[英]Activating a conda env inside a Docker container when using docker-compose to start Jupyter notebook
I have the following Dockerfile
.我有以下
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. Dockerfile 允许用户将 conda 环境文件指定为构建参数。 Here would be a typical
environment.yml file
.这是一个典型的
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.用户可以按照标准方式运行镜像,conda 环境会自动激活。 Running
跑步
$ docker run -it image_name:image_tag
yields a bash prompt within the Docker container with the conda environment activated.在激活 conda 环境的 Docker 容器中产生一个 bash 提示。
(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).现在我想使用 docker
docker-compose
在容器内启动 Jupyter notebook 服务器(使用 conda 环境文件构建,指定 Jupyter 作为依赖项)。
When I use the following docker-compose.yml
当我使用以下
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.我收到以下错误。
$ 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.我怀疑这个错误意味着没有激活conda环境。 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
.然后我尝试将
tty: true
和stdin_open: true
到docker-compose.yml
认为这应该在运行command
之前调用和交互式 bash 提示。 This resulted in the same error as above.这导致了与上述相同的错误。
I also tried defining a start-notebook.sh
script that explicitly activates the conda environment prior to running the notebook.我还尝试定义一个
start-notebook.sh
脚本,该脚本在运行笔记本之前明确激活start-notebook.sh
环境。
#!/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导致不同的错误
$ 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.此错误表明
bash
在运行脚本之前没有获取~/.bashrc
。
I tried explicitly sourcing /opt/conda/etc/profile.d/conda.sh
prior to activating the conda environment.在激活
/opt/conda/etc/profile.d/conda.sh
环境之前,我尝试明确采购/opt/conda/etc/profile.d/conda.sh
。
#!/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!这会导致不同的错误!
$ 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我可以通过运行来检查容器中可以发现哪些 conda envs
$ docker run -it nessie-py conda info --envs
which says that the environment does indeed exist.这说明环境确实存在。
$ 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.我现在没有想法。 This should be possible.
这应该是可能的。 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. 这是一个带有
docker-compose.yml
文件的项目示例,该文件指定 conda 环境并启动 Jupyter Notebook 服务器。
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.我需要的额外复杂性包括将非 root 用户添加到 Dockerfile 并创建新的 conda 环境,而不是更新默认的
base
conda 环境。
What happens is consequence of:发生的后果是:
In the docker-compose.yml
you've a typo in ip=0.0.0.0
which should be --ip=0.0.0.0
instead在
docker-compose.yml
您在ip=0.0.0.0
有一个错字,应该是--ip=0.0.0.0
Binding the host's folder into the container is overriding .bashrc
.将主机的文件夹绑定到容器是覆盖
.bashrc
。 An easy change would be mounting into a subdirectory一个简单的更改是挂载到子目录中
You need to run bash in interactive mode ( -i
) so that .bashrc
is properly read您需要以交互模式(
-i
)运行 bash 以便正确读取.bashrc
As an example, changes on these points reflected in your docker-compose.yml
:例如,这些点的更改反映在您
docker-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'
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