max-Q / Mobile] vendor: Lenovo
    driver: nouveau v: kernel arch: Lovelace pcie: speed: 16 GT/s lanes: 8
    ports: active: none empty: DP-1,HDMI-A-1,eDP-1 bus-ID: 01:00.0
    chip-ID: 10de:28e0
  Device-2: AMD Phoenix1 vendor: Lenovo driver: amdgpu v: kernel
    arch: RDNA-3 pcie: speed: 16 GT/s lanes: 16 ports: active: eDP-2 empty: DP-2,
    DP-3, DP-4, DP-5, DP-6, DP-7, DP-8, DP-9, Writeback-1 bus-ID: 65:00.0
    chip-ID: 1002:15bf temp: 39.0 C
  Device-3: Chicony Integrated Camera driver: uvcvideo type: USB rev: 2.0
    speed: 480 Mb/s lanes: 1 bus-ID: 1-3:4 chip-ID: 04f2:b7b6
  Display: x11 server: X.Org v: 1.20.14 with: Xwayland v: 24.1.0
    compositor: gnome-shell driver: X: loaded: modesetting alternate: fbdev,vesa
    dri: radeonsi gpu: amdgpu display-ID: :0 screens: 1
  Screen-1: 0 s-res: 3200x2000 s-dpi: 96
  Monitor-1: eDP-2 model: AU Optronics 0xf1a7 res: 3200x2000 dpi: 236
    diag: 406mm (16")
  API: OpenGL v: 4.6 vendor: amd mesa v: 24.1.1 glx-v: 1.4 es-v: 3.2
    direct-render: yes renderer: AMD Radeon 780M (radeonsi gfx1103_r1 LLVM
    18.1.6 DRM 3.57 6.8.11-300.fc40.x86_64) device-ID: 1002:15bf
  API: Vulkan v: 1.3.283 surfaces: xcb,xlib device: 0 type: integrated-gpu
    driver: N/A device-ID: 1002:15bf device: 1 type: discrete-gpu driver: N/A
    device-ID: 10de:28e0 device: 2 type: cpu driver: N/A device-ID: 10005:0000
  API: EGL Message: EGL data requires eglinfo. Check --recommends.
Audio:
  Device-1: NVIDIA vendor: Lenovo driver: snd_hda_intel v: kernel pcie:
    speed: 16 GT/s lanes: 8 bus-ID: 01:00.1 chip-ID: 10de:22be
  Device-2: AMD Rembrandt Radeon High Definition Audio vendor: Lenovo
    driver: snd_hda_intel v: kernel pcie: speed: 16 GT/s lanes: 16
    bus-ID: 65:00.1 chip-ID: 1002:1640
  Device-3: AMD ACP/ACP3X/ACP6x Audio Coprocessor vendor: Lenovo
    driver: snd_pci_ps v: kernel pcie: speed: 16 GT/s lanes: 16 bus-ID: 65:00.5
    chip-ID: 1022:15e2
  Device-4: AMD Family 17h/19h HD Audio vendor: Lenovo driver: snd_hda_intel
    v: kernel pcie: speed: 16 GT/s lanes: 16 bus-ID: 65:00.6 chip-ID: 1022:15e3
  API: ALSA v: k6.8.11-300.fc40.x86_64 status: kernel-api
  Server-1: JACK v: 1.9.22 status: off
  Server-2: PipeWire v: 1.0.7 status: active with: 1: pipewire-pulse
    status: active 2: wireplumber status: active 3: pipewire-alsa type: plugin
Network:
  Device-1: MEDIATEK MT7922 802.11ax PCI Express Wireless Network Adapter
    vendor: Lenovo driver: mt7921e v: kernel pcie: speed: 5 GT/s lanes: 1
    bus-ID: 03:00.0 chip-ID: 14c3:0616
  IF: wlo1 state: up mac: <filter>
Bluetooth:
  Device-1: Foxconn / Hon Hai Bluetooth 5.2 Adapter [MediaTek MT7922]
    driver: btusb v: 0.8 type: USB rev: 2.1 speed: 480 Mb/s lanes: 1
    bus-ID: 1-4:5 chip-ID: 0489:e0d8
  Report: btmgmt ID: hci0 rfk-id: 2 state: up address: <filter> bt-v: 5.2
    lmp-v: 11
Drives:
  Local Storage: total: 2.29 TiB used: 582.42 GiB (24.9%)
  ID-1: /dev/nvme0n1 vendor: Western Digital model: WD BLACK SN850X 2000GB
    size: 1.82 TiB speed: 63.2 Gb/s lanes: 4 serial: <filter> temp: 39.9 C
  ID-2: /dev/nvme1n1 vendor: Samsung model: MZVL2512HDJD-00BL2
    size: 476.94 GiB speed: 63.2 Gb/s lanes: 4 serial: <filter> temp: 37.9 C
Partition:
  ID-1: / size: 1.82 TiB used: 581.9 GiB (31.3%) fs: btrfs dev: /dev/dm-0
    mapped: luks-c081ae96-cbd6-4780-be7f-8fc06054268a
  ID-2: /boot size: 973.4 MiB used: 512.3 MiB (52.6%) fs: ext4
    dev: /dev/nvme0n1p2
  ID-3: /boot/efi size: 598.8 MiB used: 19 MiB (3.2%) fs: vfat
    dev: /dev/nvme0n1p1
  ID-4: /home size: 1.82 TiB used: 581.9 GiB (31.3%) fs: btrfs
    dev: /dev/dm-0 mapped: luks-c081ae96-cbd6-4780-be7f-8fc06054268a
Swap:
  ID-1: swap-1 type: zram size: 8 GiB used: 0 KiB (0.0%) priority: 100
    dev: /dev/zram0
Sensors:
  System Temperatures: cpu: 40.0 C mobo: N/A
  Fan Speeds (rpm): N/A
Info:
  Memory: total: 32 GiB note: est. available: 30.53 GiB used: 3.9 GiB (12.8%)
  Processes: 432 Power: uptime: 14m wakeups: 0 Init: systemd v: 255
    target: graphical (5) default: graphical
  Packages: pm: flatpak pkgs: 45 Compilers: clang: 18.1.6 gcc: 14.1.1
    Shell: Zsh v: 5.9 running-in: gnome-terminal inxi: 3.3.34

➜  ~ journalctl -p 0..3 -xb
Jun 19 10:08:27 fedora kernel: ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.GP18.SATA], AE_NOT_FOUND (20230628/dswload2-162)
Jun 19 10:08:27 fedora kernel: ACPI Error: AE_NOT_FOUND, During name lookup/catalog (20230628/psobject-220)
Jun 19 10:08:27 fedora kernel: ACPI BIOS Error (bug): Failure creating named object [\_SB.PCI0.GPP6.WLAN._S0W], AE_ALREADY_EXISTS (20230628/dswload2-326)
Jun 19 10:08:27 fedora kernel: ACPI Error: AE_ALREADY_EXISTS, During name lookup/catalog (20230628/psobject-220)
Jun 19 10:08:27 fedora kernel: ACPI BIOS Error (bug): Failure creating named object [\_SB.PCI0.GPP7.DEV0._S0W], AE_ALREADY_EXISTS (20230628/dswload2-326)
Jun 19 10:08:27 fedora kernel: ACPI Error: AE_ALREADY_EXISTS, During name lookup/catalog (20230628/psobject-220)
Jun 19 10:08:49 fedora kernel: 
Jun 19 10:08:49 fedora gdm-autologin][2028]: gkr-pam: unable to locate daemon control file
Jun 19 10:08:49 fedora abrtd[1808]: '/var/spool/abrt/Python3-2024-05-01-23:41:24-21250.new' is not a problem directory
Jun 19 10:08:50 fedora gdm[2016]: Gdm: on_display_added: assertion 'GDM_IS_REMOTE_DISPLAY (display)' failed
Jun 19 10:08:50 fedora gdm[2016]: Gdm: on_display_removed: assertion 'GDM_IS_REMOTE_DISPLAY (display)' failed
Jun 19 10:08:50 fedora abrtd[1808]: '/var/spool/abrt/Python3-2024-05-02-21:09:07-25948.new' is not a problem directory
Jun 19 10:08:50 fedora abrtd[1808]: '/var/spool/abrt/Python3-2024-05-05-23:26:23-90138.new' is not a problem directory
Jun 19 10:08:51 fedora abrtd[1808]: '/var/spool/abrt/Python3-2024-05-07-20:35:18-8235.new' is not a problem directory
Jun 19 10:08:51 fedora abrtd[1808]: '/var/spool/abrt/Python3-2024-05-21-18:02:01-3767.new' is not a problem directory
Jun 19 10:08:51 fedora systemd[2048]: Failed to start app-gnome-gnome\x2dkeyring\x2dpkcs11-2238.scope - Application launched by gnome-session-binary.
░░ Subject: A start job for unit UNIT has failed
░░ Defined-By: systemd
░░ Support: https://lists.freedesktop.org/mailman/listinfo/systemd-devel
░░ 
░░ A start job for unit UNIT has finished with a failure.
░░ 
░░ The job identifier is 179 and the job result is failed.
Jun 19 10:08:51 fedora systemd[2048]: Failed to start app-gnome-liveinst\x2dsetup-2272.scope - Application launched by gnome-session-binary.
░░ Subject: A start job for unit UNIT has failed
░░ Defined-By: systemd
░░ Support: https://lists.freedesktop.org/mailman/listinfo/systemd-devel
░░ 
░░ A start job for unit UNIT has finished with a failure.
░░ 
░░ The job identifier is 191 and the job result is failed.
Jun 19 10:08:53 fedora wpa_supplicant[2088]: bgscan simple: Failed to enable signal strength monitoring

➜  ~ lsblk -f 
NAME FSTYPE FSVER LABEL  UUID                                 FSAVAIL FSUSE% MOUNTPOINTS
zram0
                                                                             [SWAP]
nvme0n1
│                                                                            
├─nvme0n1p1
│    vfat   FAT32        EB6A-8A11                                           
├─nvme0n1p2
│    ext4   1.0          beeddacf-89bd-449b-8624-b0daa7638f6d                
└─nvme0n1p3
     crypto 2            1c5733da-d937-45b7-8a50-70cd8e180c3a                
nvme1n1
│                                                                            
├─nvme1n1p1
│    vfat   FAT32        EAA7-7E8D                             579.8M     3% /boot/efi
├─nvme1n1p2
│    ext4   1.0          20c6562b-6d47-426b-a3e6-d70aec997f1c  513.8M    40% /boot
└─nvme1n1p3
  │  crypto 2            c081ae96-cbd6-4780-be7f-8fc06054268a                
  └─luks-c081ae96-cbd6-4780-be7f-8fc06054268a
     btrfs        fedora fc614fc5-7c6a-46ad-a81b-f9a978f4672c    1.2T    31% /home
                                                                             /

This also causes firefox not to open anymore
the system goes back to normal when I restart.
Not sure what to do

1 Like
2

A Fedora Workstation 40 Live USB drive may be needed to gather information and make repairs.

Can you provide the output from df -lTH /boot /boot/efi / /home /var? This will tell us the filesystem structure, and whether a partition is full (if /var is in the root partition, you should see two entries for /).

journalctl may contain an explanation for the problem. If you can’t run it on the regular system you can boot a Live USB drive, mount the read-only partition with Gnome Disks, and then run journalctl --root=<mount point>/var/log/journal/<long hex string> .... You will need to experiment with filters to weed out massive quantities of irrelevant messages. I would start by reading man journalctl for priority options. Maybe something like journalctl --root=<...> --no-hostname -b -p 3 | cat (the |cat wraps long lines so content isn’t lost).

1 Like
3

FYI I usually use lsblk -f to see the partitions of a system and their disk usage.
It will also include any crypt info.

4

here is the output of the filesytem structure

➜  ~ df -lTH /boot /boot/efi / /home /var
Filesystem                                            Type   Size  Used Avail Use% Mounted on
/dev/nvme1n1p2                                        ext4   1.1G  412M  539M  44% /boot
/dev/nvme1n1p1                                        vfat   628M   20M  608M   4% /boot/efi
/dev/mapper/luks-c081ae96-cbd6-4780-be7f-8fc06054268a btrfs  2.0T  625G  1.4T  32% /
/dev/mapper/luks-c081ae96-cbd6-4780-be7f-8fc06054268a btrfs  2.0T  625G  1.4T  32% /home
/dev/mapper/luks-c081ae96-cbd6-4780-be7f-8fc06054268a btrfs  2.0T  625G  1.4T  32% /

I attached the journal log to the original message