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使用Docker compose启动Jupyter笔记本时,在Docker容器内激活conda env

conda docker-compose docker python

davidrpugh · 技术社区 · 7 年前

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

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.*"

用户可以标准方式运行图像,conda环境将自动激活。跑步

$ docker run -it image_name:image_tag

在激活conda环境的Docker容器中生成bash提示符。

(environment_name)$

现在我想用 docker-compose 在容器内启动Jupyter笔记本服务器(使用指定Jupyter为依赖项的conda环境文件构建)。

当我使用下面的 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

$ 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

我怀疑这个错误意味着康达环境没有被激活。然后我尝试添加 tty: true 和 stdin_open: true 到 docker-compose.yml 认为在运行 command

我还尝试定义一个 start-notebook.sh

#!/bin/bash
set -e

# activate the environment and start the notebook
conda activate nessie-py
jupyter notebook --no-browser ip=0.0.0.0

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

bash 这不是采购 ~/.bashrc 在运行脚本之前。

我试着明确地寻找资源 /opt/conda/etc/profile.d/conda.sh 在激活conda环境之前。

#!/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

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

我可以通过运行来检查容器中可发现哪些conda环境

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

也就是说环境确实存在。

$ docker run -it nessie-py_notebook-server conda info --envs
# conda environments:
#
nessie-py                /home/al-khawarizmi/.conda/envs/nessie-py
base                  *  /opt/conda

我现在没有主意了。这应该是可能的。 Here 是一个具有 docker-compose.yml 文件,指定conda环境并启动Jupyter笔记本服务器的Dockerfile。

我需要的额外复杂性包括向Dockerfile添加一个非root用户,以及创建一个新的conda环境,而不是更新默认值 base

1 回复 | 直到 7 年前

fernandezcuesta 7 年前

结果是:

在 docker-compose.yml ip=0.0.0.0 应该是哪一个 --ip=0.0.0.0
正在覆盖将主机文件夹绑定到容器中 .bashrc . 一个简单的改变是装入一个子目录
-i )所以 巴什尔先生 正确阅读

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'