Nrthugu

I have the following Dockerfile.

FROM continuumio/miniconda3:4.5.11



# create a new user (defaults to 'al-khawarizmi')

USER root

ARG username=al-khawarizmi

RUN useradd --create-home --home-dir /home/${username} ${username}

ENV HOME /home/${username}



# switch to newly created user to avoid running container as root

USER ${username}

WORKDIR $HOME



# build and activate the specified conda environment from a file (defaults to 'environment.yml')

ARG environment=environment.yml

COPY ${environment} .

RUN conda env create --file ${environment} && 

    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc &&  

    echo "conda activate $(head -1 ${environment} | cut -d' ' -f2)" >> ~/.bashrc

The Dockerfile allows the user to specify a conda environment file as a build arg. Here would be a typical environment.yml file.

name: nessie-py



channels:

  - conda-forge

  - defaults



dependencies:

  - python=3.6

  - "notebook=5.7.*"

  - "matplotlib=3.0.*"

  - "numpy=1.15.*"

  - "pandas=0.23.*"

The user can run the image in the standard way and the conda environment will be automatically activated. Running

$ docker run -it image_name:image_tag

yields a bash prompt within the Docker container with the conda environment activated.

(environment_name)$

Now I would like to use docker-compose to start a Jupyter notebook server within the container (built with a conda environment file specifying Jupyter as a dependency).

When I use the following docker-compose.yml

version: "3.7"



services:

  notebook-server:

    build:

      context: ./

    ports:

      - "8888:8888"

    volumes:

      - ./:/home/al-khawarizmi

    command: jupyter notebook --no-browser ip=0.0.0.0  

I get the following error.

$ docker-compose up

Creating network "nessie-py_default" with the default driver

Creating nessie-py_notebook-server_1 ... done

Attaching to nessie-py_notebook-server_1

notebook-server_1  | [FATAL tini (7)] exec jupyter failed: No such file or directory

nessie-py_notebook-server_1 exited with code 127

I suspected that this error meant that the conda environment is not activated. I then tried adding tty: true and stdin_open: true to the docker-compose.yml thinking that this should invoke and interactive bash prompt prior to running the command. This resulted in the same error as above.

I also tried defining a start-notebook.sh script that explicitly activates the conda environment prior to running the notebook.

#!/bin/bash

set -e



# activate the environment and start the notebook

conda activate nessie-py

jupyter notebook --no-browser ip=0.0.0.0

results in a different error

$ docker-compose up

Creating network "nessie-py_default" with the default driver

Creating nessie-py_notebook-server_1 ... done

Attaching to nessie-py_notebook-server_1

notebook-server_1  | 

notebook-server_1  | CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.

notebook-server_1  | If your shell is Bash or a Bourne variant, enable conda for the current user with

notebook-server_1  | 

notebook-server_1  |     $ echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc

notebook-server_1  | 

notebook-server_1  | or, for all users, enable conda with

notebook-server_1  | 

notebook-server_1  |     $ sudo ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh

notebook-server_1  | 

notebook-server_1  | The options above will permanently enable the 'conda' command, but they do NOT

notebook-server_1  | put conda's base (root) environment on PATH.  To do so, run

notebook-server_1  | 

notebook-server_1  |     $ conda activate

notebook-server_1  | 

notebook-server_1  | in your terminal, or to put the base environment on PATH permanently, run

notebook-server_1  | 

notebook-server_1  |     $ echo "conda activate" >> ~/.bashrc

notebook-server_1  | 

notebook-server_1  | Previous to conda 4.4, the recommended way to activate conda was to modify PATH in

notebook-server_1  | your ~/.bashrc file.  You should manually remove the line that looks like

notebook-server_1  | 

notebook-server_1  |     export PATH="/opt/conda/bin:$PATH"

notebook-server_1  | 

notebook-server_1  | ^^^ The above line should NO LONGER be in your ~/.bashrc file! ^^^

notebook-server_1  | 

notebook-server_1  | 

nessie-py_notebook-server_1 exited with code 1

This error suggests that bash is not sourcing ~/.bashrc prior to running the script.

I tried explicitly sourcing /opt/conda/etc/profile.d/conda.sh prior to activating the conda environment.

#!/bin/bash

set -e



# activate the environment and start the notebook

. /opt/conda/etc/profile.d/conda.sh

conda activate nessie-py

jupyter notebook --no-browser ip=0.0.0.0

which results in a different error!

$ docker-compose up

Creating network "nessie-py_default" with the default driver

Creating nessie-py_notebook-server_1 ... done

Attaching to nessie-py_notebook-server_1

notebook-server_1  | Could not find conda environment: nessie-py

notebook-server_1  | You can list all discoverable environments with `conda info --envs`.

notebook-server_1  | 

nessie-py_notebook-server_1 exited with code 1

I can check to see which conda envs are discoverable in the container by running

$ docker run -it nessie-py conda info --envs

which says that the environment does indeed exist.

$ docker run -it nessie-py_notebook-server conda info --envs

# conda environments:

#

nessie-py                /home/al-khawarizmi/.conda/envs/nessie-py

base                  *  /opt/conda

I am out of ideas at this point. This should be possible. Here is an example of a project with a docker-compose.yml file, a Dockerfile that specifies a conda environment and starts a Jupyter notebook server.

The additional complexities that I need include adding a non-root user to the Dockerfile and creating a new conda environment instead of updating the default base conda environment.

What happens is consequence of:

1. In the docker-compose.yml you've a typo in ip=0.0.0.0 which should be --ip=0.0.0.0 instead




2. Binding the host's folder into the container is overriding .bashrc. An easy change would be mounting into a subdirectory




3. You need to run bash in interactive mode (-i) so that .bashrc is properly read

As an example, changes on these points reflected in yourdocker-compose.yml:

version: "3.7"



    services:

      notebook-server:

        build:

          context: ./

        ports:

          - "8888:8888"

        volumes:

          - ./:/home/al-khawarizmi/hosthome

        command: bash -ic 'jupyter notebook --no-browser --ip=0.0.0.0'