Broken BIOS after kernel and linux-firmware upgrade

tomaqa · 2017-02-05 13:09:46

I've read many issues here caused by kernel upgrade to 4.9 version, but none has exactly fit my problem.

I upgraded all packages (-Syu), which included linux (4.8.13 -> 4.9.6) and linux-firmware (20161005 -> 20161222), see pacman log for details.
After powering on next day, computer seems to be completely broken. The major problem is that the display is blank all the time from startup and booting does not work for any (well, tested only 1) attached hard drive, even live CD did not work. Even external VGA display does not work.
Concretely: firstly it waits for BIOS password, which is obviously recognized (it reacts somehow only on correct password). Then nothing is happening regardless on attached device. For instance at live CD, CD-ROM does not seem to be performing anything (except of initial loading at startup). Despite this, I tried to simulate to boot live system and type reboot, but with no reaction.

The kernel itself was broken too, but I fixed it on another machine with linux-lts and now it works fine there (HDD is OK now), but the problem with my original machine is obviously still the same.
I assume that linux-firmware has done some changes to the NVRAM. I tried to restart it by erasing CMOS battery overnight, but with no success.
Note that I have not been using intel-ucode at all.

My point is: is there a way to repair the machine although I have almost no access to interact with it?
I also don't want to waste too much time on fixing this, it depends on how much complicated the suggested solution would be.

Thank you very much for any response.

-----------------------------------------------------------

pacman.log (only from the fateful day):

[2017-01-27 15:21] [PACMAN] Running 'pacman -Syu'
[2017-01-27 15:21] [PACMAN] synchronizing package lists
[2017-01-27 15:21] [PACMAN] starting full system upgrade
[2017-01-27 15:24] [ALPM] running '70-dkms-remove.hook'...
[2017-01-27 15:24] [ALPM-SCRIPTLET] ==> No kernel 3.17.6-1-ARCH modules. You must install them to use DKMS!
[2017-01-27 15:24] [ALPM-SCRIPTLET] ==> dkms remove vboxguest/5.1.12_OSE -k 4.8.13-1-ARCH
[2017-01-27 15:24] [ALPM-SCRIPTLET] ==> No kernel 3.17.6-1-ARCH modules. You must install them to use DKMS!
[2017-01-27 15:24] [ALPM-SCRIPTLET] ==> dkms remove vboxhost/5.1.12_OSE -k 4.8.13-1-ARCH
[2017-01-27 15:24] [ALPM-SCRIPTLET] rmdir: failed to remove '': No such file or directory
[2017-01-27 15:24] [ALPM-SCRIPTLET] rmdir: failed to remove '': No such file or directory
[2017-01-27 15:25] [ALPM] transaction started
[2017-01-27 15:25] [ALPM] upgraded kbd (2.0.3-1 -> 2.0.4-1)
[2017-01-27 15:25] [ALPM] upgraded pango (1.40.3-1 -> 1.40.3-2)
[2017-01-27 15:25] [ALPM] upgraded chromium (55.0.2883.87-1 -> 56.0.2924.76-1)
[2017-01-27 15:25] [ALPM] upgraded gnupg (2.1.17-4 -> 2.1.18-1)
[2017-01-27 15:25] [ALPM] upgraded lib32-openssl (1:1.0.2.j-1 -> 1:1.0.2.k-1)
[2017-01-27 15:25] [ALPM] upgraded libproxy (0.4.13-1 -> 0.4.13-2)
[2017-01-27 15:25] [ALPM] upgraded linux-firmware (20161005.9c71af9-1 -> 20161222.4b9559f-2)
[2017-01-27 15:25] [ALPM] upgraded linux (4.8.13-1 -> 4.9.6-1)
[2017-01-27 15:25] [ALPM-SCRIPTLET] >>> Updating module dependencies. Please wait ...
[2017-01-27 15:25] [ALPM] upgraded linux-headers (4.8.13-1 -> 4.9.6-1)
[2017-01-27 15:25] [ALPM] upgraded python2-pygments (2.1.3-2 -> 2.2.0-1)
[2017-01-27 15:25] [ALPM] upgraded rest (0.8.0-1 -> 0.8.0-2)
[2017-01-27 15:25] [ALPM] upgraded vhba-module (20161009-2 -> 20161009-7)
[2017-01-27 15:25] [ALPM-SCRIPTLET]   > Updating module dependencies...
[2017-01-27 15:25] [ALPM] upgraded virtualbox-host-dkms (5.1.12-2 -> 5.1.14-1)
[2017-01-27 15:25] [ALPM] upgraded virtualbox (5.1.12-2 -> 5.1.14-1)
[2017-01-27 15:25] [ALPM-SCRIPTLET] 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
[2017-01-27 15:25] [ALPM] upgraded virtualbox-ext-vnc (5.1.12-2 -> 5.1.14-1)
[2017-01-27 15:25] [ALPM-SCRIPTLET] 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
[2017-01-27 15:25] [ALPM] upgraded virtualbox-guest-dkms (5.1.12-2 -> 5.1.14-1)
[2017-01-27 15:25] [ALPM] upgraded virtualbox-guest-iso (5.1.12-1 -> 5.1.14-1)
[2017-01-27 15:25] [ALPM] upgraded virtualbox-guest-utils (5.1.12-2 -> 5.1.14-1)
[2017-01-27 15:26] [ALPM] upgraded xfsprogs (4.8.0-1 -> 4.9.0-1)
[2017-01-27 15:26] [ALPM] transaction completed
[2017-01-27 15:26] [ALPM] running '70-dkms-install.hook'...
[2017-01-27 15:26] [ALPM-SCRIPTLET] ==> dkms install vboxguest/5.1.14_OSE -k 4.9.6-1-ARCH
[2017-01-27 15:26] [ALPM-SCRIPTLET] ==> No kernel 3.17.6-1-ARCH modules. You must install them to use DKMS!
[2017-01-27 15:26] [ALPM-SCRIPTLET] ==> dkms install vboxhost/5.1.14_OSE -k 4.9.6-1-ARCH
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> No kernel 3.17.6-1-ARCH modules. You must install them to use DKMS!
[2017-01-27 15:27] [ALPM] running '99-linux.hook'...
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Starting build: 4.9.6-1-ARCH
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [base]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [udev]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [autodetect]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [modconf]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [filesystems]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [keyboard]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [fsck]
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux.img
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Image generation successful
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Starting build: 4.9.6-1-ARCH
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [base]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [udev]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [modconf]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [block]
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: aic94xx
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: wd719x
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [filesystems]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [keyboard]
[2017-01-27 15:27] [ALPM-SCRIPTLET]   -> Running build hook: [fsck]
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Creating gzip-compressed initcpio image: /boot/initramfs-linux-fallback.img
[2017-01-27 15:27] [ALPM-SCRIPTLET] ==> Image generation successful
[2017-01-27 15:27] [ALPM] running 'gtk-update-icon-cache.hook'...
[2017-01-27 15:27] [ALPM] running 'systemd-sysusers.hook'...
[2017-01-27 15:27] [ALPM] running 'systemd-tmpfiles.hook'...
[2017-01-27 15:27] [ALPM] running 'texinfo-install.hook'...
[2017-01-27 15:27] [ALPM] running 'update-desktop-database.hook'...
[2017-01-27 15:27] [ALPM] running 'update-mime-database.hook'...
[2017-01-27 15:30] [PACMAN] Running 'pacman --color auto -S --asdeps --needed extra/yasm'
[2017-01-27 15:31] [ALPM] transaction started
[2017-01-27 15:31] [ALPM] installed yasm (1.3.0-1)
[2017-01-27 15:31] [ALPM] transaction completed
[2017-01-27 15:41] [PACMAN] Running 'pacman --color auto -U /home/tomaqa/Temp/yaourt-tmp-tomaqa/PKGDEST.2LV/ffmpeg0.10-0.10.16-3-x86_64.pkg.tar.xz'
[2017-01-27 15:41] [ALPM] transaction started
[2017-01-27 15:41] [ALPM] upgraded ffmpeg0.10 (0.10.16-2 -> 0.10.16-3)
[2017-01-27 15:41] [ALPM] transaction completed
[2017-01-27 15:45] [PACMAN] Running 'pacman --color auto -U /home/tomaqa/Temp/yaourt-tmp-tomaqa/PKGDEST.nvN/gstreamer0.10-0.10.36-6-x86_64.pkg.tar.xz'
[2017-01-27 15:45] [ALPM] transaction started
[2017-01-27 15:45] [ALPM] upgraded gstreamer0.10 (0.10.36-4 -> 0.10.36-6)
[2017-01-27 15:45] [ALPM] transaction completed
[2017-01-27 15:45] [PACMAN] Running 'pacman --color auto -S --asdeps --needed extra/gtk-doc'
[2017-01-27 15:45] [ALPM] transaction started
[2017-01-27 15:45] [ALPM] installed docbook-xml (4.5-6)
[2017-01-27 15:45] [ALPM] installed docbook-xsl (1.79.1-2)
[2017-01-27 15:45] [ALPM] installed source-highlight (3.1.8-11)
[2017-01-27 15:45] [ALPM] installed glib2-docs (2.50.2-1)
[2017-01-27 15:45] [ALPM] installed gtk-doc (1.25+33+g567353f-1)
[2017-01-27 15:45] [ALPM] transaction completed
[2017-01-27 15:45] [ALPM] running 'texinfo-install.hook'...

/proc/version :

Linux version 4.4.46-1-lts (builduser@andyrtr) (gcc version 6.3.1 20170109 (GCC) ) #1 SMP Wed Feb 1 17:39:10 CET 2017

uname -a:

Linux tomas-ntb 4.4.46-1-lts #1 SMP Wed Feb 1 17:39:10 CET 2017 x86_64 GNU/Linux

I also discovered that I have installed grub with grub-install --target=i386-pc --recheck --debug ..., I don't know whether this could have caused any issues.

Affected machine: Asus K52J laptop, motherboard Asus K52JK, with processor Intel i3-core.

Tell me for any others logs or other files, but some of them would not be available now since I'm running the same system but on different machine.

Last edited by tomaqa (2017-02-05 13:11:32)

Head_on_a_Stick · 2017-02-05 15:11:19

Are you sure that the monitor is not just broken?

If you can see it, try disabling UEFI mode from the firmware ("BIOS") options screen to eliminate NVRAM problems.

tomaqa · 2017-02-05 18:14:45

As I've mentioned, I'm quite sure that the display is not the only issue, because the system was not responding in all cases I've come through. And I think that the problem must be in firmware, because it happened after the upgrade and it worked a day before, then it only laid on the table during the night :-)

I don't see anything, but despite this I've tried to configure "BIOS" blindly using this video.
I'm not sure which items should I configure. I assume these options should be handled: restore default settings, Security/Secure boot and Boot/Launch {CSM,PXE...}.
I tried provided steps in the video and now the situation is that I have detached HDD and am trying to operate somehow with live CD, which obviously loads somehow, but none option takes any reaction, that is, Power off and Reboot does not work and booting live arch system gets stuck somewhere and only hard reset helps. As I don't see anything, I can't determine whether at least the live CD's menu has loaded or not, I only hear CD-ROM noise.

Can you please give me an advice how should I configure the BIOS?
Thank you.

Last edited by tomaqa (2017-02-05 18:17:37)

Head_on_a_Stick · 2017-02-05 19:15:08

tomaqa wrote:

Can you please give me an advice how should I configure the BIOS?

Sorry, no, I'm not sure how you can do that

I did have a similar experience a while back though when attempting to dual-boot GNU/Linux with OpenBSD — my laptop's (UEFI) firmware didn't seem to like the OpenBSD disklabel on the internal SSD and that also completely "bricked" the device, it was exactly as you describe with your machine, a black screen, completely unresponsive and unbootable even with live USB sticks or CD/DVDs.

My eventual "solution" was to prise the SSD out of the laptop, attach it to another machine, boot an Arch live ISO and then to run:

# sgdisk --zap-all /dev/sda

I think I may even have had to manually scrape zeros onto the drive with a magnetized needle...

EDIT: I am *not* suggesting that you use that command, it will completely wipe your drive.

Last edited by Head_on_a_Stick (2017-02-05 19:17:43)

R00KIE · 2017-02-06 13:33:40

tomaqa wrote:

Concretely: firstly it waits for BIOS password, which is obviously recognized (it reacts somehow only on correct password). Then nothing is happening regardless on attached device.

I would also guess either a broken monitor or broken gpu.

Updating linux-firmware does not (or should not) do changes to your hardware, it contains firmware that needs to be loaded every time you bring up some pieces of hardware (for hardware that needs the firmware to be uploaded every time).

seth · 2017-02-06 15:45:55

I'm not sure how this would have happend, but a system with fucked up nvram is virtually bricked - unless there's some HW reset switch, you need to flash it from outside.

Iff you're lucky, you need to totally unpower the system (unplug ac/dc & battery, maybe cmos) and you might have to press some magic key combo in addition.
Consult the boards/books manual and/or asus for this, nobody here can probably tell.

The nvram could probably have been left in a bad state and operate on a junk resolution or so. If the system posts and boots and you got ssh access, you *might* ninja yourself out by xrandr to VGA or some such - but that's the voodoo approach :-(

R00KIE · 2017-02-09 15:23:59

Seth's voodoo approach idea might work if you can manage to boot and ssh in from another machine, at least you'll be able to poke and prod the system, see the dmesg output and try to find clues as to why it doesn't work as expected.

Restoring it to normal might be tricky though if it involves bad, corrupted or missing uefi variables, that is one of my gripes with uefi, for all its advantages it is too easy to break it beyond easy repair.

killer1804 · 2017-02-11 15:07:43

try to unplug ALL devices from MB, and plug it againe.

Arch Linux

#1 2017-02-05 13:09:46

Broken BIOS after kernel and linux-firmware upgrade

#2 2017-02-05 15:11:19

Re: Broken BIOS after kernel and linux-firmware upgrade

#3 2017-02-05 18:14:45

Re: Broken BIOS after kernel and linux-firmware upgrade

#4 2017-02-05 19:15:08

Re: Broken BIOS after kernel and linux-firmware upgrade

#5 2017-02-06 13:33:40

Re: Broken BIOS after kernel and linux-firmware upgrade

#6 2017-02-06 15:45:55

Re: Broken BIOS after kernel and linux-firmware upgrade

#7 2017-02-09 15:23:59

Re: Broken BIOS after kernel and linux-firmware upgrade

#8 2017-02-11 15:07:43

Re: Broken BIOS after kernel and linux-firmware upgrade

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