diff options
Diffstat (limited to 'topics')
| -rw-r--r-- | topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi | 40 |
1 files changed, 39 insertions, 1 deletions
diff --git a/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi b/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi index f10aa21..3371067 100644 --- a/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi +++ b/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi @@ -68,4 +68,42 @@ root@genenetwork: cd /export/source/fallback-debug/genenetwork3 root@genenetwork /export/source/fallback-debug/genenetwork3# PYTHONPATH=/gnu/store/yi76sybwqql4ky60yahv91z57srb2fr0-profile/lib/python3.10/site-packages /gnu/store/hhn20xg4vag4xiib2d7d4c1vkm09dcav-gunicorn-20.1.0/bin/gunicorn --workers 1 --timeout 1200 --bind 127.0.0.1:8893 --env GN3_CONF=/gnu/store/592bscjpr6xyz8asn743iqzgczg8l947-gn3.conf --env GN3_SECRETS=/etc/genenetwork/gn3-secrets.py --chdir /export/source/fallback-debug/genenetwork3 --log-level debug --log-file gn3.log --reload --env HOME=/tmp gn3.app:create_app\(\) ``` -Note that gunicorn also has a `--pythonpath` switch, but I could not get that to work. Make sure you are loading gn3 code from your source dir (e.g. by introducing an error). +Make sure you are loading gn3 code from your source dir (e.g. by introducing an error). The commit for sharing sources is at + +=> https://git.genenetwork.org/gn-machines/commit/?id=0d551870499c886f900a5b87b2040db25e9a00cc + +Anyway, at this stage I can edit GN3 code outside the container and it will update with gunicorn. It leads to solving the shared path issue. But first we want to also run GN2 inside the system container. + +# GN2 in a system container + +We clone genenetwork2 in the source path, next we take a hint from shepherd: + +``` +/gnu/store/1gd9nsy4cps8fnrd1avkc9l01l7ywiai-guile-3.0.9/bin/guile --no-auto-compile /gnu/store/vg8q4kdnkzy7skv04z57ngm8rqn7kvhd-gunicorn-genenetwork2-pola-wrapper --workers 20 --timeout 1200 --bind 127.0.0.1:8892 --env GN2_PROFILE=/gnu/store/jl6x90wdbwbs7c7zxnyz2kfd0qx8bf5h-profile --env GN2_SETTINGS=/gnu/store/gn9pr6kvmf1zlaskd1bqn1dssx4sy5lw-gn2.conf --env HOME=/tmp gn2.wsgi +``` + +and we tell herd to stop genenetwork2. + +``` + PYTHONPATH=/gnu/store/yi76sybwqql4ky60yahv91z57srb2fr0-profile/lib/python3.10/site-packages /gnu/store/1gd9nsy4cps8fnrd1avkc9l01l7ywiai-guile-3.0.9/bin/guile --no-auto-compile /gnu/store/vg8q4kdnkzy7skv04z57ngm8rqn7kvhd-gunicorn-genenetwork2-pola-wrapper --workers 20 --timeout 1200 --bind 127.0.0.1:8892 --env GN2_PROFILE=/gnu/store/jl6x90wdbwbs7c7zxnyz2kfd0qx8bf5h-profile --env GN2_SETTINGS=/gnu/store/gn9pr6kvmf1zlaskd1bqn1dssx4sy5lw-gn2.conf --chdir /export/source/fallback-debug/genenetwork2 --env HOME=/tmp gn2.wsgi +``` + +and we get an Error: can't chdir to '/export/source/fallback-debug/genenetwork2'. Now I banged my head against the wall for a while and realized, after a back-and-forth with Arun, that guile starts a container without that path being visible! So we run GN2 and GN3 as *containers* inside a guix system container (a VM). OK, that means, next to specifying the path in the build, we also have to specify the source path inside the container definition. The upside is being explicit. The downside may be performance - we'll have to look into that later. This link suggests running a container in a VM is 40% slower: + +=> https://blog.nestybox.com/2020/09/23/perf-comparison.html + +But, we'll have to look into such optimizations later. + +After adding the source dir and changing the permissions of the secrets file I can + +``` +/export/source/fallback-debug/genenetwork2# /gnu/store/1gd9nsy4cps8fnrd1avkc9l01l7ywiai-guile-3.0.9/bin/guile --no-auto-compile /gnu/store/47vplgxkcwd7vk3r71qvvfkwr9rcqlsl-gunicorn-genenetwork2-pola-wrapper --workers 1 --timeout 1200 --bind 127.0.0.1:8892 --env GN2_PROFILE=/gnu/store/jl6x90wdbwbs7c7zxnyz2kfd0qx8bf5h-profile --env GN2_SETTINGS=/gnu/store/gn9pr6kvmf1zlaskd1bqn1dssx4sy5lw-gn2.conf --chdir /export/source/fallback-debug/genenetwork2 --pythonpath=/gnu/store/hvv0r5nzhbbsnd9s68cmx5q0sznjhnrp-profile/lib/python3.10/site-packages --log-level debug --log-file /tmp/gn2.log --reload --env HOME=/tmp gn2.wsgi +``` + +Note that we need the --pythonpath. I pick up that profile from pola-wrapper. + +# Fixing shared paths + +By default both GN2 and GN3 run as containers. We pass temporary files through the file sytem, so let's try and fix that first. The good news is that they only have to share the TMPDIR. First we share a new directory under /var/tmp for the system container. Next we have to tell GN2 and GN3 system containers to use /var/tmp/gn2. This was done in commit + +=> https://git.genenetwork.org/gn-machines/commit/?id=831cf86b4fbf7b054640fa46eede6040ad01340f |