Can't update to Bazzite 42 nor do almost anything. Input/output error

Bazzite
1

Hi, I’m quite new to Bazzite and I’m facing some problems at updating. After running

ujust update that is the result:

error: Importing: Checking out base commit: Input/output error
System update failed:
0: Command failed: /usr/bin/rpm-ostree upgrade
1: /usr/bin/rpm-ostree failed: exit status: 1

Location:
src/steps/os/linux.rs:228

My rpm-ostree status returns as follows:

State: idle
Deployments:
● ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:5bb32b035ce0678ada4b86f4899c7e237887c02038e077934b214f27866de14a
Version: 41.20241030 (2024-10-31T01:20:26Z)

ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Digest: sha256:5bb32b035ce0678ada4b86f4899c7e237887c02038e077934b214f27866de14a
Version: 41.20241030 (2024-10-31T01:20:26Z)
LayeredPackages: coolercontrol liquidctl sunshine
LocalPackages: lact-0.5.6-0.x86_64

I tried to rpm-ostree reset and rpm-ostree uninstall the tree packets that show on layered but nothing works.

Lastly I tried a rebase from bazzite with sudo rpm-ostree rebase ostree-unverified-registry:ghcr.io/ublue-os/bazzite:stable:

Pulling manifest: ostree-unverified-registry:ghcr.io/ublue-os/bazzite:stable
Importing: ostree-unverified-registry:ghcr.io/ublue-os/bazzite:stable (digest: sha256:8d929716c9c5102f9b91fb830d21d5c3f9b6bfe0f63476722ff08a5a07c43276)
ostree chunk layers already present: 72
error: Importing: Checking out base commit: Input/output error

Next i tried to nuke the repo:

sudo ostree admin unlock

sudo mv /sysroot/ostree/repo /sysroot/ostree/repo.bak

But still tells me that is read only.

I’m quite a bit lost here. The system keeps working well and

smartctl -a /dev/nvme0

return Media and Data Integrity Errors: 0, so it doesn’t seems a disk error.

All help would be appreciated. Thank you!

2

Check dmesg to see what kernel has to say about I/O errors.

Even if your NVMe is functioning correctly, maybe your file system got corrupted. Run appropriate fsck command for your file system. If this is BTRFS, just a note that BTRFS can be wonky if metadata space is filled up so you can check that up also.

1 Like
3

The dmesg just after running a update gets this warnings and errors:

[10223.160715] BTRFS warning (device nvme0n1p3): csum failed root 258 ino 1880106 off 0 csum 0xfa3fb031 expected csum 0x44a6d8bf mirror 1
[10223.160722] BTRFS error (device nvme0n1p3): bdev /dev/nvme0n1p3 errs: wr 0, rd 0, flush 0, corrupt 174331, gen 0
[10223.160742] BTRFS warning (device nvme0n1p3): csum failed root 258 ino 1880106 off 0 csum 0xfa3fb031 expected csum 0x44a6d8bf mirror 1
[10223.160744] BTRFS error (device nvme0n1p3): bdev /dev/nvme0n1p3 errs: wr 0, rd 0, flush 0, corrupt 174332, gen 0

I tried btrfs check, but the it doesn’t work because it is mounted. Is it “safe” to run the --force flag? this are my partitions:

image
image739×223 44.4 KB

Thank you!

4

You probably shouldn’t do it on the live system. Can you get a USB (like what you used to install bazzite) and boot from it, then run the check from there?

And everything else on the system works normally, like shutdown, etc, except rpm-ostree update?

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5

Everything normal works. Day to day usage is working nice, but when i try anything with rpm-ostree or some commands trying to fix it I get this error. Will try booting from live USB now, but yesterday i tried to reinstall only formating the / partition (got scared and bailed to try other things first) and i didn’t saw live boot option. I try again and tell you the results.

6

I’m back! The simple btrfsck didn’t throw any errors. (can’t post two images asa new user).

But when i ran in with the --check-data-csum a lot of errors (i think) appeal:

IMG_20250417_221211852
IMG_20250417_2212118523072×4096 3.87 MB

I was reading the --repair flag but got scared. I don’t want to fuck my sistem more. Could you give me a thumbs up as that is the command i need to run?

Thank you all!

7

To be honest, if it were me, I would focus on verifying my backups and reinstall instructions are in order and reinstall.

This of course relies upon your intuition that the hardware is in good working order.

I am wary of situations like this. Namely: what is still messed up after the repair that I won’t realize until 6 months from now?

But please do wait for others to potentially chime in.

My $0.02.

1 Like
8

Back everything up that you need to back up now while you can, first. Then just try it, and if it doesn’t work, reinstall.

Do you have a backup? If not, make one now. It obviously won’t include the corrupted data, but losing only that is better than losing everything.

Once you have a backup, just run the check command in repair mode. It may fix things. If it does, then you’re fine. If it doesn’t, or it makes things worse, just nuke the volume and restore from the backup.

In either case, you should probably look into what caused this issue in the first place

1 Like
9

If everything normal works, that’s a good opportunity to back up what is important to you.
The backup also shouldn’t be over your one and only backup.

@jude beat me to it.

Do a backup. Save a kitten. :cat:

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10

Ah yes, BTRFS. Unfortunately, I don’t have much experience with troubleshooting and repairing BTRFS so I can’t be of much help… and all my experience with BTRFS is in fact… bad :unamused:

A reinstall is probably a much more time saving option that going down the rabbit hole of repairing the damaged BTRFS.