Arch Linux

bosco

Member

Registered: 2019-02-26

Posts: 16

[SOLVED] Kernel got deleted from the EFI partition

I was facing issues with my installation today. I updated all my packages with sudo pacman -Syu and went on using my laptop as normal until my lunch break, where I shut it down.
Upon rebooting I found that the systemd boot menu, instead of having normal, fallback and reboot into firmware options, it only showed me the last one.
I booted from a usb live environment, mounted the drive (btrfs partition scheme)and chrooted into my enviroment and saw that everything was there. I ran sudo pacman -Syu again to see if the issue will fix itself (it didn't), and then went on to assume it is, as it often is in these cases, related to the bootlader. bootctl update skipped coppying the boot entries so I ran bootctl install much to no avail. I eventually ran bootctl with no arguments and it showed that the entry was broken since the kernel and initramfs files weren't in the location specified in the entry. I moved over to /boot and confirmed that, in fact, those files weren't there. I ran pacman -S linux and that fixed it so I'm no in dire need for help at the moment, but it leaves me to wonder, what could've caused those files to be deleted in the first place? How could I avoid it happening again?.

Last edited by bosco (2024-05-07 16:00:57)

V1del

Forum Moderator

Registered: 2012-10-16

Posts: 25,230

Re: [SOLVED] Kernel got deleted from the EFI partition

They will get deleted on kernel updates but should get regenerated again. Maybe check/post your pacman.log of the faulty transaction. Is your /boot partition close to being out of space?

Last edited by V1del (2024-05-06 16:37:08)

bosco

Member

Registered: 2019-02-26

Posts: 16

Re: [SOLVED] Kernel got deleted from the EFI partition

[2024-05-06T10:33:29+0200] [PACMAN] Running 'pacman --sync -y -u --'
[2024-05-06T10:33:29+0200] [PACMAN] synchronizing package lists
[2024-05-06T10:33:30+0200] [PACMAN] starting full system upgrade
[2024-05-06T10:35:09+0200] [ALPM] running '60-mkinitcpio-remove.hook'...
[2024-05-06T10:35:10+0200] [ALPM] running '71-dkms-remove.hook'...
[2024-05-06T10:35:10+0200] [ALPM-SCRIPTLET] ==> dkms remove --no-depmod binder/1 -k 6.8.8-arch1-1
[2024-05-06T10:35:10+0200] [ALPM-SCRIPTLET] ==> depmod 6.8.8-arch1-1
[2024-05-06T10:35:12+0200] [ALPM] running 'ghc-unregister.hook'...
[2024-05-06T10:35:13+0200] [ALPM] transaction started
[2024-05-06T10:35:13+0200] [ALPM] upgraded tzdata (2024a-1 -> 2024a-2)
[2024-05-06T10:35:13+0200] [ALPM] upgraded glibc (2.39-2 -> 2.39-4)
[2024-05-06T10:35:13+0200] [ALPM-SCRIPTLET] Generating locales...
[2024-05-06T10:35:14+0200] [ALPM-SCRIPTLET]   en_US.UTF-8... done
[2024-05-06T10:35:14+0200] [ALPM-SCRIPTLET] Generation complete.
[2024-05-06T10:35:14+0200] [ALPM] upgraded abseil-cpp (20240116.1-1 -> 20240116.2-1)
[2024-05-06T10:35:14+0200] [ALPM] upgraded zlib (1:1.3.1-1 -> 1:1.3.1-2)
[2024-05-06T10:35:14+0200] [ALPM] upgraded ncurses (6.4_20230520-2 -> 6.4_20230520-3)
[2024-05-06T10:35:14+0200] [ALPM] upgraded pcre2 (10.43-3 -> 10.43-4)
[2024-05-06T10:35:14+0200] [ALPM] upgraded libsysprof-capture (46.0-1 -> 46.0-2)
[2024-05-06T10:35:14+0200] [ALPM] upgraded glib2 (2.80.0-3 -> 2.80.0-4)
[2024-05-06T10:35:14+0200] [ALPM] upgraded harfbuzz (8.4.0-1 -> 8.4.0-2)
[2024-05-06T10:35:17+0200] [ALPM] upgraded android-studio (2023.2.1.25-1 -> 2023.3.1.18-1)
[2024-05-06T10:35:17+0200] [ALPM] upgraded openssl (3.2.1-1 -> 3.3.0-1)
[2024-05-06T10:35:17+0200] [ALPM] upgraded python-orjson (3.10.1-2 -> 3.10.3-1)
[2024-05-06T10:35:17+0200] [ALPM] upgraded systemd-libs (255.5-3 -> 255.5-4)
[2024-05-06T10:35:17+0200] [ALPM] upgraded libpsl (0.21.2-1 -> 0.21.5-1)
[2024-05-06T10:35:17+0200] [ALPM] upgraded libproxy (0.5.5-1 -> 0.5.6-1)
[2024-05-06T10:35:17+0200] [ALPM] upgraded llvm-libs (17.0.6-3 -> 17.0.6-4)
[2024-05-06T10:35:17+0200] [ALPM] upgraded libelf (0.191-1 -> 0.191-2)
[2024-05-06T10:35:17+0200] [ALPM] upgraded hwdata (0.381-1 -> 0.382-1)
[2024-05-06T10:35:17+0200] [ALPM] upgraded systemd (255.5-3 -> 255.5-4)
[2024-05-06T10:35:19+0200] [ALPM] upgraded qt6-base (6.7.0-3 -> 6.7.0-5)
[2024-05-06T10:35:19+0200] [ALPM] upgraded minizip (1:1.3.1-1 -> 1:1.3.1-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded qt6-positioning (6.7.0-1 -> 6.7.0-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded fribidi (1.0.13-2 -> 1.0.14-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded libvpl (2.10.2-1 -> 2.11.0-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded sdl2 (2.30.2-1 -> 2.30.3-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded mpg123 (1.32.5-1 -> 1.32.6-1)
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[2024-05-06T10:35:19+0200] [ALPM] upgraded spirv-tools (2023.6-1 -> 2024.1-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded glslang (14.0.0-2 -> 14.1.0-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded libdovi (3.3.0-1 -> 3.3.0-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded shaderc (2023.8-1 -> 2024.0-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded fftw (3.3.10-6 -> 3.3.10-7)
[2024-05-06T10:35:19+0200] [ALPM] upgraded anki (24.04.1-1.1 -> 24.04.1-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded libgit2 (1:1.7.2-1 -> 1:1.8.0-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded bat (0.24.0-1 -> 0.24.0-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded boost-libs (1.83.0-6 -> 1.83.0-7)
[2024-05-06T10:35:19+0200] [ALPM] upgraded btrfs-progs (6.8-3 -> 6.8.1-1)
[2024-05-06T10:35:19+0200] [ALPM] upgraded libisl (0.26-1 -> 0.26-2)
[2024-05-06T10:35:19+0200] [ALPM] upgraded jansson (2.14-3 -> 2.14-4)
[2024-05-06T10:35:20+0200] [ALPM] upgraded rust (1:1.77.2-1 -> 1:1.78.0-1)
[2024-05-06T10:35:20+0200] [ALPM] upgraded cargo-binstall (1.6.4-1 -> 1.6.5-1)
[2024-05-06T10:35:20+0200] [ALPM] upgraded gtk-update-icon-cache (1:4.14.3-1 -> 1:4.14.4-1)
[2024-05-06T10:35:20+0200] [ALPM] upgraded tracker3 (3.7.2-1 -> 3.7.3-1)
[2024-05-06T10:35:20+0200] [ALPM] upgraded chromium (124.0.6367.91-1 -> 124.0.6367.118-1)
[2024-05-06T10:35:20+0200] [ALPM] upgraded compiler-rt (17.0.6-1 -> 17.0.6-2)
[2024-05-06T10:35:20+0200] [ALPM] upgraded db5.3 (5.3.28-4 -> 5.3.28-5)
[2024-05-06T10:35:20+0200] [ALPM] upgraded exiv2 (0.28.2-3 -> 0.28.2-4)
[2024-05-06T10:35:20+0200] [ALPM] upgraded eza (0.18.13-1 -> 0.18.14-6)
[2024-05-06T10:35:21+0200] [ALPM] upgraded firefox (125.0.3-1 -> 125.0.3-2)
[2024-05-06T10:35:21+0200] [ALPM] upgraded fwupd (1.9.18-2 -> 1.9.19-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gendesk (1.0.9-3 -> 1.0.9-4)
[2024-05-06T10:35:21+0200] [ALPM] upgraded github-cli (2.48.0-2 -> 2.49.0-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gitui (0.26.1-1 -> 0.26.1-5)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gn (0.2157.22581fb4-1 -> 0.2165.f284b6b4-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gstreamer (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gst-plugins-base-libs (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gst-libav (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gst-plugins-bad-libs (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gst-plugins-base (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gst-plugins-good (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gst-plugins-ugly (1.24.2-2 -> 1.24.3-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded gtk4 (1:4.14.3-1 -> 1:4.14.4-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded harfbuzz-icu (8.4.0-1 -> 8.4.0-2)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-marshalling (2.3.0-43 -> 2.3.1-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-aeson (2.3.0.1-29 -> 2.3.0.1-30)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-classes (2.3.0-48 -> 2.3.0-49)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-typing (0.1.1-2 -> 0.1.1-3)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-objectorientation (2.3.0-44 -> 2.3.0-45)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-packaging (2.3.1-9 -> 2.3.1-10)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua (2.3.0-47 -> 2.3.0-48)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-list (1.1.1-55 -> 1.1.1-56)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-module-doclayout (1.1.0-53 -> 1.1.0-54)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-module-path (1.1.0-48 -> 1.1.0-49)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-module-system (1.1.0.1-22 -> 1.1.0.1-23)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-module-text (1.1.0.1-22 -> 1.1.0.1-23)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-module-version (1.1.0-48 -> 1.1.0-49)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-hslua-module-zip (1.1.1-17 -> 1.1.1-18)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-libyaml (0.1.2-346 -> 0.1.4-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-yaml (0.11.11.2-44 -> 0.11.11.2-45)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-typst (0.3.2.1-27 -> 0.3.2.1-28)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-pandoc (3.1.8-21 -> 3.1.8-22)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-pandoc-lua-marshal (0.2.3-4 -> 0.2.3-5)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-pandoc-lua-engine (0.2.1.2-7 -> 0.2.1.2-9)
[2024-05-06T10:35:21+0200] [ALPM] upgraded haskell-pandoc-server (0.1.0.5-24 -> 0.1.0.5-25)
[2024-05-06T10:35:21+0200] [ALPM] upgraded hslua-cli (1.4.1-44 -> 1.4.1-45)
[2024-05-06T10:35:21+0200] [ALPM] upgraded imagemagick (7.1.1.31-1 -> 7.1.1.32-1)
[2024-05-06T10:35:21+0200] [ALPM] upgraded iproute2 (6.8.0-1 -> 6.8.0-2)
[2024-05-06T10:35:21+0200] [ALPM] upgraded irssi (1.4.5-2 -> 1.4.5-3)
[2024-05-06T10:35:21+0200] [ALPM] upgraded jemalloc (1:5.3.0-3 -> 1:5.3.0-4)
[2024-05-06T10:35:21+0200] [ALPM] upgraded lib32-glibc (2.39-2 -> 2.39-4)
[2024-05-06T10:35:22+0200] [ALPM] upgraded libbsd (0.12.2-1 -> 0.12.2-2)
[2024-05-06T10:35:22+0200] [ALPM] upgraded libmfx (23.2.2-2 -> 23.2.2-3)
[2024-05-06T10:35:22+0200] [ALPM] upgraded libplist (2.4.0-2 -> 2.5.0-1)
[2024-05-06T10:35:23+0200] [ALPM] upgraded libreoffice-fresh (24.2.2-3 -> 24.2.3-1)
[2024-05-06T10:35:23+0200] [ALPM] warning: /etc/mkinitcpio.conf installed as /etc/mkinitcpio.conf.pacnew
[2024-05-06T10:35:23+0200] [ALPM] upgraded mkinitcpio (38.1-1 -> 39-1)
[2024-05-06T10:35:23+0200] [ALPM] upgraded linux (6.8.8.arch1-1 -> 6.8.9.arch1-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded linux-headers (6.8.8.arch1-1 -> 6.8.9.arch1-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded llvm (17.0.6-3 -> 17.0.6-4)
[2024-05-06T10:35:25+0200] [ALPM] upgraded python-tqdm (4.66.2-2 -> 4.66.4-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded meson (1.4.0-4 -> 1.4.0-5)
[2024-05-06T10:35:25+0200] [ALPM] upgraded mobile-broadband-provider-info (20230416-1 -> 20240407-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded mold (2.30.0-1 -> 2.31.0-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded msmtp (1.8.25-2 -> 1.8.26-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded msmtp-mta (1.8.25-2 -> 1.8.26-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded nchat-git (4.41.r42.gdc566175-1 -> 4.41.r43.gb10e9072-1)
[2024-05-06T10:35:25+0200] [ALPM] upgraded tree-sitter (0.22.5-1 -> 0.22.6-1)
[2024-05-06T10:35:25+0200] [ALPM] error: problem occurred while upgrading neovim
[2024-05-06T10:35:25+0200] [ALPM] upgraded neovim (0.9.5-5 -> 0.9.5-6)
[2024-05-06T10:35:25+0200] [ALPM] transaction failed
[2024-05-06T10:37:11+0200] [PACMAN] Running 'pacman --sync -y -u --'
[2024-05-06T10:37:11+0200] [PACMAN] synchronizing package lists
[2024-05-06T10:37:13+0200] [PACMAN] starting full system upgrade
[2024-05-06T10:37:18+0200] [ALPM] transaction started
[2024-05-06T10:37:18+0200] [ALPM] upgraded nim (2.0.2-1 -> 2.0.4-1)
[2024-05-06T10:37:18+0200] [ALPM] upgraded nwg-displays (0.3.16-2 -> 0.3.18-1)
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[2024-05-06T10:37:21+0200] [ALPM] upgraded zellij (0.40.0-1 -> 0.40.1-1)
[2024-05-06T10:37:21+0200] [ALPM] transaction completed
[2024-05-06T10:37:22+0200] [ALPM] running '30-systemd-daemon-reload-system.hook'...
[2024-05-06T10:37:22+0200] [ALPM] running '30-systemd-daemon-reload-user.hook'...
[2024-05-06T10:37:22+0200] [ALPM] running '30-systemd-tmpfiles.hook'...
[2024-05-06T10:37:22+0200] [ALPM] running '30-systemd-update.hook'...
[2024-05-06T10:37:22+0200] [ALPM] running 'gtk-update-icon-cache.hook'...
[2024-05-06T10:37:22+0200] [ALPM] running 'texinfo-install.hook'...
[2024-05-06T10:37:22+0200] [ALPM] running 'update-desktop-database.hook'...
[2024-05-06T10:37:23+0200] [ALPM] running 'update-vlc-plugin-cache.hook'...
[2024-05-06T10:38:04+0200] [PACMAN] Running 'pacman --upgrade --noconfirm -- /home/bosco/.cache/paru/clone/bun-bin/bun-bin-1.1.7-1-x86_64.pkg.tar.zst'
[2024-05-06T10:38:04+0200] [ALPM] transaction started
[2024-05-06T10:38:05+0200] [ALPM] upgraded bun-bin (1.1.6-1 -> 1.1.7-1)
[2024-05-06T10:38:05+0200] [ALPM] transaction completed
[2024-05-06T10:38:05+0200] [ALPM] running '30-systemd-update.hook'...
[2024-05-06T10:38:17+0200] [PACMAN] Running 'pacman --upgrade --noconfirm -- /home/bosco/.cache/paru/clone/mise-bin/mise-bin-2024.5.2-1-x86_64.pkg.tar.zst'
[2024-05-06T10:38:17+0200] [ALPM] transaction started
[2024-05-06T10:38:17+0200] [ALPM] upgraded mise-bin (2024.4.10-1 -> 2024.5.2-1)
[2024-05-06T10:38:17+0200] [ALPM] transaction completed
[2024-05-06T10:38:17+0200] [ALPM] running '30-systemd-update.hook'...
[2024-05-06T10:39:26+0200] [PACMAN] Running 'pacman --upgrade --noconfirm -- /home/bosco/.cache/paru/clone/mongodb-compass/mongodb-compass-1.43.0-1-x86_64.pkg.tar.zst'
[2024-05-06T10:39:26+0200] [ALPM] transaction started
[2024-05-06T10:39:27+0200] [ALPM] upgraded mongodb-compass (1.42.5-1 -> 1.43.0-1)
[2024-05-06T10:39:27+0200] [ALPM] transaction completed
[2024-05-06T10:39:27+0200] [ALPM] running '30-systemd-update.hook'...
[2024-05-06T10:39:27+0200] [ALPM] running 'update-desktop-database.hook'...
[2024-05-06T10:39:36+0200] [PACMAN] Running 'pacman --upgrade --noconfirm -- /home/bosco/.cache/paru/clone/spaceship-prompt/spaceship-prompt-4.15.2-1-any.pkg.tar.zst'
[2024-05-06T10:39:36+0200] [ALPM] transaction started
[2024-05-06T10:39:36+0200] [ALPM] upgraded spaceship-prompt (4.15.1-1 -> 4.15.2-1)
[2024-05-06T10:39:36+0200] [ALPM] transaction completed
[2024-05-06T10:39:36+0200] [ALPM] running '30-systemd-update.hook'...
[2024-05-06T10:39:43+0200] [PACMAN] Running 'pacman --upgrade --noconfirm -- /home/bosco/.cache/paru/clone/sherlock-git/sherlock-git-r2192.49b190f-1-any.pkg.tar.zst'
[2024-05-06T10:39:43+0200] [ALPM] transaction started
[2024-05-06T10:39:43+0200] [ALPM] upgraded sherlock-git (r2146.9137ee4-1 -> r2192.49b190f-1)
[2024-05-06T10:39:43+0200] [ALPM] transaction completed
[2024-05-06T10:39:43+0200] [ALPM] running '30-systemd-update.hook'...
[2024-05-06T10:39:51+0200] [PACMAN] Running 'pacman --upgrade --noconfirm -- /home/bosco/.cache/paru/clone/tree-sitter-python-git/tree-sitter-python-git-0.21.0.r5.g71778c2-1-x86_64.pkg.tar.zst'
[2024-05-06T10:39:51+0200] [ALPM] transaction started
[2024-05-06T10:39:51+0200] [ALPM] upgraded tree-sitter-python-git (0.21.0.r3.gb466ffb-1 -> 0.21.0.r5.g71778c2-1)
[2024-05-06T10:39:51+0200] [ALPM] transaction completed
[2024-05-06T10:39:51+0200] [ALPM] running '30-systemd-update.hook'...

Is your /boot partition close to being out of space?

lsblk says it's 512M and du on the partition when mounted says 90M so unless I checked it wrong, far from it

Last edited by bosco (2024-05-07 07:32:34)

V1del

Forum Moderator

Registered: 2012-10-16

Posts: 25,230

Re: [SOLVED] Kernel got deleted from the EFI partition

[2024-05-06T10:35:09+0200] [ALPM] running '60-mkinitcpio-remove.hook'...

This removes your existing kernels prior to transaction, file system conflict checks should've already happened at this point.

Then you die in the middle of transaction

[2024-05-06T10:35:25+0200] [ALPM] error: problem occurred while upgrading neovim
[2024-05-06T10:35:25+0200] [ALPM] upgraded neovim (0.9.5-5 -> 0.9.5-6)
[2024-05-06T10:35:25+0200] [ALPM] transaction failed

and the post transaction hooks that would run and regenerate your kernel images never ran.

Main question which unexpected event occurred here, did you interrupt this with Ctrl+C or so/RAM issues, neovim running at the same time leading to some logical conflict?

bosco

Member

Registered: 2019-02-26

Posts: 16

Re: [SOLVED] Kernel got deleted from the EFI partition

Main question which unexpected event occurred here, did you interrupt this with Ctrl+C or so/RAM issues, neovim running at the same time leading to some logical conflict?

I don't think I interrupted the upgrade and I have 16GB of ram on a fairly lightweight system, I do however have Neovim open most of the time on that laptop so it's likely that.
Thank you