Help potentially important warning in journal regarding boot efi being corrupted

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1

I was looking at my journal and found a troubling message:

FAT-fs (nvme1n1p1): Volume was not properly unmounted. Some data may be corrupt. Please run fsck.

It seems to indicate that there may be corruption in my /boot/efi partition. I haven’t really had any problems even though this log seems to persist between boots.

Full error and warning output with journalctl -b -1 -k -p warning:

Aug 11 02:12:21 fedora kernel: ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.GP18.SATA], AE_NOT_FOUND (20240322/dswload2-162)
Aug 11 02:12:21 fedora kernel: ACPI Error: AE_NOT_FOUND, During name lookup/catalog (20240322/psobject-220)
Aug 11 02:12:21 fedora kernel: ACPI BIOS Error (bug): Failure creating named object [\_SB.PCI0.GPP6.WLAN._S0W], AE_ALREADY_EXISTS (20240322/dswload2-326)
Aug 11 02:12:21 fedora kernel: ACPI Error: AE_ALREADY_EXISTS, During name lookup/catalog (20240322/psobject-220)
Aug 11 02:12:23 fedora kernel: i8042: PNP: PS/2 appears to have AUX port disabled, if this is incorrect please boot with i8042.nopnp
Aug 11 02:12:23 fedora kernel: device-mapper: core: CONFIG_IMA_DISABLE_HTABLE is disabled. Duplicate IMA measurements will not be recorded in the IMA log.
Aug 11 02:12:26 fedora kernel: amdgpu 0000:06:00.0: [drm] REG_WAIT timeout 1us * 1000 tries - dcn314_dsc_pg_control line:223
Aug 11 02:12:26 fedora kernel: amdgpu 0000:06:00.0: [drm] REG_WAIT timeout 1us * 1000 tries - dcn314_dsc_pg_control line:231
Aug 11 02:12:26 fedora kernel: amdgpu 0000:06:00.0: [drm] REG_WAIT timeout 1us * 1000 tries - dcn314_dsc_pg_control line:239
Aug 11 02:12:26 fedora kernel: amdgpu 0000:06:00.0: [drm] REG_WAIT timeout 1us * 1000 tries - dcn314_dsc_pg_control line:247
Aug 11 02:13:07 fedora kernel: ideapad_acpi VPC2004:00: Unknown keyboard type: 1
Aug 11 02:13:07 fedora kernel: Bluetooth: hci0: HCI Enhanced Setup Synchronous Connection command is advertised, but not supported.
Aug 11 02:13:07 fedora kernel: FAT-fs (nvme1n1p1): Volume was not properly unmounted. Some data may be corrupt. Please run fsck.
Aug 11 02:13:08 fedora kernel: nvidia: loading out-of-tree module taints kernel.
Aug 11 02:13:08 fedora kernel: nvidia: module license 'NVIDIA' taints kernel.
Aug 11 02:13:08 fedora kernel: Disabling lock debugging due to kernel taint
Aug 11 02:13:08 fedora kernel: nvidia: module license taints kernel.
Aug 11 02:13:08 fedora kernel: 
Aug 11 02:13:08 fedora kernel: NVRM: loading NVIDIA UNIX x86_64 Kernel Module  555.58.02  Tue Jun 25 01:39:15 UTC 2024
Aug 11 02:13:08 fedora kernel: nvidia_uvm: module uses symbols nvUvmInterfaceDisableAccessCntr from proprietary module nvidia, inheriting taint.
Aug 11 02:13:08 fedora kernel: block nvme0n1: No UUID available providing old NGUID
Aug 11 02:13:08 fedora kernel: ACPI Warning: \_SB.NPCF._DSM: Argument #4 type mismatch - Found [Buffer], ACPI requires [Package] (20240322/nsarguments-61)
Aug 11 02:13:08 fedora kernel: ACPI Warning: \_SB.PCI0.GPP0.PEGP._DSM: Argument #4 type mismatch - Found [Buffer], ACPI requires [Package] (20240322/nsarguments-61)
Aug 11 02:13:08 fedora kernel: ACPI BIOS Error (bug): Could not resolve symbol [\_SB.PCI0.GPP0.PEGP.GPS.NVD1], AE_NOT_FOUND (20240322/psargs-330)
Aug 11 02:13:08 fedora kernel: ACPI Error: Aborting method \_SB.PCI0.GPP0.PEGP.GPS due to previous error (AE_NOT_FOUND) (20240322/psparse-529)
Aug 11 02:13:08 fedora kernel: ACPI Error: Aborting method \_SB.PCI0.GPP0.PEGP._DSM due to previous error (AE_NOT_FOUND) (20240322/psparse-529)
Aug 11 02:13:09 fedora kernel: r8169 0000:02:00.0: Direct firmware load for rtl_nic/rtl8168h-2.fw failed with error -2
Aug 11 02:13:09 fedora kernel: r8169 0000:02:00.0: Unable to load firmware rtl_nic/rtl8168h-2.fw (-2)
Aug 11 02:13:09 fedora kernel: nvidia-modeset: WARNING: GPU:0: Unable to read EDID for display device DP-2
Aug 11 02:13:09 fedora kernel: nvidia-modeset: WARNING: GPU:0: Unable to read EDID for display device DP-2
Aug 11 02:13:11 fedora kernel: warning: `QSampleCache::L' uses wireless extensions which will stop working for Wi-Fi 7 hardware; use nl80211
Aug 11 02:13:55 fedora kernel: kauditd_printk_skb: 62 callbacks suppressed

Running sudo fsck /dev/nvme1n1p1 results in:

fsck from util-linux 2.40.1
fsck.fat 4.2 (2021-01-31)
There are differences between boot sector and its backup.
This is mostly harmless. Differences: (offset:original/backup)
  65:01/00
1) Copy original to backup
2) Copy backup to original
3) No action
[123?q]? 3
Dirty bit is set. Fs was not properly unmounted and some data may be corrupt.
1) Remove dirty bit
2) No action
[12?q]? 2
/dev/nvme1n1p1: 13 files, 1905/1046526 clusters

I mainly want to know if this is something that needs to be fixed ASAP or if it’s something that’s relatively common and harmless (I’ve seen a number of logs posted on this forum with this message, but that was never the topic of the thread). If it needs to be fixed ASAP, then I just wanted to check in to see if running fsck is the way to go here.

In general, I’m also wondering if all of the error messages that I posted above are OK or if I need to do something. I’ve been running this system for a few months and I upgraded from F39 to F40 relatively soon after installation (some weeks). I also followed a guide on sysguides to have enrypted boot with btrfs snapshots using snapper.

This is a multi-boot laptop, as I also have Windows 11 and Linux Mint installed, both on a separate disk. However, I rarely boot into them.

inxi 
System:
  Kernel: 6.10.3-200.fc40.x86_64 arch: x86_64 bits: 64
  Desktop: KDE Plasma v: 6.1.3 Distro: Fedora Linux 40 (Forty)
Machine:
  Type: Laptop System: LENOVO product: 82Y9 v: Legion Slim 5 16APH8
    serial: <superuser required>
  Mobo: LENOVO model: LNVNB161216 v: SDK0T76463 WIN
    serial: <superuser required> UEFI: LENOVO v: M3CN42WW date: 01/11/2024
Battery:
  ID-1: BAT1 charge: 61.3 Wh (75.2%) condition: 81.5/80.0 Wh (101.9%)
  ID-2: hidpp_battery_0 charge: 99% condition: N/A
CPU:
  Info: 8-core model: AMD Ryzen 7 7840HS w/ Radeon 780M Graphics bits: 64
    type: MT MCP cache: L2: 8 MiB
  Speed (MHz): avg: 1619 min/max: 400/5137 cores: 1: 400 2: 400 3: 400
    4: 400 5: 400 6: 3537 7: 3782 8: 400 9: 400 10: 400 11: 3768 12: 3767
    13: 400 14: 400 15: 3282 16: 3770
Graphics:
  Device-1: NVIDIA AD106M [GeForce RTX 4070 Max-Q / Mobile] driver: nvidia
    v: 555.58.02
  Device-2: AMD Phoenix1 driver: amdgpu v: kernel
  Device-3: Luxvisions Innotech Integrated Camera driver: uvcvideo type: USB
  Display: wayland server: X.org v: 1.20.14 with: Xwayland v: 24.1.2
    compositor: kwin_wayland driver: X: loaded: amdgpu,nvidia
    unloaded: fbdev,modesetting,nouveau,vesa dri: radeonsi gpu: nvidia,amdgpu
    resolution: 1: 2048x1152 2: 2048x1280
  API: EGL v: 1.5 drivers: kms_swrast,nvidia,radeonsi,swrast
    platforms: gbm,wayland,x11,surfaceless,device
  API: OpenGL v: 4.6.0 compat-v: 4.5 vendor: amd mesa v: 24.1.5 renderer: AMD
    Radeon 780M (radeonsi gfx1103_r1 LLVM 18.1.6 DRM 3.57
    6.10.3-200.fc40.x86_64)
  API: Vulkan v: 1.3.283 drivers: N/A surfaces: xcb,xlib,wayland
Audio:
  Device-1: NVIDIA AD106M High Definition Audio driver: snd_hda_intel
  Device-2: AMD Rembrandt Radeon High Definition Audio driver: snd_hda_intel
  Device-3: AMD ACP/ACP3X/ACP6x Audio Coprocessor driver: snd_pci_ps
  Device-4: AMD Family 17h/19h HD Audio driver: snd_hda_intel
  API: ALSA v: k6.10.3-200.fc40.x86_64 status: kernel-api
  Server-1: PipeWire v: 1.0.7 status: active
Network:
  Device-1: Realtek RTL8111/8168/8211/8411 PCI Express Gigabit Ethernet
    driver: r8169
  IF: enp2s0 state: down mac: <filter>
  Device-2: MEDIATEK MT7922 802.11ax PCI Express Wireless Network Adapter
    driver: mt7921e
  IF: wlo1 state: up mac: <filter>
  IF-ID-1: virbr0 state: down mac: <filter>
  IF-ID-2: virbr1 state: down mac: <filter>
Bluetooth:
  Device-1: Foxconn / Hon Hai Bluetooth 5.2 Adapter [MediaTek MT7922]
    driver: btusb type: USB
  Report: btmgmt ID: hci0 rfk-id: 2 state: down bt-service: enabled,running
    rfk-block: hardware: no software: yes address: <filter> bt-v: 5.2
Drives:
  Local Storage: total: 2.29 TiB used: 792.2 GiB (33.9%)
  ID-1: /dev/nvme0n1 vendor: SK Hynix model: HFS512GEJ9X115N
    size: 476.94 GiB
  ID-2: /dev/nvme1n1 vendor: Crucial model: CT2000T500SSD8 size: 1.82 TiB
Partition:
  ID-1: / size: 1.82 TiB used: 792.19 GiB (42.6%) fs: btrfs dev: /dev/dm-0
  ID-2: /boot/efi size: 3.99 GiB used: 7.4 MiB (0.2%) fs: vfat
    dev: /dev/nvme1n1p1
  ID-3: /home size: 1.82 TiB used: 792.19 GiB (42.6%) fs: btrfs
    dev: /dev/dm-0
  ID-4: /opt size: 1.82 TiB used: 792.19 GiB (42.6%) fs: btrfs
    dev: /dev/dm-0
  ID-5: /var/log size: 1.82 TiB used: 792.19 GiB (42.6%) fs: btrfs
    dev: /dev/dm-0
  ID-6: /var/tmp size: 1.82 TiB used: 792.19 GiB (42.6%) fs: btrfs
    dev: /dev/dm-0
Swap:
  ID-1: swap-1 type: zram size: 8 GiB used: 0 KiB (0.0%) dev: /dev/zram0
Sensors:
  System Temperatures: cpu: 42.9 C mobo: 40.0 C
  Fan Speeds (rpm): N/A
Info:
  Memory: total: 32 GiB note: est. available: 30.53 GiB used: 8.56 GiB (28.0%)
  Processes: 455 Uptime: 49m Shell: Bash inxi: 3.3.34

Other threads about this:

2

That will always happen unless you disable “Fast Startup” in Windows. Otherwise it doesn’t fully shutdown leaving the partition marked as dirty.

In the past, this didn’t impact the ESP but recently I have been seeing this issue more frequently with people who dual-boot.

2 Likes
3

Removed audio, bluetooth, f39

4

Did you run that while the device was mounted? Doing so can easily destroy the file system if it is forced while mounted.
In general never run fsck on a mounted file system

As noted above, Using windows fast boot can cause this. Please turn off fast boot and make certain it remains off within windows.

2 Likes
5

OK, I may have run it while I was booted into Fedora, so I will avoid that from now on. However, one thing to note is that Fast Startup is turned off in Windows and has been for a long time. I only ever login to that OS very rarely, too. It is a vendor-specific distribution of Windows, though (from Lenovo for the Legion Laptop) and I have run a few updates there. Idk if that might cause this issue?

Perhaps fast boot was turned on at some point before.

Either way, do I need to use a live boot usb and run fsck from there?

6

No,
simply

  1. boot windows and make certain fast boot is disabled before shutdown. I understand that some windows updates with win 11 may automatically turn that back on so check every time you boot windows before shutting down.
  2. boot fedora then
  3. sudo umount /boot/efi
  4. sudo fsck.vfat /dev/nvme1n1p1and pay attention to what it tells you. Fix any problems found.
  5. after step 4 completes then sudo mount -a to remount the device.
1 Like
7

OK, thanks! I’m about to do that after a quick backup. The fast startup checkbox is unchecked in the control panel, but I can also try running powercfg /h off.

How should I interpret the boot backup output of fsck in my original post? Which option would make sense to choose?

Edit: I’ve done the steps that you’ve outlined and, after booting up again, the corruption warning isn’t present in the journal for this boot.

Notably, once I ran the fsck, I first got the boot backup message telling me that there was some mismatch between the boot sector and the backup, but since it told me that it was mostly harmless and I wasn’t sure what option to choose there, I simply chose “No action.”

Then I got the dirty bit dialogue, where I chose to remove the dirty bit.

For future reference, I made sure to run powercfg /h off as admin in Windows, turning off hibernation completely (which also makes the fast startup option disappear in the control panel, just as a PSA).

I then made sure that I had the right partition name for the /boot/efi by running lsblk, because the label for my two nvme drives tends to switch between nvme0 and nvme1 for me between boots (idk why this happens, but it hasnt really cause problems).

After that, I followed the steps for unmounting the /boot/efi and running fsck.

8

The backup copy should be identical to the original/current. You would normally copy the original over the backup (the first option) unless you believe there is some problem/corruption in the original. Since you said that you haven’t noticed any problems with the current copy (missing files, won’t boot, etc.), you should choose the first option. Updating/overwriting the backup should be a safe operation, but making a full backup of your ESP beforehand is still a good idea.

Edit: Actually, looking back at your original report, the only difference between the boot sector and its backup was one bit at offset 65. That happens to be the “dirty bit”, so you are fine just by clearing the dirty bit (clearing the dirty bit on your current boot sector had the side-effect of bringing your original and backup copies into agreement).

2 Likes
9

This is why linux uses UUIDs now to identify devices and file systems. The name is assigned in the order devices are configured and is not always consistent.

1 Like
10

Some windows updates require updating multiple times, and hybernation/fastboot is used so the reboots occur quickly and without any opportunity to interrupt. I recently got stuck in a loop where booting went directly to Windows 10 and ignored efforts to invoke the grub2 menu. There were a bunch of Windows 10 updates, so I left the system running overnight. The next a new update had arrived, but after that was applied booting only went to Windows. I could boot linux (installed on a USB drive) using Windows Setting/System/Rescue to enable booting from USB. Fastboot was not enabled in Windows, but I think that only applies to normal shutdown, so if there are pending updates you appear to be stuck until they have all been applied. It may be that one of the updates was temporarily unavailable either to fix a problem with the update or just an overloaded server.

1 Like