Unable to update using ujust update

Hello, I'm getting an error when trying to update using the terminal and the error message is a bit too cryptic for me to understand. Here's the message in text format as well:
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Importing: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable (digest: sha256:72ae13c334ed9db3fc0eee5707d94e9d7d669fd413ea90b49043bdf1e55d51f7)
ostree chunk layers already present: 16
ostree chunk layers needed: 57 (3.9 GB)
[0/57] Fetching ostree chunk 04a738d1adc8304e07a (275.0 MB)... done
error: Importing: Unencapsulating base: Layer sha256:04a738d1adc8304e07a76d2aac8ddb4419e6462c67400847d1ef8030fe6d4813: Importing objects: Importing object 46/d38e9f5cdaea03d99ab9f61fe66be91a939ac710ba7de2a39a99b8924aa632.file: Processing content object 46d38e9f5cdaea03d99ab9f61fe66be91a939ac710ba7de2a39a99b8924aa632: fstatat(46/d38e9f5cdaea03d99ab9f61fe66be91a939ac710ba7de2a39a99b8924aa632.file): 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
Pulling manifest: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable
Importing: ostree-image-signed:docker://ghcr.io/ublue-os/bazzite:stable (digest: sha256:72ae13c334ed9db3fc0eee5707d94e9d7d669fd413ea90b49043bdf1e55d51f7)
ostree chunk layers already present: 16
ostree chunk layers needed: 57 (3.9 GB)
[0/57] Fetching ostree chunk 04a738d1adc8304e07a (275.0 MB)... done
error: Importing: Unencapsulating base: Layer sha256:04a738d1adc8304e07a76d2aac8ddb4419e6462c67400847d1ef8030fe6d4813: Importing objects: Importing object 46/d38e9f5cdaea03d99ab9f61fe66be91a939ac710ba7de2a39a99b8924aa632.file: Processing content object 46d38e9f5cdaea03d99ab9f61fe66be91a939ac710ba7de2a39a99b8924aa632: fstatat(46/d38e9f5cdaea03d99ab9f61fe66be91a939ac710ba7de2a39a99b8924aa632.file): 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
Thank you in advance :)
No description
No description
42 Replies
Kalker
KalkerOP2w ago
Sorry for the bump, but I'm really not sure what do to Even after multiple restarts I still get the Input/Output error
renner
renner2w ago
post the full output of rpm-ostree status, including the rollbacks
Kalker
KalkerOP2w ago
Here is the full output of rpm-ostree status after running the rpm-ostree cleanup -m -b -p -r Kyle gave me
No description
sunny.ayyl
sunny.ayyl2w ago
I don't know much, but do you have any spaces left in your computer, just curious
Kalker
KalkerOP2w ago
Dolphin says I have 384 GB free, which should be enough I'd hope haha
renner
renner2w ago
Oh right, my bad I don't know what the source of this error could be at the top of my head Do sudo rpm-ostree reset This will remove all your layered packages and reboot and try again
sunny.ayyl
sunny.ayyl2w ago
GitHub
Input/output error · Issue #4568 · coreos/rpm-ostree
Host system details State: idle Deployments: fedora:fedora/38/x86_64/silverblue Version: 38.20230830.0 (2023-08-30T00:49:28Z) BaseCommit: 20e6c5c20307f6bcdc7371be020e2e88c7a4ec3d31abd46d0add5011d03...
Kalker
KalkerOP2w ago
This also gave me the same error unfortunately
jc@bazzite:~$ sudo rpm-ostree reset
[sudo] password for jc:
Staging deployment... done
error: Staging deployment: Initializing deployment: Checking out deployment tree: Opening content object 496f5f5dc7b5c875ad19e670a8a1ecb20cc19628f117a692e8ec3a866275e11b: fstat: Input/output error
jc@bazzite:~$
jc@bazzite:~$ sudo rpm-ostree reset
[sudo] password for jc:
Staging deployment... done
error: Staging deployment: Initializing deployment: Checking out deployment tree: Opening content object 496f5f5dc7b5c875ad19e670a8a1ecb20cc19628f117a692e8ec3a866275e11b: fstat: Input/output error
jc@bazzite:~$
sunny.ayyl
sunny.ayyl2w ago
Hmm, you did this already didn't you, sorry, I missed it
renner
renner2w ago
Oh yeah, probably disk failure I assume. How old is the SSD? Backup your important data When my disk died I got mountains of errors on my desktops. Didn't survive a reboot after that
Kalker
KalkerOP2w ago
The SSD I bought in early september 2023, so not too old I forget if I've tried those but I'll give them a try again
renner
renner2w ago
This is SATA or nvme? Not some hacky USB Adapter perhaps?
Kalker
KalkerOP2w ago
It's a pcie 4 nvme Plugged in the motherboard
sunny.ayyl
sunny.ayyl2w ago
I think you did run the first two commands, so it might be a hardware issue, doesn't hurt trying it again, but yeah
Kalker
KalkerOP2w ago
This doesn't seem to have done anything unfortunately Outside of updating the system seems to be working generally fine, I can install games, flatpaks, and reboot without issues But if this really is the nvme dying for some reason or other I'll have to reinstall I suppose
renner
renner2w ago
Can you check smart status in settings/kinfocenter just in case? search for smart in settings
Kalker
KalkerOP2w ago
Of course, just a second
Kalker
KalkerOP2w ago
No description
Kalker
KalkerOP2w ago
And this is what the show details button gives me
smartctl 7.4 2023-08-01 r5530 [x86_64-linux-6.11.10-304.bazzite.fc41.x86_64] (local build)
Copyright (C) 2002-23, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Number: Samsung SSD 980 PRO 2TB
Serial Number: S69ENF0W776487D
Firmware Version: 5B2QGXA7
PCI Vendor/Subsystem ID: 0x144d
IEEE OUI Identifier: 0x002538
Total NVM Capacity: 2,000,398,934,016 [2.00 TB]
Unallocated NVM Capacity: 0
Controller ID: 6
NVMe Version: 1.3
Number of Namespaces: 1
Namespace 1 Size/Capacity: 2,000,398,934,016 [2.00 TB]
Namespace 1 Utilization: 1,586,811,924,480 [1.58 TB]
Namespace 1 Formatted LBA Size: 512
Namespace 1 IEEE EUI-64: 002538 b731b4b8f6
Local Time is: Sat Jan 11 19:14:46 2025 CET
Firmware Updates (0x16): 3 Slots, no Reset required
Optional Admin Commands (0x0017): Security Format Frmw_DL Self_Test
Optional NVM Commands (0x0057): Comp Wr_Unc DS_Mngmt Sav/Sel_Feat Timestmp
Log Page Attributes (0x0f): S/H_per_NS Cmd_Eff_Lg Ext_Get_Lg Telmtry_Lg
Maximum Data Transfer Size: 128 Pages
Warning Comp. Temp. Threshold: 82 Celsius
Critical Comp. Temp. Threshold: 85 Celsius

Supported Power States
St Op Max Active Idle RL RT WL WT Ent_Lat Ex_Lat
0 + 8.49W - - 0 0 0 0 0 0
1 + 4.48W - - 1 1 1 1 0 200
2 + 3.18W - - 2 2 2 2 0 1000
3 - 0.0400W - - 3 3 3 3 2000 1200
4 - 0.0050W - - 4 4 4 4 500 9500

Supported LBA Sizes (NSID 0x1)
Id Fmt Data Metadt Rel_Perf
0 + 512 0 0
smartctl 7.4 2023-08-01 r5530 [x86_64-linux-6.11.10-304.bazzite.fc41.x86_64] (local build)
Copyright (C) 2002-23, Bruce Allen, Christian Franke, www.smartmontools.org

=== START OF INFORMATION SECTION ===
Model Number: Samsung SSD 980 PRO 2TB
Serial Number: S69ENF0W776487D
Firmware Version: 5B2QGXA7
PCI Vendor/Subsystem ID: 0x144d
IEEE OUI Identifier: 0x002538
Total NVM Capacity: 2,000,398,934,016 [2.00 TB]
Unallocated NVM Capacity: 0
Controller ID: 6
NVMe Version: 1.3
Number of Namespaces: 1
Namespace 1 Size/Capacity: 2,000,398,934,016 [2.00 TB]
Namespace 1 Utilization: 1,586,811,924,480 [1.58 TB]
Namespace 1 Formatted LBA Size: 512
Namespace 1 IEEE EUI-64: 002538 b731b4b8f6
Local Time is: Sat Jan 11 19:14:46 2025 CET
Firmware Updates (0x16): 3 Slots, no Reset required
Optional Admin Commands (0x0017): Security Format Frmw_DL Self_Test
Optional NVM Commands (0x0057): Comp Wr_Unc DS_Mngmt Sav/Sel_Feat Timestmp
Log Page Attributes (0x0f): S/H_per_NS Cmd_Eff_Lg Ext_Get_Lg Telmtry_Lg
Maximum Data Transfer Size: 128 Pages
Warning Comp. Temp. Threshold: 82 Celsius
Critical Comp. Temp. Threshold: 85 Celsius

Supported Power States
St Op Max Active Idle RL RT WL WT Ent_Lat Ex_Lat
0 + 8.49W - - 0 0 0 0 0 0
1 + 4.48W - - 1 1 1 1 0 200
2 + 3.18W - - 2 2 2 2 0 1000
3 - 0.0400W - - 3 3 3 3 2000 1200
4 - 0.0050W - - 4 4 4 4 500 9500

Supported LBA Sizes (NSID 0x1)
Id Fmt Data Metadt Rel_Perf
0 + 512 0 0
=== START OF SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

SMART/Health Information (NVMe Log 0x02)
Critical Warning: 0x00
Temperature: 43 Celsius
Available Spare: 100%
Available Spare Threshold: 10%
Percentage Used: 1%
Data Units Read: 137,815,429 [70.5 TB]
Data Units Written: 94,606,396 [48.4 TB]
Host Read Commands: 1,072,480,013
Host Write Commands: 1,309,177,016
Controller Busy Time: 8,137
Power Cycles: 573
Power On Hours: 666
Unsafe Shutdowns: 29
Media and Data Integrity Errors: 0
Error Information Log Entries: 0
Warning Comp. Temperature Time: 0
Critical Comp. Temperature Time: 0
Temperature Sensor 1: 43 Celsius
Temperature Sensor 2: 54 Celsius

Error Information (NVMe Log 0x01, 16 of 64 entries)
No Errors Logged

Read Self-test Log failed: Invalid Field in Command (0x002)
=== START OF SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

SMART/Health Information (NVMe Log 0x02)
Critical Warning: 0x00
Temperature: 43 Celsius
Available Spare: 100%
Available Spare Threshold: 10%
Percentage Used: 1%
Data Units Read: 137,815,429 [70.5 TB]
Data Units Written: 94,606,396 [48.4 TB]
Host Read Commands: 1,072,480,013
Host Write Commands: 1,309,177,016
Controller Busy Time: 8,137
Power Cycles: 573
Power On Hours: 666
Unsafe Shutdowns: 29
Media and Data Integrity Errors: 0
Error Information Log Entries: 0
Warning Comp. Temperature Time: 0
Critical Comp. Temperature Time: 0
Temperature Sensor 1: 43 Celsius
Temperature Sensor 2: 54 Celsius

Error Information (NVMe Log 0x01, 16 of 64 entries)
No Errors Logged

Read Self-test Log failed: Invalid Field in Command (0x002)
renner
renner2w ago
Unsafe Shutdowns: 29
Do you often hard-reset your PC or lose power?
sunny.ayyl
sunny.ayyl2w ago
Uh, oh, I do that occasionally :dispair:, lesson learned (not op, but still)
Kalker
KalkerOP2w ago
I try shutting down the PC safely but I've had the power go off a couple of times yeah That said the last version I have is from the 16th and I don't think I've had the power randomly go off since then, dunno if that matters
renner
renner2w ago
Mine says almost a thousand, was troubleshooting something lol It should be fine as long as there are no writes(?)
sunny.ayyl
sunny.ayyl2w ago
ah yes, do as I say, not as I do /joking :clueless:
renner
renner2w ago
try sudo journalctl -b 0 --dmesg | grep -i btrfs | fpaste this will filter the btrfs filesystem stuff from your current boot and upload it to a pastebin
Kalker
KalkerOP2w ago
Sorry for the delay, but I'm getting a journalctl-b command not found error
renner
renner2w ago
it is missing a space, I made typo
Kalker
KalkerOP2w ago
Ah, that did the trick Here's the link: https://paste.centos.org/view/08de8013 I am seeing a lot of critical lines :MonkaS:
renner
renner2w ago
BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096 Do you have important data on this drive?
Kalker
KalkerOP2w ago
The home folder, but I think that's it
renner
renner2w ago
Make a backup your filesystem is (partly) corrupted. It could be that a simple scrub could fix that but I'm no expert on the topic of btrfs
Kalker
KalkerOP2w ago
I'll make a backup and then try a scrub
renner
renner2w ago
sudo btrfs scrub start / and then to watch progress watch sudo btrfs scrub status / keep another terminal open in the background with sudo journalctl --dmesg --follow to see what it does also check if the files are actually legit and you can open them (on the backup drive)
Kalker
KalkerOP2w ago
Will do! I'll report back when I'm done :)
sunny.ayyl
sunny.ayyl2w ago
Good luck!
Kalker
KalkerOP2w ago
Thank you :) Heya, I did the btrfs scrub, there were 2 uncorrectable errors apparently
Scrub started: Sat Jan 11 21:39:29 2025
Status: finished
Duration: 0:05:26
Total to scrub: 1.04TiB
Rate: 3.27GiB/s
Error summary: csum=2
Corrected: 0
Uncorrectable: 2
Unverified: 0
Scrub started: Sat Jan 11 21:39:29 2025
Status: finished
Duration: 0:05:26
Total to scrub: 1.04TiB
Rate: 3.27GiB/s
Error summary: csum=2
Corrected: 0
Uncorrectable: 2
Unverified: 0
It doesn't sound like a lot but I don't know how bad that is
Kalker
KalkerOP2w ago
Hmm, the 2 files I have aren't critical, one is from a game and the other is from discord I can just delete them and repair the game later probably
renner
renner2w ago
yes, delete them, verify the game in steam and at the worst you'll have to login to discord again doesn't explain why your update is failing tho some sector of your filesystem/disk is probably borked
Kalker
KalkerOP2w ago
I think those were not actually the files but rather warnings Actually no I deleted the file but still getting an error :Thonking: After deleting the 2 files I no longer have any errors, but the upgrade still doesn't work Now that I backed up my files I'll probably just reinstall I guess Maybe get a UPS just to make sure I don't have more power issues
renner
renner2w ago
i should someday get one myself could do the btrfs check if you are curious if you don't give a shit, I absoluetly understand
Kalker
KalkerOP2w ago
I had this popup on the terminal with dsmeg when I tried updating
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: SELinux: inode_doinit_use_xattr: getxattr returned 5 for dev=nvme0n1p3 ino=9937
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: SELinux: inode_doinit_use_xattr: getxattr returned 5 for dev=nvme0n1p3 ino=9937
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: SELinux: inode_doinit_use_xattr: getxattr returned 5 for dev=nvme0n1p3 ino=9937
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: SELinux: inode_doinit_use_xattr: getxattr returned 5 for dev=nvme0n1p3 ino=9937
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 4096
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
Jan 11 23:10:34 bazzite kernel: BTRFS critical (device nvme0n1p3): unable to find chunk map for logical 72058819940335616 length 16384
So I think there's probably some errors still

Did you find this page helpful?