[SOLVED] Input/output errors after pacman upgrade kernel panic

brandon.arnold · 2024-04-20 18:42:24

tl;dr: Try reinstalling the glibc package.

---

I believe my experience is a variation of this issue, and I have confirmed another person on IRC with the same problem. We all use the nvidia package/driver.

After `pacman -Syu` last night, my system went into a kernel panic (flashing caps key) during the "Reloading system manager configuration..." post-install hook. After this, the system would not boot (literally boots directly into the firmware configuration / BIOS menu).

I booted into the Arch USB installation media to go through the Pacman crashes during an upgrade steps. I found a number of packages needed to be installed again with `--overwrite`, but then got a curious error in the post-install hooks here, too:

"call to execv failed (Input/output error)"

And it turns out I can't even chroot into my system, which also fails with "Input/output error."

Another person (Guest91) on IRC has confirmed they are also working through this issue. We have been recommended to try reinstalling all packages, by piping into pacstrap. But the Input/output error is happening here, too.

I'm not convinced both our drives are going out. This seems like it could be something else, possibly recoverable? Any advice?

Last edited by brandon.arnold (2024-04-20 21:26:45)

brandon.arnold · 2024-04-20 20:06:58

Update: After reinstalling glibc, I can successfully chroot now. But I'm still not able to boot. It goes directly into offering to boot into the laptop firmware menu.

One thing that is concerning is the step in the Wiki: "After the upgrade, one way to double-check for not upgraded but still broken packages: find /mnt/usr/lib -size 0"

When I run `find /mnt/usr/lib -size 0` I get an extremely long output (30540 lines).

Last edited by brandon.arnold (2024-04-20 20:11:55)

brandon.arnold · 2024-04-20 20:35:07

Update: I wasn't able to reinstall packages, because all the PGP files were of 0 size. I decided to remove those and remove the keyring as well, but after:

After:
rm -fR /etc/pacman.d/gnupg
pacman-key --init

I get gpg: error while loading shared libraries: /usr/lib/libsqlite3.so.0: file too short

SO it would seem that even files that are depended on by pacman-key are messed up and need reinstalling!

seth · 2024-04-20 20:43:10

I found a number of packages needed to be installed again with `--overwrite`, but then got a curious error in the post-install hooks here, too:

Don't.

Boot the iso, mount the root of the installed system int /mnt and a possible boot partition into /mnt/boot
Do not attempt to chroot, there's probably too much damage on the installed system to reliably use the chroot.
Use "pacman --root /mnt --cachedir /mnt/var/cache/pacman/pkg" (not! --sysroot, as that chroots into the system) and just re-install all packages

You'll most likely have to do this in two steps:
The first on with "--dbonly", the second one without.
The first one will fix the metadata of the installed packages so you're not running into file conflicts from that (and won't have to use --override which would be too tedious to use narrowly and the global glob might accidendatlly steam-roll over files you rather didn't want to touch)

brandon.arnold · 2024-04-20 21:21:55

I appreciate your help, Seth. Trying what you suggested, things are all very much better, from the USB installation media. Although I do see a lot of ldconfig: File ... is empty, not checked errors during the pacman install. I can arch-chroot again and generally commands just work.

Rebooting, the firmware isn't booting to my disk still. I wonder if it's because UEFI isn't seeing the right place to boot; investigating.

brandon.arnold · 2024-04-20 21:23:00

All right, after reinstalling linux and linux-headers, the post-install fixed boot and we're back in order. Thank you so much!

seth · 2024-04-20 21:26:22

I do see a lot of ldconfig: File ... is empty, not checked errors during the pacman install.

You'll get those from some pacman hooks running before the packages finally get sanitized.
You can run a final "ldconfig" (as root on the installed system) - it should not produce any errors and update the cache (if that's actually still required)

Rebooting, the firmware isn't booting to my disk still. I wonder if it's because UEFI isn't seeing the right place to boot; investigating.

What is your bootloader?

Last edited by seth (2024-04-20 21:27:12)

brandon.arnold · 2024-04-20 21:28:01

Haha. Thanks again.

Arch Linux

#1 2024-04-20 18:42:24

[SOLVED] Input/output errors after pacman upgrade kernel panic

#2 2024-04-20 20:06:58

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

#3 2024-04-20 20:35:07

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

#4 2024-04-20 20:43:10

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

#5 2024-04-20 21:21:55

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

#6 2024-04-20 21:23:00

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

#7 2024-04-20 21:26:22

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

#8 2024-04-20 21:28:01

Re: [SOLVED] Input/output errors after pacman upgrade kernel panic

Board footer