Cannot boot after partially upgrading openssl

[sasetz]

Hello everyone,

Today I messed up pretty badly. Initially I just wanted to install PostgreSQL and when I did and tried to configure it with initd, but it needed library libssl.so.3. I went to install it, with these commands:

pacman -Sy
pacman -S openssl

After this, I couldn’t do basically anything on the system, even boot. I found a post on Arch forums about the exact same issue, so I tried to follow the solution. I created a live CD (Manjaro Gnome, I run Plasma) and unpacked the libraries libcrypto.so.1.1 and libssl.so.1.1 to /usr/lib. After doing this, everything booted and started working again, and I proceeded to upgrade the whole system (pacman -Syu). During this, pacman was printing error messages such as this

[2022-11-28T12:48:35+0100] [ALPM-SCRIPTLET] depmod: /usr/lib/libcrypto.so.3: version `OPENSSL_3.0.0' not found (required by depmod)

First time, the update failed, so I started it again, and it succeeded. But the system broke again, I could not do anything and most commands were giving similar messages as pacman did. I cannot boot to the system at all, GRUB does not start, and I just wait indefinitely watching the ASUS logo, although previously GRUB was showing, and I was able to choose between Windows and Manjaro, right now I have to use boot menu to access Windows. Also, there were messages about what is wrong (that libcrypto.so.1.1 was missing), but now there is just this logo.

After this, I found a post about similar boot problem, successfully chrooted to the system, but my pacman is working and has nothing to update, plus, pacman --sysroot /mnt -Syu exited with an error that it cannot find the /etc/pacman.conf file, although it exists. At this point, I don’t know what to do, any help would be useful

Also, I want to mention that if I press ESC when booting to the Manjaro partition, before showing the ASUS logo it actually opens the boot menu but with only two options: Manjaro and additional options, Windows is not present there. And the font there seems weird, it is definitely different from how it was before, if this information helps

I use ASUS Tuf FX516PC laptop with two NVMes: the stock one with 512GB has Windows 10 and the other one with 1TB runs Manjaro KDE Plasma
Pacman version is 6.0.2

[zbe]

@sasetz

pacman -Sy
pacman -S openssl

Who told you to use these commands? Please read official docs, ie. archwiki on pacman (or anything else) before using it.

Be sure that mirrors are synced and try upgrading again. Also try reinstalling all kernels you have.

[freggel.doe]

@sasetz

I cannot boot to the system at all

• boot from manjaro iso
• manjaro-chroot -a into your installation
• fully update the system:

# pacman -Syu

also see

[Fix] Can’t login - black screen & chroot guide

Original author on old forum @AlManja If you are stuck and you can’t log into your system, use one of these steps below. They are sorted from easiest at the top. Start with the first step and if it doesn’t work, try with the next one and so on… Once you get access to the system, then proceed with updating the system or installing/removing packages, checking log files… Steps (you only need one) are: log to tty terminal boot without X chroot auto (with manjaro-chroot) chroot (with manjaro-chro…

[sasetz]

Thank you for your answer. Yes, I already figured that I shouldn’t have done that. Actually, I skipped the pacman -Syu command, so it is really just my fault

I can’t link the post that I followed, but the commands were there:

sudo sed -i 's/ trap/#trap/' /usr/lib/manjaro-tools/util-mount.sh
exit | manjaro-chroot -a
pacman-mirrors -f5
pacman --sysroot /mnt -Syu

pacman-mirrors -f5 successfully runs, but the last command fails, saying that /etc/pacman.conf does not exist. It exists, though. When I run pacman -Syu, it says that everything is up-to-date

[zbe]

Keep in mind that this just mounts everything for chroot, enters it and then exits it. --sysroot command is performed outside of chroot, so any subsequent pacman -Syu is done on live iso image.

Insted of --sysroot command try doing something like (you can selectively add what’s in brackets if without fails)

pacman -r /mnt -Syu --cachedir /mnt/var/cache/pacman/pkg [ --dbpath /mnt/var/lib/pacman ] [ --gpgdir /mnt/etc/pacman.d/gnupg ]

[sasetz]

Thank you for your answer. manjaro-chroot does not work, it says that I don’t have /dev/sda (I only have /dev/nvme...), so I chrooted without it. pacman -Syu runs without a problem, it says that my system is up-to-date. I will now try running pacman -Syyu and the commands that zbe suggested to me

[zbe]

@sasetz

manjaro-chroot does not work, it says that I don’t have /dev/sda (I only have /dev/nvme...), so I chrooted without it.

It’s same command in “my” list of commands and you haven’t mentioned anything. Please post actual preformatted output of commands you run. “it says this and that” doesn’t help.

@sasetz

I will now try running pacman -Syyu

Again, if you read pacman wiki, you’d know this command is useless in your case.

@sasetz

and the commands that zbe suggested to me

Add your kernels too after -Syu.

[sasetz]

$ sudo pacman -r /mnt -Syu --cachedir /mnt/var/cache/pacman/pkg

Output

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
 there is nothing to do

$ sudo pacman -r /mnt -Syu linux515 --cachedir /mnt/var/cache/pacman/pkg

Output

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
warning: linux515-5.15.78-1 is up to date -- reinstalling
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Packages (1) linux515-5.15.78-1

Total Installed Size:  104.72 MiB
Net Upgrade Size:        0.00 MiB

:: Proceed with installation? [Y/n] 
(1/1) checking keys in keyring                                 [##################################] 100%
(1/1) checking package integrity                               [##################################] 100%
error: linux515: signature from "Manjaro Build Server <build@manjaro.org>" is unknown trust
:: File /mnt/var/cache/pacman/pkg/linux515-5.15.78-1-x86_64.pkg.tar.zst is corrupted (invalid or corrupted package (PGP signature)).
Do you want to delete it? [Y/n] n
error: failed to commit transaction (invalid or corrupted package (PGP signature))
Errors occurred, no packages were upgraded.

I run those commands under normal user in live CD, no sudo -i, no chroot. I am not sure, should I delete the corrupted signature? This is what the same command returns when run chrooted into /mnt:

pacman -Syu linux515

Output

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
warning: linux515-5.15.78-1 is up to date -- reinstalling
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Packages (1) linux515-5.15.78-1

Total Installed Size:  104.72 MiB
Net Upgrade Size:        0.00 MiB

:: Proceed with installation? [Y/n] 
(1/1) checking keys in keyring                                 [##################################] 100%
(1/1) checking package integrity                               [##################################] 100%
(1/1) loading package files                                    [##################################] 100%
(1/1) checking for file conflicts                              [##################################] 100%
(1/1) checking available disk space                            [##################################] 100%
:: Running pre-transaction hooks...
(1/2) Creating Timeshift snapshot before upgrade...
==> skipping timeshift-autosnap due skipRsyncAutosnap in /etc/timeshift-autosnap.conf set to TRUE.
(2/2) Remove upgraded DKMS modules
:: Processing package changes...
(1/1) reinstalling linux515                                    [##################################] 100%
:: Running post-transaction hooks...
(1/7) Arming ConditionNeedsUpdate...
(2/7) Updating module dependencies...
(3/7) Install DKMS modules
==> ERROR: Missing 5.15.78-1-MANJARO kernel headers for module tuxedo-keyboard/3.1.1.
(4/7) Updating linux initcpios...
==> Building image from preset: /etc/mkinitcpio.d/linux515.preset: 'default'
  -> -k /boot/vmlinuz-5.15-x86_64 -c /etc/mkinitcpio.conf -g /boot/initramfs-5.15-x86_64.img
==> Starting build: 5.15.78-1-MANJARO
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [autodetect]
  -> Running build hook: [modconf]
  -> Running build hook: [block]
  -> Running build hook: [keyboard]
  -> Running build hook: [keymap]
  -> Running build hook: [consolefont]
==> WARNING: consolefont: no font found in configuration
  -> Running build hook: [resume]
  -> Running build hook: [filesystems]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating gzip-compressed initcpio image: /boot/initramfs-5.15-x86_64.img
==> Image generation successful
==> Building image from preset: /etc/mkinitcpio.d/linux515.preset: 'fallback'
  -> -k /boot/vmlinuz-5.15-x86_64 -c /etc/mkinitcpio.conf -g /boot/initramfs-5.15-x86_64-fallback.img -S autodetect
==> Starting build: 5.15.78-1-MANJARO
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [modconf]
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: bfa
==> WARNING: Possibly missing firmware for module: qed
==> WARNING: Possibly missing firmware for module: qla2xxx
==> WARNING: Possibly missing firmware for module: qla1280
  -> Running build hook: [keyboard]
  -> Running build hook: [keymap]
  -> Running build hook: [consolefont]
==> WARNING: consolefont: no font found in configuration
  -> Running build hook: [resume]
  -> Running build hook: [filesystems]
  -> Running build hook: [fsck]
==> Generating module dependencies
==> Creating gzip-compressed initcpio image: /boot/initramfs-5.15-x86_64-fallback.img
==> Image generation successful
(5/7) Updating Kernel initcpios for Nvidia-DRM...
(6/7) Refreshing PackageKit...
Error connecting: Could not connect: No such file or directory
error: command failed to execute correctly
(7/7) Updating Grub-Bootmenu
Generating grub configuration file ...
Found theme: /usr/share/grub/themes/manjaro/theme.txt
Found linux image: /boot/vmlinuz-5.15-x86_64
Found initrd image: /boot/intel-ucode.img /boot/initramfs-5.15-x86_64.img
Found initrd fallback image: /boot/initramfs-5.15-x86_64-fallback.img
Warning: os-prober will be executed to detect other bootable partitions.
Its output will be used to detect bootable binaries on them and create new boot entries.
ERROR: mkdir /var/lock/dmraid
grub-probe: error: cannot find a GRUB drive for /dev/sda1.  Check your device.map.
grub-probe: error: cannot find a GRUB drive for /dev/sda1.  Check your device.map.
Adding boot menu entry for UEFI Firmware Settings ...
Found memtest86+ image: /boot/memtest86+/memtest.bin
/usr/bin/grub-probe: warning: unknown device type nvme0n1.
done

[zbe]

@sasetz

==> ERROR: Missing 5.15.78-1-MANJARO kernel headers for module tuxedo-keyboard/3.1.1.

Beside missing headers (install them) and whatever that grub-probe error is, it’s fine.

What exactly happens when you boot? Post more output.

[sasetz]

How do I install the headers exactly? I don’t really know and certainly don’t want to guess

The problem is, there is no output. When I boot, the initial ASUS logo flashes, as always, then black screen for a moment. During this black screen I can press esc to open the weird GRUB (?) with the only Manjaro, no Windows (usually there is a Manjaro option and a Windows one). After I select Manjaro in that menu or if I just never pressed esc to begin with, it just goes to ASUS logo again. No output, no console as usual, not even a black screen. The disk light isn’t flashing, so I assume it’s just sitting there doing nothing. I’ve waited for ~10 minutes for it to do anything just to be sure, but nothing came of it. Also I tried to view boot logs chrooted, but yeah, it didn’t work

journalctl -b

-- No entries --

[sasetz]

Wait, it seems I found the command to install the headers. It failed (I ran it chrooted):

pacman -S linux515-headers

Output

resolving dependencies...
looking for conflicting packages...

Packages (2) pahole-1:1.24-1  linux515-headers-5.15.78-1

Total Download Size:    32.07 MiB
Total Installed Size:  137.46 MiB

:: Proceed with installation? [Y/n] 
:: Retrieving packages...
 linux515-headers-5.15.78-1-x...    31.8 MiB  86.5 MiB/s 00:00 [##################################] 100%
 pahole-1:1.24-1-x86_64            312.1 KiB  43.5 MiB/s 00:00 [##################################] 100%
 Total (2/2)                        32.1 MiB  85.1 MiB/s 00:00 [##################################] 100%
(2/2) checking keys in keyring                                 [##################################] 100%
(2/2) checking package integrity                               [##################################] 100%
(2/2) loading package files                                    [##################################] 100%
(2/2) checking for file conflicts                              [##################################] 100%
(2/2) checking available disk space                            [##################################] 100%
:: Processing package changes...
(1/2) installing pahole                                        [##################################] 100%
(2/2) installing linux515-headers                              [##################################] 100%
:: Running post-transaction hooks...
(1/4) Arming ConditionNeedsUpdate...
(2/4) Updating module dependencies...
(3/4) Install DKMS modules
==> dkms install --no-depmod tuxedo-keyboard/3.1.1 -k 5.15.78-1-MANJARO
/usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file: /usr/lib/libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file)
/usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file: /usr/lib/libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file)
/usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file: /usr/lib/libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file)
/usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file: /usr/lib/libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file)
/usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file: /usr/lib/libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /usr/lib/modules/5.15.78-1-MANJARO/build/scripts/sign-file)
==> depmod 5.15.78-1-MANJARO
(4/4) Refreshing PackageKit...
Error connecting: Could not connect: No such file or directory
error: command failed to execute correctly

[zbe]

@sasetz

How do I install the headers exactly?

Package is called linuxXY-headers, XY depending on kernel.

@sasetz

black screen

Try removing ‘quiet’ from /etc/default/grub and run update-grub.

You can try reinstalling grub - consult manjaro wiki page. But I don’t see how grub itself could break because of partial upgrade, so before that I’d reinstall every package (in chroot):

edited:

pacman -Qnq | pacman -Syu openssl-1.1 -

[sasetz]

I will try to boot again and see if something is happening, probably going to take a while, since I am on live CD right now

Here is the full output of the command: Output: pacman -Qnq | pacman -Syu openssl-1.1 - - Pastebin.com

pacman -Qnq | pacman -Syu openssl-1.1 -

Partial output

<...>
 numlockx-1.2-5-x86_64               6.4 KiB  1067 KiB/s 00:00 [##################################] 100%
 lib32-libxdamage-1.1.5-2-x86_64 is up to date
 lib32-libxcomposite-0.4.5-2-x86_64 is up to date
 bashrc-manjaro-5.1.016-2-any is up to date
 pulseaudio-alsa-1:1.2.7.1-1-x86_64 is up to date
 dnssec-anchors-20190629-3-any       3.0 KiB   749 KiB/s 00:00 [##################################] 100%
 Total (499/499)                   182.3 MiB  21.2 MiB/s 00:09 [##################################] 100%
(1772/1772) checking keys in keyring                           [##################################] 100%
(1772/1772) checking package integrity                         [##################################] 100%
(1772/1772) loading package files                              [##################################] 100%
(1772/1772) checking for file conflicts                        [##################################] 100%
error: failed to commit transaction (conflicting files)
openssl-1.1: /usr/lib/libcrypto.so.1.1 exists in filesystem
openssl-1.1: /usr/lib/libssl.so.1.1 exists in filesystem
Errors occurred, no packages were upgraded.

libcrypto.so.1.1 is a link to libcrypto.so, but libssl.so.1.1 isn’t

And for the grub update, after I deleted quiet:

update-grub

Output

Generating grub configuration file ...
Found theme: /usr/share/grub/themes/manjaro/theme.txt
Found linux image: /boot/vmlinuz-5.15-x86_64
Found initrd image: /boot/intel-ucode.img /boot/initramfs-5.15-x86_64.img
Found initrd fallback image: /boot/initramfs-5.15-x86_64-fallback.img
Warning: os-prober will be executed to detect other bootable partitions.
Its output will be used to detect bootable binaries on them and create new boot entries.
grub-probe: error: cannot find a GRUB drive for /dev/sda1.  Check your device.map.
grub-probe: error: cannot find a GRUB drive for /dev/sda1.  Check your device.map.
Adding boot menu entry for UEFI Firmware Settings ...
Found memtest86+ image: /boot/memtest86+/memtest.bin
/usr/bin/grub-probe: warning: unknown device type nvme0n1.
done

I really don’t know why I this happens with Grub, could I mess something up when I changed UEFI boot order? Because I didn’t do anything related to booting apart from that

Nevermind, Manjaro booted fine… What should I do now? Should I update the system?
And also I didn’t see Grub appear, but that may be just because I booted directly into Manjaro, I’ll check and edit if Grub is fine too

Edited: Grub is fine, but it doesn’t see Windows. I’ll try to fix this and see what is wrong. Thank you for your tremendous help, my exams are safe now!

How I fixed Grub from my Manjaro installation:

sudo rm /etc/grub.d/60_memtest86+
sudo update-grub

[zbe]

@sasetz

openssl-1.1: /usr/lib/libcrypto.so.1.1 exists in filesystem
openssl-1.1: /usr/lib/libssl.so.1.1 exists in filesystem

That happens when you manually copy files under system dirs.

https://wiki.archlinux.org/title/pacman#"Failed_to_commit_transaction_(conflicting_files)"_error

@sasetz

Nevermind, Manjaro booted fine…

Heh what? You didn’t do anything. Package reinstall failed.

@sasetz

could I mess something up when I changed UEFI boot order? Because I didn’t do anything related to booting apart from that

…