swupd update is not setting new kernel as default to boot after updating kernel-native bundle

[Senary6]

Recently the WiFi on my NUC8i7BEH stopped working see issue https://github.com/clearlinux/distribution/issues/2767 for more details

Running bootctl set-default Clear-linux-native-6.0.9-1209.conf fixed the issue of the WiFi Firmware not loading. However after running swupd updateand getting an update to kernel-native bundle then rebooting, Clear Linux is still running the 6.0.9-1209 instead of the new 6.0.9-1214 kernel

uname -r 6.0.9-1209.native

running bootctl list after updating to 37680

Boot Loader Entries:
         type: Boot Loader Specification Type #1 (.conf)
        title: Clear Linux OS (Clear-linux-native-6.0.9-1214.conf)
           id: Clear-linux-native-6.0.9-1214.conf
       source: /boot/loader/entries/Clear-linux-native-6.0.9-1214.conf
        linux: /EFI/org.clearlinux/kernel-org.clearlinux.native.6.0.9-1214
       initrd: /EFI/org.clearlinux/freestanding-00-early-ucode.cpio
               /EFI/org.clearlinux/freestanding-i915-firmware.cpio.zstd
      options: root=PARTUUID=40f5f694-258d-4437-bf3c-4cbeb90a456a quiet console=tty0 console=ttyS0,115200n8 cryptomgr.notests init=/usr/bin/initra-desktop initcall_debug intel_iommu=igfx_off kvm-intel.nested=1 no_timer_check nore>

         type: Boot Loader Specification Type #1 (.conf)
        title: Clear Linux OS (Clear-linux-native-6.0.9-1209.conf) (default) (selected)
           id: Clear-linux-native-6.0.9-1209.conf
       source: /boot/loader/entries/Clear-linux-native-6.0.9-1209.conf
        linux: /EFI/org.clearlinux/kernel-org.clearlinux.native.6.0.9-1209
       initrd: /EFI/org.clearlinux/freestanding-00-early-ucode.cpio
               /EFI/org.clearlinux/freestanding-i915-firmware.cpio.zstd
      options: root=PARTUUID=40f5f694-258d-4437-bf3c-4cbeb90a456a quiet console=tty0 console=ttyS0,115200n8 cryptomgr.notests init=/usr/bin/initra-desktop initcall_debug intel_iommu=igfx_off kvm-intel.nested=1 no_timer_check nore>

         type: Automatic
        title: EFI Default Loader
           id: auto-efi-default
       source: /sys/firmware/efi/efivars/LoaderEntries-4a67b082-0a4c-41cf-b6c7-440b29bb8c4f

         type: Automatic
        title: Reboot Into Firmware Interface
           id: auto-reboot-to-firmware-setup
       source: /sys/firmware/efi/efivars/LoaderEntries-4a67b082-0a4c-41cf-b6c7-440b29bb8c4f

running swupd update

sudo swupd update
Update started
Preparing to update from 37640 to 37680
Downloading packs for:
 - NetworkManager
 - NetworkManager-extras
 - Sphinx
 - alsa-utils
 - binutils
 - c-basic
 - cloud-api
 - clr-network-troubleshooter
 - desktop
 - desktop-apps
 - desktop-gnomelibs
 - dev-utils
 - devpkg-NetworkManager
 - devpkg-SDL2
 - devpkg-Vulkan-Headers
 - devpkg-Vulkan-Loader
 - devpkg-colord
 - devpkg-cryptsetup
 - devpkg-cups
 - devpkg-gdk-pixbuf
 - devpkg-gobject-introspection
 - devpkg-harfbuzz
 - devpkg-lcms2
 - devpkg-libXpm
 - devpkg-libpng
 - devpkg-mediasdk
 - devpkg-pango
 - devpkg-systemd
 - devpkg-vala
 - emacs-x11
 - firefox
 - flare
 - flatpak
 - games
 - games-dev
 - gdb
 - gedit
 - gimp
 - glibc-locale
 - gnome-calculator
 - gnome-disk-utility
 - gvim
 - hardware-uefi
 - kernel-native
 - lib-imageformat
 - lib-opengl
 - lib-poppler
 - lib-samba
 - libX11client
 - libstdcpp
 - linux-tools
 - llvm
 - lm-sensors
 - lutris
 - openblas
 - os-core
 - os-core-dev
 - os-core-legacy
 - os-core-plus
 - os-core-update
 - parallel
 - perl-basic
 - perl-basic-dev
 - polkit
 - python-extras
 - python3-basic
 - qt-basic
 - seahorse
 - spice-gtk
 - stress-ng
 - supertuxkart
 - sysadmin-basic
 - tcl-basic
 - vim
 - virt-manager
 - wine
 - x11-server
 [100%]

Finishing packs extraction...

Statistics for going from version 37640 to version 37680:

    changed bundles   : 77
    new bundles       : 0
    deleted bundles   : 0

    changed files     : 3582
    new files         : 9325
    deleted files     : 197
    largest pack      : devpkg-vala 18080Kb

Validate downloaded files
 [100%]

No extra files need to be downloaded
 [100%]

Installing files...
 [100%]

Update was applied
Calling post-update helper scripts
External command: none
External command: clr_debug_fuse.service: restarted (the binary was updated)
External command: pacdiscovery.service: restarted (the binary was updated)
External command: tallow.service: restarted (the binary was updated)
External command: pacrunner.service: restarted (the binary was updated)
External command: systemd-journald.service: restarted (the binary was updated)
External command: mcelog.service: restarted (the binary was updated)
External command: systemd-resolved.service: restarted (the binary was updated)
External command: (Took 7 seconds)
External command: systemd-timesyncd.service: restarted (the binary was updated)
Update took 211.5 seconds, 144 MB transferred
Update successful - System updated from version 37640 to version 37680

[paulcarroty]

Is ls /boot empty?

[anciubo]

Try clr-boot-manager set-timeout 10 After rebooting you will get a kernel list where you can choose which one to boot from this article

[Senary6]

After some investigation it appears that the existence of the EFI variable LoaderEntryDefault will override the /boot/loader/loader.conf file. Going into the boot loader and deselecting the default entry by pressing the d key seems to have resolved the problem.

The boot loader is accessible by pressing any key while the computer is booting up. I tried ESC,Left Control,Left Shift and random letter keys on my keyboard.

What I think happened is that I accidentally went into the boot loader and created a default Entry for the 5.17.4-1139.native kernel by hitting the d key which overrode the loader.conf file, Unfortunately running bootctl set-default Clear-linux-native-6.0.9-1209.conf would have changed LoaderEntryDefault variable and destroyed the evidence for this.

So this appears to be a case of human error.

Some links

https://unix.stackexchange.com/questions/459389/systemd-boot-skips-boot-menu-and-ignores-settings-in-loader-loader-con https://superuser.com/questions/1346163/how-to-safely-set-change-remove-values-of-efi-variables

Edit: Apologies for For closing and opening the issue I am new to GitHub.

[Senary6]

My system has updated to 37720 The kernel I am running is 6.0.11-1216.native, so it seems that the issues has been resolved and no-one has replied about my human error hypothesis. So I am closing the issue as caused by human error accidentally setting the default kernel in systemd-boot.