bug#58783: Strange booting/reproducibility issue

[Denis 'GNUtoo' Carikli]

Hi,

On an i686 computer[1], I've a Guix installation on an HDD, and if I do
> guix pull -M 1 -c 1
and that I then do
> sudo -E guix system reconfigure -M 1 -c 1 system.scm

I get the following boot failure[2]:
> GC Warning: pthread_getattr_np or pthread_attr_getstack failed for
> main thread GC Warning: Couldn't read /proc/stat
> Welcome, this is GNU's early boot Guile.
> Use 'gnu.repl' for an initrd REPL.
> 
> loading kernel modules...
> Enter passphrase for /dev/sda2: 
> /dev/mapper/cryptroot: recovering journal
> /dev/mapper/cryptroot: clean, 702176/9773056 files, 8418369/39071232
> blocks ice-9/boot-9.scm:1685:16: In procedure raise-exception:
> In procedure mkdir: File exists
> 
> Entering a new prompt.  Type `,bt' for a backtrace or `,q' to
> continue. GNU Guile 3.0.7
> Copyright (C) 1995-2021 Free Software Foundation, Inc.
> 
> Guile comes with ABSOLUTELY NO WARRANTY; for details type `,show w'.
> This program is free software, and you are welcome to redistribute it
> under certain conditions; type `,show c' for details.
> 
> Enter `,help' for help.
> scheme@(guile-user)> 

If I use the same system.scm (attached) and that I produce an image
with the build_init.sh script (attached) which setups an encrypted
partition and uses guix system init, and that I then copy the resulting
image to an USB drive with ddrescue, It then boots fine.

Since the system ends up not booting anymore when I try to guix pull
and guix system reconfigure the system on the HDD, to boot I simply
select a known booting old revision in the grub menu, so I can easily
test things.

Though I'm not sure where to look. Is there anything I can do to get
more contexts or logs? Should I try loglevel=8 ?

References:
-----------
[1] The computer is a Thinkpad X60 with only an external display running
    Coreboot with SeaBIOS.
[2] The boot log was captured by adding console=ttyS0,115200 to the
    command line arguments in grub and by capturing the messages
    through a serial port.

Denis.

build_init.sh
Description: application/shellscript

;; Copyright (C) 2022 Denis 'GNUtoo' Carikli <gnu...@cyberdimension.org>
;;
;; This program is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;;
;; This program is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with this program.  If not, see <https://www.gnu.org/licenses/>.

(use-modules
  (gnu)
  (gnu packages admin)
  (gnu packages emacs)
  (gnu packages gnome)
  (gnu packages ntp)
  (gnu packages screen)
  (gnu packages vim))
(use-package-modules version-control xdisorg)
(use-service-modules desktop networking sddm ssh xorg)

(operating-system
  (locale "en_US.utf8")
  (timezone "Europe/Paris")
  (keyboard-layout
    (keyboard-layout "us" "altgr-intl"))
  (host-name "x60-base")
  (users (cons* (user-account
                  (name "gnutoo")
                  (comment "GNUtoo")
                  (group "users")
                  (home-directory "/home/gnutoo")
                  (supplementary-groups
                    '("wheel" "netdev" "audio" "video")))
                %base-user-accounts))
  (packages
    (append
      (list (specification->package "nss-certs")
        emacs
        git
        gvfs
        htop
        ntp
        redshift-wayland
        screen
        vim)
      %base-packages))
  (services
    (append
     (list
      (elogind-service)
      (service openssh-service-type
	       (openssh-configuration
		(permit-root-login #t)
		(password-authentication? #f)
		(challenge-response-authentication? #f)
                (use-pam? #f)
		;; (authorized-keys
		;; `(("root", (local-file "gnutoo.pub"))))))
                ))
            (service tor-service-type)
            ;; (service dhcp-client-service-type)
            (service xfce-desktop-service-type)
            (set-xorg-configuration
             (xorg-configuration
              (keyboard-layout keyboard-layout))
             sddm-service-type))
      %base-services))
  (bootloader
    (bootloader-configuration
      (bootloader grub-bootloader)
      (targets '("/dev/sda"))
      (terminal-outputs '(console))
      (keyboard-layout keyboard-layout)))
  (mapped-devices
    (list (mapped-device
            (source
              (uuid "12345678-abcd-1234-1234-1234567899ab"))
            (target "cryptroot")
            (type luks-device-mapping))))
  (file-systems
    (cons* (file-system
             (mount-point "/")
             (device "/dev/mapper/cryptroot")
             (type "ext4")
             (dependencies mapped-devices))
           %base-file-systems)))

pgp1Q9Z_qjwM6.pgp
Description: OpenPGP digital signature