Comments (8)
razrotenberg
commented on May 20, 2024
1
Ok thanks for sharing!
I'm closing this issue for now.
We can reopen it any time if you will get this error again 👌
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InCogNiTo124
commented on May 20, 2024
version: latest
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razrotenberg
commented on May 20, 2024
Hi @InCogNiTo124 !
So sorry for the late reply, truth is that for some reason I wasn't notified about this issue so I just didn't see it 😅
I reran the Docker image and the conda install command.
Then, running genv command works for me so unfortunately I'm unable to reproduce the issue.
I wonder if it was a problem in a previous version of Genv and now it is solved.
Do you mind trying the same thing once again and making sure genv is of version 0.4.0?
You can verify the version using the command conda list | grep genv.
If this still fails, can you run the following commands and share their outputs here:
which genvtype genvls -la /opt/conda/bin/genvls -la /opt/conda/opt/genv/conda list | grep genv
Waiting for hearing from you and thanks for reaching out!
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InCogNiTo124
commented on May 20, 2024
hey @razrotenberg!
Unfortunately the issue persists for me. This is our Dockerfile:
FROM jupyterhub/singleuser:3.1.0
RUN apt update && apt install -y ffmpeg libsm6 libxext6 git
RUN conda install -y -c conda-forge genv jupyterlab_genvbuilding the image with docker buildx build --no-cache -t singleuser . and accesing JupyterLab through JupyterHub, but it isn't resolved. Here are the command outputs:
msmetko@5ef780f06b03:~/work$ which genv
/opt/conda/bin/genv
msmetko@5ef780f06b03:~/work$ type genv
genv is hashed (/opt/conda/bin/genv)
msmetko@5ef780f06b03:~/work$ ls -la /opt/conda/bin/genv
lrwxrwxrwx 1 root users 24 Jan 13 12:17 /opt/conda/bin/genv -> ../opt/genv/libexec/genv
msmetko@5ef780f06b03:~/work$ ls -la /opt/conda/opt/genv/
total 112
drwxr-sr-x 11 root users 4096 Jan 13 12:17 .
drwxr-sr-x 3 root users 4096 Jan 13 12:17 ..
-rwxrwxr-x 2 root root 68 Dec 22 20:48 .bashrc
drwxr-sr-x 2 root users 4096 Jan 13 12:17 bin
-rw-rw-r-- 1 root users 2478 Jan 13 12:17 build_env_setup.sh
-rwxrwxrwx 2 root root 444 Dec 22 20:56 conda_build.sh
drwxr-sr-x 3 root users 4096 Jan 13 12:17 docs
drwxr-sr-x 2 root users 4096 Jan 13 12:17 exe
-rw-rw-r-- 2 root root 92 Dec 22 20:48 .flake8
drwxr-sr-x 3 root users 4096 Jan 13 12:17 .github
-rw-rw-r-- 2 root root 42 Dec 22 20:48 .gitignore
drwxr-sr-x 2 root users 4096 Jan 13 12:17 images
drwxr-sr-x 2 root users 4096 Jan 13 12:17 libexec
-rw-rw-r-- 2 root root 34523 Dec 22 20:48 LICENSE
-rw-rw-r-- 2 root root 842 Dec 22 20:56 metadata_conda_debug.yaml
drwxr-sr-x 2 root users 4096 Jan 13 12:17 py
-rw-rw-r-- 2 root root 5331 Dec 22 20:48 README.md
drwxr-sr-x 2 root users 4096 Jan 13 12:17 shims
drwxr-sr-x 2 root users 4096 Jan 13 12:17 .vscode
msmetko@5ef780f06b03:~/work$ conda list | grep genv
genv 0.4.0 ha770c72_0 conda-forge
jupyterlab_genv 0.1.2 pyhd8ed1ab_0 conda-forgefrom genv.
InCogNiTo124
commented on May 20, 2024
However, I sort of managed to make it run with this:
msmetko@5ef780f06b03:~/work$ /opt/conda/opt/genv/bin/genv
Usage: genv <command>
Available commands:
activate Activate environment
attach Attach devices to this environment
commands List all available genv commands
config Configure this environment
deactivate Deactivate environment
detach Detach devices from this environment
devices Print information of devices
envs Print information of active environments
exec Run a genv executable
help Print this help message
home Display the directory containing the configuration of this environment
init Add genv support to your shell
remote Query genv on remote hosts
root Display the root directory where genv is installed
status Show status of the current environmentfrom genv.
razrotenberg
commented on May 20, 2024
I'm trying to reproduce what you are seeing.
For some reason I can't build the Docker image with the Dockerfile and command that you shared here 🤷
I have another question though, how do you run the bash inside the container?
I wonder if it's something related to this because part of the Genv installation in Conda is the initialization of the shell.
It might be something with the container entrypoint/command that the shell is not initialized properly.
Can you please try running the following command and then check if genv works properly?
source /opt/conda/etc/conda/activate.d/genv_activate.sh
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InCogNiTo124
commented on May 20, 2024
Sorry for the delay! Work got in the way ://
Running the command above resulted with:
$ source /opt/conda/etc/conda/activate.d/genv_activate.sh
No such command 'init'
/opt/conda/bin/genv: line 28: genv-help: command not found
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InCogNiTo124
commented on May 20, 2024
I discovered the problem may be connected to the fact that, while building the image, the commands are run as root, but when the built container is started, we switch it up to another user so permissions get all mixed up. Imma look into it in the future.
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