summaryrefslogtreecommitdiff
path: root/miscellaneous/broken-guix-on-tux04-20241108.org
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2024-11-08 11:20:48 -0600
committerFrederick Muriuki Muriithi2024-11-08 11:21:21 -0600
commitd785b06643b5e5a2470fd0da075dcf77bda82d16 (patch)
tree2d4d84a944deaf7b8020b6344a3d244782aa2fad /miscellaneous/broken-guix-on-tux04-20241108.org
parent5414baf24a3fe44be4891fc2a5f4a20dac66453a (diff)
downloadgn-gemtext-d785b06643b5e5a2470fd0da075dcf77bda82d16.tar.gz
Add troubleshooting transcript for broken guix on tux04.
Diffstat (limited to 'miscellaneous/broken-guix-on-tux04-20241108.org')
-rw-r--r--miscellaneous/broken-guix-on-tux04-20241108.org162
1 files changed, 162 insertions, 0 deletions
diff --git a/miscellaneous/broken-guix-on-tux04-20241108.org b/miscellaneous/broken-guix-on-tux04-20241108.org
new file mode 100644
index 0000000..a3eb550
--- /dev/null
+++ b/miscellaneous/broken-guix-on-tux04-20241108.org
@@ -0,0 +1,162 @@
+* 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!