* Broken Guix on Tux04 Troubleshooting Log

Noticed at arount 15:30 (UTC-0500) that guix broke for no apparent reason and I
could no longer do ~guix pull~ without a "Segmentation fault" error.

I could not even do a ~guix search~ without the error.

Began today (2024-11-08UTC-0500) by attempting a pull, and still got the Segmentation fault.

Try checking out an older generation

#+begin_src sh
  $ /home/fredm/opt/guix/bin/guix -p ~/opt/guix --list-generations
  ⋮
  $ /home/fredm/opt/guix/bin/guix -p ~/opt/guix --delete-generations=46
  ⋮
  Segmentation fault
  $ /home/fredm/opt/guix/bin/guix -p ~/opt/guix --delete-generations=40..47
  ⋮
  Segmentation fault
#+end_src

Try pulling with someone else's guix:

#+begin_src bash
  /var/guix/profiles/per-user/aruni/current-guix/bin/guix --profile=/export3/local/home/fredm/opt/guix --channels=channels.scm
#+end_src

#+begin_example
(repl-version 0 1 1)
Backtrace:
           1 (primitive-load "/gnu/store/2lpf5rl0dhq1v8wjfnfmglvr0p2?")
In ice-9/boot-9.scm:
   2007:7  0 (error _ . _)

ice-9/boot-9.scm:2007:7: In procedure error:
inferior failed "/gnu/store/5rac7n9ya6qrpbz42gpn96sa47dkz7rj-guix-2394a7f5f"
#+end_example

Fine, maybe the issue is my profile: delete all links and do a ~guix gc~ to clear any issues.

Upgrade guix daemon

#+begin_src bash
  $ sudo -i /var/guix/profiles/per-user/aruni/current-guix/bin/guix pull
  ⋮
  $ sudo systemctl stop guix-daemon.service
  $ sudo systemctl start guix-daemon.service
  $ sudo systemctl status guix-daemon.service
#+end_src

Try again: No success.

Try:
#+begin_src shell
  $ /var/guix/profiles/per-user/aruni/current-guix/bin/guix describe --format=channels > channels-aruni.scm
  $ /var/guix/profiles/per-user/aruni/current-guix/bin/guix pull -C channels-aruni.scm -p /home/fredm/opt/guix
  $ /home/fredm/opt/guix/bin/guix search python-requests
#+end_src

Okay, now that gives me an output!

Try pulling latest channels:

#+begin_src shell
  $ /home/fredm/opt/guix/bin/guix pull -C channels.scm -p ~/opt/guix
  ⋮
  Building from these channels:
  guix-bioinformaticshttps://git.genenetwork.org/guix-bioinformatics    3659ecd
  guix-forgehttps://git.systemreboot.net/guix-forge/    9864821
  guix-past https://gitlab.inria.fr/guix-hpc/guix-past  5fb77cc
  guix      https://git.savannah.gnu.org/git/guix.git   2394a7f
  ⋮
  building /gnu/store/gzm7jb7hj2bmfhdjzsprar8lacz34ncr-guix-past.drv...
  -builder for `/gnu/store/gzm7jb7hj2bmfhdjzsprar8lacz34ncr-guix-past.drv' failed with exit code 1
  build of /gnu/store/gzm7jb7hj2bmfhdjzsprar8lacz34ncr-guix-past.drv failed
  View build log at '/var/log/guix/drvs/gz/m7jb7hj2bmfhdjzsprar8lacz34ncr-guix-past.drv.gz'.
  cannot build derivation `/gnu/store/rwarhjfc9kymw5k5wvl0pz658bmmmqvh-profile.drv': 1 dependencies couldn't be built
  guix pull: error: build of `/gnu/store/rwarhjfc9kymw5k5wvl0pz658bmmmqvh-profile.drv' failed
#+end_src

Okay, view the logs:
#+begin_src sh
  $ gunzip -kc /var/log/guix/drvs/gz/m7jb7hj2bmfhdjzsprar8lacz34ncr-guix-past.drv.gz
  (repl-version 0 1 1)
  Backtrace:
             1 (primitive-load "/gnu/store/2lpf5rl0dhq1v8wjfnfmglvr0p2?")
  In ice-9/boot-9.scm:
     2007:7  0 (error _ . _)
  
  ice-9/boot-9.scm:2007:7: In procedure error:
  inferior failed "/gnu/store/5rac7n9ya6qrpbz42gpn96sa47dkz7rj-guix-2394a7f5f"
#+end_src

Oh boy!

How about  we start with @aruni's channels and pin everything except
=guix-bioinformatics= in the code below:
#+begin_src scheme
  (list (channel
         (name 'guix-bioinformatics)
         (url "https://git.genenetwork.org/guix-bioinformatics")
         (branch "master"))
        (channel
         (name 'guix-forge)
         (url "https://git.systemreboot.net/guix-forge/")
         (branch "main")
         (commit
          "9864821f976b3de355138c12f287a19fdced67df")
         (introduction
          (make-channel-introduction
           "0432e37b20dd678a02efee21adf0b9525a670310"
           (openpgp-fingerprint
            "7F73 0343 F2F0 9F3C 77BF  79D3 2E25 EE8B 6180 2BB3"))))
        (channel
         (name 'guix-past)
         (url "https://gitlab.inria.fr/guix-hpc/guix-past")
         (branch "master")
         (commit
          "5fb77cce01f21a03b8f5a9c873067691cf09d057")
         (introduction
          (make-channel-introduction
           "0c119db2ea86a389769f4d2b9c6f5c41c027e336"
           (openpgp-fingerprint
            "3CE4 6455 8A84 FDC6 9DB4  0CFB 090B 1199 3D9A EBB5"))))
        (channel
         (name 'guix)
         (url "https://git.savannah.gnu.org/git/guix.git")
         (branch "master")
         (commit
          "b0b988c41c9e0e591274495a1b2d6f27fcdae15a")
         (introduction
          (make-channel-introduction
           "9edb3f66fd807b096b48283debdcddccfea34bad"
           (openpgp-fingerprint
            "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA")))))
#+end_src
Put the code above in =channels.scm= and retry:

#+begin_src sh
  $ /home/fredm/opt/guix/bin/guix pull -C channels.scm -p ~/opt/guix
  ⋮
  Building from these channels:
    guix-bioinformaticshttps://git.genenetwork.org/guix-bioinformatics    3659ecd
    guix-forgehttps://git.systemreboot.net/guix-forge/    9864821
    guix-past https://gitlab.inria.fr/guix-hpc/guix-past  5fb77cc
    guix      https://git.savannah.gnu.org/git/guix.git   b0b988c
  ⋮
#+end_src

Success!

Okay, now, try rebuilding the container:
#+begin_src sh
  $ env PATH="/home/fredm/opt/guix/bin:${PATH}" ./production-deploy.sh
#+end_src

Success!

Check that https://gn2-fred.genenetwork.org/ is up and running: Yes!

Okay. We are back!