diff options
| -rw-r--r-- | issues/gn-uploader/build-uploader-container-20240321.org | 219 | ||||
| -rw-r--r-- | issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi | 2 |
2 files changed, 220 insertions, 1 deletions
diff --git a/issues/gn-uploader/build-uploader-container-20240321.org b/issues/gn-uploader/build-uploader-container-20240321.org index d1086df..3511e23 100644 --- a/issues/gn-uploader/build-uploader-container-20240321.org +++ b/issues/gn-uploader/build-uploader-container-20240321.org @@ -201,3 +201,222 @@ Restart all containers: $ sudo systemctl start genenetwork-container.service $ sudo systemctl start genenetwork-development-container.service #+END_SRC + +* Log 2024-03-21T14:57+03:00UTC + +** Reset profile + +List installed packages +#+begin_src shell + /usr/local/guix-profiles/guix-daemon/bin/guix \ + package -p ~/opt/guix --list-installed +#+end_src + +which gave: +#+begin_example +guix-past 921f845 out /gnu/store/7sljixsgvsgdiafshqybdrl8m0f2j8v5-guix-past +guix b0b988c out /gnu/store/dhisx07fngb69qkj4gnlzz5iyakw25zy-guix-b0b988c41 +guix-bioinformatics 2fdbf24 out /gnu/store/4vgrwfaxbvixh1jpsq9wqnm5jc7rhd0r-guix-bioinformatics +guix-forge 6c622a6 out /gnu/store/5bc8079iyd8z3n4l3np09yqgqhdzailv-guix-forge +gn-auth ade6c76 out /gnu/store/l52qdmn3c3liz0pywkndn9j49a9axh6i-gn-auth +gn-uploader 3958ce4 out /gnu/store/adqg6vxq9z2ds0y6a275yqaijv3vslpw-gn-uploader +#+end_example + +remove all installed packages +#+begin_src shell + /usr/local/guix-profiles/guix-daemon/bin/guix \ + package -p ~/opt/guix -r guix-past guix guix-bioinformatics guix-forge \ + gn-auth gn-uploader +#+end_src + +Verify everything was uninstalled by listing packages again as done previously. + +Now list generations: +#+begin_src shell + /usr/local/guix-profiles/guix-daemon/bin/guix \ + package -p ~/opt/guix --list-generations +#+end_src + +which gave (truncated for readability): +#+begin_example +Generation 7 Nov 12 2023 20:45:25 + guix-past 1e25b23 out /gnu/store/91yjvk23arknxlavd1m7rbva3qnrx6fp-guix-past + guix 330b94e out /gnu/store/rsb6nqychig8qdan23rj6w5m7q2kha22-guix-330b94e8b + ︙ + ,- guix b0b988c out /gnu/store/8qrhzflvlp71ijsg6wv13fpcsxxq0n52-guix-b0b988c41 + +Generation 16 Mar 21 2024 07:04:36 (current) + ,- gn-uploader 3958ce4 out /gnu/store/adqg6vxq9z2ds0y6a275yqaijv3vslpw-gn-uploader + ,- gn-auth ade6c76 out /gnu/store/l52qdmn3c3liz0pywkndn9j49a9axh6i-gn-auth + ,- guix-forge 6c622a6 out /gnu/store/5bc8079iyd8z3n4l3np09yqgqhdzailv-guix-forge + ,- guix-bioinformatics 2fdbf24 out /gnu/store/4vgrwfaxbvixh1jpsq9wqnm5jc7rhd0r-guix-bioinformatics + ,- guix b0b988c out /gnu/store/dhisx07fngb69qkj4gnlzz5iyakw25zy-guix-b0b988c41 + ,- guix-past 921f845 out /gnu/store/7sljixsgvsgdiafshqybdrl8m0f2j8v5-guix-past +#+end_example + +Delete all generations except latest +#+begin_src shell + /usr/local/guix-profiles/guix-daemon/bin/guix \ + package -p ~/opt/guix --delete-generations=7..16 +#+end_src + +giving +#+begin_example +guix package: warning: not removing generation 16, which is current +deleting /home/fredm/opt/guix-7-link +deleting /home/fredm/opt/guix-8-link +deleting /home/fredm/opt/guix-9-link +deleting /home/fredm/opt/guix-10-link +deleting /home/fredm/opt/guix-11-link +deleting /home/fredm/opt/guix-12-link +deleting /home/fredm/opt/guix-13-link +deleting /home/fredm/opt/guix-14-link +deleting /home/fredm/opt/guix-15-link +︙ +#+end_example + +Now delete symlinks to ensure next ~guix gc~ cleans up correctly +#+begin_src shell + rm -fv ~/opt/guix* +#+end_src + +Now recreate a new profile with minimal channels: + +#+begin_src shell + /usr/local/guix-profiles/guix-daemon/bin/guix \ + pull -p ~/opt/guix -C minimal-channels.scm +#+end_src + +Where =minimal-channels.scm= has the following content: + +#+begin_src scheme + (list + (channel + (name 'guix-bioinformatics) + (url "https://git.genenetwork.org/guix-bioinformatics/") + (branch "master")) + (channel + (name 'guix-past) + (url "https://gitlab.inria.fr/guix-hpc/guix-past") + (introduction + (make-channel-introduction + "0c119db2ea86a389769f4d2b9c6f5c41c027e336" + (openpgp-fingerprint + "3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5"))))) +#+end_src + +Let's see what the new profile has: +#+begin_src shell + ~/opt/guix/bin/guix describe +#+end_src + +which gives: +#+begin_example +Generation 1 Mar 21 2024 07:34:58 (current) + guix-bioinformatics 2fdbf24 + repository URL: https://git.genenetwork.org/guix-bioinformatics/ + branch: master + commit: 2fdbf2445e5293ba9a12b154c58774e73dfeabe5 + guix-past 921f845 + repository URL: https://gitlab.inria.fr/guix-hpc/guix-past + branch: master + commit: 921f845dc0dec9f052dcda479a15e787f9fd5b0a + guix b0b988c + repository URL: https://git.savannah.gnu.org/git/guix.git + branch: master + commit: b0b988c41c9e0e591274495a1b2d6f27fcdae15a +#+end_example + +Awesome. Now, let's add the profile to the front of the path and build the container afresh: +#+begin_src shell + $ cd /home/fredm/gn-machines + $ export PATH="/home/fredm/opt/guix/bin:${PATH}" + $ ./uploader-deploy.sh +#+end_src + +I get: +#+begin_example +guix system: error: failed to load 'uploader.scm': +ice-9/boot-9.scm:3330:6: In procedure resolve-interface: +no code for module (forge acme) +#+end_example + + I need the =guix-forge= channel too. Add it to the channels: + +#+begin_src scheme + ;; minimal-channels.scm + (list + (channel + (name 'guix-bioinformatics) + (url "https://git.genenetwork.org/guix-bioinformatics/") + (branch "master")) + (channel + (name 'guix-past) + (url "https://gitlab.inria.fr/guix-hpc/guix-past") + (introduction + (make-channel-introduction + "0c119db2ea86a389769f4d2b9c6f5c41c027e336" + (openpgp-fingerprint + "3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5")))) + (channel + (name 'guix-forge) + (url "https://git.systemreboot.net/guix-forge/") + (branch "main") + (introduction + (make-channel-introduction + "0432e37b20dd678a02efee21adf0b9525a670310" + (openpgp-fingerprint + "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3"))))) + +#+end_src + +Pull guix with new =minimal-channels.scm=, and check to see what the profile contains: +#+begin_src shell + ~/opt/guix/bin/guix describe +#+end_src +giving +#+begin_example +Generation 2 Mar 21 2024 07:49:01 (current) + guix-bioinformatics 2fdbf24 + repository URL: https://git.genenetwork.org/guix-bioinformatics/ + branch: master + commit: 2fdbf2445e5293ba9a12b154c58774e73dfeabe5 + guix-past 921f845 + repository URL: https://gitlab.inria.fr/guix-hpc/guix-past + branch: master + commit: 921f845dc0dec9f052dcda479a15e787f9fd5b0a + guix-forge 6c622a6 + repository URL: https://git.systemreboot.net/guix-forge/ + branch: main + commit: 6c622a67051c22eeefe37eedb17d427fbb70c99b + guix b0b988c + repository URL: https://git.savannah.gnu.org/git/guix.git + branch: master + commit: b0b988c41c9e0e591274495a1b2d6f27fcdae15a +#+end_example + +Attempt to rebuild the container: +#+begin_src shell + ./uploader-deploy.sh +#+end_src + +Success!!! + +Stop the currently running container +#+begin_src shell + sudo systemctl stop genenetwork-uploader-container.service +#+end_src + +Delete logs and check they are gone: +#+begin_src shell + $ sudo rm -fv /export2/guix-containers/genenetwork/uploader/var/log/gunicorn-g*.log + $ ls /export2/guix-containers/genenetwork/uploader/var/log/ +#+end_src + += /export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= +still rears its ugly head 😭. + +Start the container for now: +#+begin_src shell + sudo systemctl start genenetwork-uploader-container.service +#+end_src diff --git a/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi b/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi index e8f0c56..d2c33e8 100644 --- a/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi +++ b/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi @@ -28,4 +28,4 @@ However, when I look at the logs, it seems the container is instead running the instead, which seems to be stuck on an older commit without fixes for a circular import bug I'd fixed. -=> https://github.com/genenetwork/gn-gemtext-threads/blob/1c50ad278bb91d899909e9aa78304dfcebbabf9c/issues/gn-uploader/build-uploader-container-20240321.org Troubleshooting log: 2024-03-21 +=> https://github.com/genenetwork/gn-gemtext-threads/blob/main/issues/gn-uploader/build-uploader-container-20240321.org Troubleshooting log: 2024-03-21 |