diff options
| -rw-r--r-- | issues/gn-uploader/build-uploader-container-20240321.org | 203 | ||||
| -rw-r--r-- | issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi | 2 |
2 files changed, 205 insertions, 0 deletions
diff --git a/issues/gn-uploader/build-uploader-container-20240321.org b/issues/gn-uploader/build-uploader-container-20240321.org new file mode 100644 index 0000000..d1086df --- /dev/null +++ b/issues/gn-uploader/build-uploader-container-20240321.org @@ -0,0 +1,203 @@ +#+STARTUP: content +#+TITLE: Building Uploader Container (2024-03-21) +#+AUTHOR: Frederick Muriuki Muriithi +#+OPTIONS: ^:{} + +* Log + +Fix the [[https://git.genenetwork.org/gn-uploader/commit/?id=3958ce457f621f1b75fa8843ba859d8e6015a6c7][channel introduction documentation]] on =gn-uploader= + +On =tux02= do: +#+BEGIN_SRC shell +$ guix pull -p ~/opt/guix -C channels.scm +#+END_SRC +where =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-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")))) + (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 'gn-auth) + (url "https://git.genenetwork.org/gn-auth") + (branch "main")) + (channel + (name 'gn-uploader) + (url "https://git.genenetwork.org/gn-uploader") + (branch "main") + (introduction + (make-channel-introduction + "93c77842315d304abbfc27d78d98b7d42da32a61" + (openpgp-fingerprint + "F370 F409 854B 90E3 52F3 AB01 362B 0BB8 B81D 5A42"))))) +#+END_SRC + +Pull was successful! + +After that, we get the following on =tux02=: +#+BEGIN_SRC shell + $ ~/opt/guix/bin/guix describe --format=channels + hint: Consider installing the `glibc-locales' package and defining + `GUIX_LOCPATH', along these lines: + + guix install glibc-locales + export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale" + + See the "Application Setup" section in the manual, for more info. + + (list (channel + (name 'gn-uploader) + (url "https://git.genenetwork.org/gn-uploader") + (branch "main") + (commit + "3958ce457f621f1b75fa8843ba859d8e6015a6c7") + (introduction + (make-channel-introduction + "93c77842315d304abbfc27d78d98b7d42da32a61" + (openpgp-fingerprint + "F370 F409 854B 90E3 52F3 AB01 362B 0BB8 B81D 5A42")))) + (channel + (name 'gn-auth) + (url "https://git.genenetwork.org/gn-auth") + (branch "main") + (commit + "ade6c76208bd45c24cdd0e73bf3570e6a2bfa131")) + (channel + (name 'guix-forge) + (url "https://git.systemreboot.net/guix-forge/") + (branch "main") + (commit + "6c622a67051c22eeefe37eedb17d427fbb70c99b") + (introduction + (make-channel-introduction + "0432e37b20dd678a02efee21adf0b9525a670310" + (openpgp-fingerprint + "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) + (channel + (name 'guix-bioinformatics) + (url "https://git.genenetwork.org/guix-bioinformatics/") + (branch "master") + (commit + "2fdbf2445e5293ba9a12b154c58774e73dfeabe5")) + (channel + (name 'guix) + (url "https://git.savannah.gnu.org/git/guix.git") + (branch "master") + (commit + "b0b988c41c9e0e591274495a1b2d6f27fcdae15a") + (introduction + (make-channel-introduction + "9edb3f66fd807b096b48283debdcddccfea34bad" + (openpgp-fingerprint + "BBB0 2DDF 2CEA F6A8 0D1D E643 A2A0 6DF2 A33A 54FA")))) + (channel + (name 'guix-past) + (url "https://gitlab.inria.fr/guix-hpc/guix-past") + (branch "master") + (commit + "921f845dc0dec9f052dcda479a15e787f9fd5b0a") + (introduction + (make-channel-introduction + "0c119db2ea86a389769f4d2b9c6f5c41c027e336" + (openpgp-fingerprint + "3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5"))))) +#+END_SRC + +Now, build the container: +#+BEGIN_SRC shell + env PATH="/home/fredm/opt/guix/bin:${PATH}" ./uploader-deploy.sh + ︙ + successfully built /gnu/store/0fwp30li4ngfmradkiyc81cdmapm04bf-gn-uploader-0.0.1-a4ed5d82.drv + ︙ + /gnu/store/4rfwx4d376kbql9y31cfldf3prcfrvx2-run-container + ︙ +#+END_SRC + +Restart the container +#+BEGIN_SRC shell + $ sudo systemctl stop genenetwork-uploader-container.service + $ sudo systemctl start genenetwork-uploader-container.service + $ sudo systemctl status genenetwork-uploader-container.service +#+END_SRC + +Check logs in =/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= + +Still getting: +#+BEGIN_EXAMPLE +︙ +2024-03-21 02:18:29 from gn2.wqflask.oauth2.checks import user_logged_in +2024-03-21 02:18:29 File "/gnu/store/2qhgkf5j649kv57nw4lzsbwlnb1790vq-profile/lib/python3.10/site-packages/gn2/wqflask/oauth2/checks.py", line 10, i +n <module> +2024-03-21 02:18:29 from .client import authserver_uri, oauth2_clientid, oauth2_clientsecret +2024-03-21 02:18:29 ImportError: cannot import name 'authserver_uri' from partially initialized module 'gn2.wqflask.oauth2.client' (most likely due to + a circular import) (/gnu/store/2qhgkf5j649kv57nw4lzsbwlnb1790vq-profile/lib/python3.10/site-packages/gn2/wqflask/oauth2/client.py) +2024-03-21 02:18:29 [2024-03-21 02:18:29 +0000] [9] [INFO] Worker exiting (pid: 9) +︙ +#+END_EXAMPLE + +When we verify where this comes from: +#+BEGIN_SRC shell + $ ls -l /gnu/store/2qhgkf5j649kv57nw4lzsbwlnb1790vq-profile/lib/python3.10/site-packages/ | grep gn2 + lrwxrwxrwx 1 root root 104 Dec 31 1969 gn2 -> /gnu/store/vfa2zdla7ixbb2l5i7k6xnlh5d1rshz9-genenetwork2-3.11-4.1e81c74/lib/python3.10/site-packages/gn2 +#+END_SRC + +We see that the code being run is from [[https://github.com/genenetwork/genenetwork2/commit/1e81c74ee8752ad2913b4e610ba7575638755385][GeneNetwork2: commit 1e81c74]] from +05^{th} March 2024. In [[https://git.genenetwork.org/guix-bioinformatics/tree/gn/packages/genenetwork.scm?id=2fdbf2445e5293ba9a12b154c58774e73dfeabe5#n190][=guix-bioinformatics=, however]], we have specified a newer +[[https://github.com/genenetwork/genenetwork2/commit/b9e04ad79e0039edba25d58f8bc03e4d2a17583b][commit b9e04ad7]] from 07^{th} March 2024. + + Stop uploader service and delete logs: +#+BEGIN_SRC shell + $ sudo systemctl stop genenetwork-uploader-container.service + $ sudo rm -fv /export2/guix-containers/genenetwork/uploader/var/log/gunicorn-g* + removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log' + removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork3.log' + removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-gn-auth.log' + removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-gn-uploader.log' + $ ls /export2/guix-containers/genenetwork/uploader/var/log/ + debug gunicorn-genenetwork2.log mcron.log messages mysqld.log nscd.log secure.1.gz wtmp + guix-daemon.log maillog mcron.log.1.gz messages.1.gz nginx secure virtuoso.log +#+END_SRC + +The file =/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= is still showing up. + +Stop all containers for good measure: +#+BEGIN_SRC shell + $ sudo systemctl stop genenetwork-uploader-container.service + $ sudo systemctl stop genenetwork-container.service + $ sudo systemctl stop genenetwork-development-container.service + $ sudo rm -fv /export2/guix-containers/genenetwork/uploader/var/log/gunicorn-g* + removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log' + $ ls /export2/guix-containers/genenetwork/uploader/var/log/ + debug gunicorn-genenetwork2.log mcron.log messages mysqld.log nscd.log secure.1.gz wtmp + guix-daemon.log maillog mcron.log.1.gz messages.1.gz nginx secure virtuoso.log +#+END_SRC + +The file =/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= is still showing up. + +Something else is running and recreating the file and I have no idea what it is. + +Restart all containers: +#+BEGIN_SRC shell + $ sudo systemctl start genenetwork-uploader-container.service + $ sudo systemctl start genenetwork-container.service + $ sudo systemctl start genenetwork-development-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 c0562ad..fe372c9 100644 --- a/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi +++ b/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi @@ -27,3 +27,5 @@ 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. + +=> ./issues/gn-uploader/build-uploader-container-20240321.org Troubleshooting log: 2024-03-21 |