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mamba-org / gator

Conda environment and package management extension from within Jupyter
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no_conda_kernels is not finding conda #72

Closed dbkinghorn closed 4 years ago

dbkinghorn commented 4 years ago

Description

Installing from conda-forge for JupyterLab 2.2.5 (served from JupyterHub)

Install completes but on starting up Conda Package Manager from JLab gives 2 boxes;

"An error occured while listing Conda environments" " ... I know you want to give up, but wait a bit longer..." Waiting doesn't help :-)

In the system log there is this,

Aug 22 00:08:48 i7ml jupyterhub[24643]: [Errno 2] No such file or directory: 'conda' Aug 22 00:08:48 i7ml jupyterhub[24643]: [E 2020-08-22 00:08:48.089 SingleUserNotebookApp manager:91] [nb_conda_kernels] couldn't call conda:

Looks like it is not finding conda? Maybe need a full path to the system conda (in /opt/conda/bin) ??

Any ideas for a fix/workaround would be appreciated. Thanks

fcollonval commented 4 years ago

Hey @dbkinghorn thanks for reaching out. The main trouble is to get conda activated (i.e. available) in the user single server. This depends on the spawner you are using. But basically, you need the single server user to load conda (like conda init does by adding commands to shell init script).

Usually you will get it to work by ensuring . /path/to/conda-installation/etc/profile.d/conda.sh is executed at the start of the single user server.

dbkinghorn commented 4 years ago

Thank you!
It looked like it was something like that but, for the user, conda.sh has been sourced and conda is on PATH. (as seen from the jlab terminal) However, I'm using JupyterHub to launch the single user servers (default) and I installed the extension with sudo so the extension is available to all users ...and root does not source /etc/profile.d/conda.sh

As a workaround/fix I added a link to the system /opt/conda/bin/conda in /usr/local/sbin so root can find it ... that worked

Keep up the good work :-)