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Tuesday, 23rd of May 2023, 15:53:33 UTC
15:54:36
bike
it works. very nice. next, jupyter...
16:28:51
drmeister
yitzi: On the cluster jupyterlab has lost the ability to display sdf files with the sdf viewer. I see this when I run `jupyter-labextension list`
16:28:52
drmeister
https://www.irccloud.com/pastebin/KA0tUF8B/
16:30:24
yitzi
Try running the install line from cando-user-install
16:30:44
yitzi
https://github.com/cando-developers/cando/blob/fdf1ce9b473669dc12368add791f6ed24a86954d/cando-user-install#L6-L8
16:31:04
bike
if i want to add a cando kernel to this hub, do i need to make kernel json files for each user?
16:32:52
yitzi
Quicklisp will need to be setup also. You could try running cando-user-install inside each account and that should do everything
16:33:07
drmeister
https://www.irccloud.com/pastebin/1TpvzexC/
16:33:17
drmeister
The jupyterlab on the cluster in the apptainer is 4.0.0
16:33:34
yitzi
bike: But there are also ways of installing system wide
16:33:36
drmeister
The jupyterlab on zeus is 3.6.1
16:34:13
drmeister
Are we about to lose all of our hard work with widgets when jupyterlab goes 4.0.0?
16:34:17
bike
i gues i can just try cando-user-install
16:34:52
yitzi
drmeister: No, I already updated for all that stuff. I use v4 on Arch.
16:35:08
bike
well, it complains about not being able to find jupyter-lab(extension), like it did on zeus
16:35:42
drmeister
I'll stay quiet - you guys are doing important work.
16:36:04
yitzi
Bike: I think you need to login via the terminal from the hub page
16:37:23
yitzi
Probably after you login in to the specific user
16:37:45
yitzi
drmeister: Did you get an error message?
16:38:09
bike
wants node.js and npm. ok, sure
16:40:21
bike
and now it's out of storage...
17:01:03
bike
now ona new instance it won't let me install cando because it can't get libfmt9 and a few other things, so i must have screwed something up
17:03:25
bike
ok yeah deleting the source and readding it worked.
17:08:14
bike
okay, so now i run cando-user-install, and it gets an error with permission denied on /opt/tljh/user/share/jupyter/lab/extensions, which i suppose is where jupyter is
17:08:26
bike
should i do sudo cando-user-install? does that even make sense?
17:10:14
yitzi
edit cando-user-install and comment out L5-L8 and try again
17:11:34
bike
ok. do i not need the jupyter extensions installed?
17:11:47
yitzi
We'll install those system wide
17:14:08
bike
well, cando-user-install kept going past those lines anyway. it's loading flexi streams right now.
17:14:25
yitzi
Get a cup of coffee...or three.
17:15:35
yitzi
In the admin tljh termina do jupyter-labextension install @jupyter-widgets/jupyterlab-manager @jupyter-widgets/jupyterlab-sidecar cytoscape-clj kekule-clj ngl-clj resizable-box-clj jupyterlab-debugger-restarts jupyterlab-molviewer
17:16:29
bike
oh, i mean, i was running cando-user-install in that terminal too
17:16:45
bike
should i just run that command separately with sudo?
17:17:59
yitzi
cando-user-install will need to be run in each user's account
17:18:34
yitzi
There maybe a hook to accomplish that...but we should try it manually first.
17:19:30
yitzi
I'll see if there is a way to detect a user writable lab extension folder so it can skip those step if needed.
18:03:47
bike
kernel seems to be dying at startup. can i get at the logs somehow? or, is this just the image save thing again
18:26:11
yitzi
Is jupyter-console installed?
18:27:45
yitzi
Bike: make a folder ~/.local/share/jupyter/cando_slow
18:28:00
yitzi
~/.local/share/jupyter/kernels/cando_slow
18:28:11
yitzi
and create kernel.json https://plaster.tymoon.eu/view/3796
18:39:56
bike
oh so maybe i just didn't install the jupyterlab dependencies. but then when i did that it fails because... node.js is an old version, i think?
18:40:14
bike
error lib0@0.2.63: The engine "node" is incompatible with this module. Expected version ">=14". Got "12.22.9"
18:40:41
bike
should i not have installed node from debian?
18:41:49
yitzi
Probably not. Debian is decrepit
18:42:25
yitzi
Remove it and try installing it using conda from inside the admin console
18:43:01
yitzi
conda install -c conda-forge nodejs
18:49:12
bike
now if i run jupyter-labextension it says to install node with version >= 12. it runs a binary called 'node' from within tljh, but it seems to be... version 6?
18:49:59
yitzi
Do conda search -f nodejs
18:51:03
bike
conda list shows version 6.13.1. conda search says "Loading channels: failed"
18:52:13
yitzi
Try doing conda update nodejs
18:52:56
yitzi
You may need to do conda update -c conda-forge nodejs
19:01:28
bike
conda update nodejs says i have a million conflicts, so i guess i'll try the conda forge thing
19:03:16
yitzi
I hate conda. It is incredibly dumb.
19:03:54
bike
i've not had a great time with it.
19:04:13
bike
well, this says it failed to solve the environment also.
19:05:53
bike
not sure what i could have done to cause these million conflicts
19:07:50
bike
well ater the update i have a node version 14, so here we go again
19:08:30
bike
nope, now when i run jupyter-labextension it fails immediately with "No module named 'six'"
19:09:11
yitzi
No. Use conda to remove nodejs first.
19:09:14
bike
or just more conda-forge, i guess
19:10:04
yitzi
Then how about this? https://github.com/nodesource/distributions#using-debian-as-root-5
19:16:16
bike
ok, after some stuff that seems to have worked, and node --version says v20. but i get the same error about 'six' from jupyter-labextension.
19:17:02
yitzi
Is it complaining about node or npm?
19:18:37
yitzi
I meant which one is it saying version 6?
19:19:24
bike
it's not. it's saying it's trying to load a module called 'six' and not finding it.
19:20:21
yitzi
conda install -c conda-forge si
19:26:01
bike
ok. now the extensions are installed. thanks.
19:26:17
bike
don't feel obligated to handhold me through this, i'm sure you have better things to do
19:26:49
bike
so i guess i'll try the slow cando thing next.
19:27:33
yitzi
No worries. I am just grading papers
19:28:46
yitzi
Is jupyter-console installed?
19:29:06
yitzi
Make the kernel.json file...then just start cando and do (ql:quickload cando-jupyter) ... when it is done exit cando. Then restart the hub.
19:33:32
bike
i think this is just a jupyter notebook rather than lab, though. not sure of the difference still.
19:34:17
yitzi
To get lab you need to change the spawn url
19:34:54
yitzi
https://jupyterlab.readthedocs.io/en/latest/user/jupyterhub.html
19:36:18
bike
ok. great. something is working.
19:36:23
yitzi
I think you can change that in the Hub settings verus per user
21:53:33
drmeister
How are things going? Is there a jupyterhub?
22:06:58
bike
let me make an account for you and set things up hopefully.
22:16:31
bike
cando-user-install takes a bit.
22:28:21
bike
drmeister: messaged on google
Wednesday, 24th of May 2023, 3:53:33 UTC