我有下面的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
Dockerfile允许用户指定一个conda环境文件作为构建参数。下面是一个典型的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.*"
用户可以以标准方式运行映像,conda环境将自动激活。运行
$ docker run -it image_name:image_tag
在Docker容器中生成一个bash提示符,并激活conda环境。
(environment_name)$
现在,我想使用docker-compose
在容器中启动Jupyter笔记本服务器(使用conda环境文件构建,该文件将Jupyter指定为依赖项)。
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
出现以下错误。
$ 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
我怀疑这个错误意味着conda环境没有激活。然后我尝试将tty: true
和stdin_open: true
添加到docker-compose.yml
中,认为这应该在运行command
之前调用交互式bash提示符。这导致了与上面相同的错误。
我还尝试定义一个start-notebook.sh
脚本,在运行笔记本之前显式激活conda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
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
此错误表示bash
在运行脚本之前未获取~/.bashrc
。
我尝试在激活conda环境之前显式获取/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
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
$ docker run -it nessie-py conda info --envs
它说环境确实存在。
$ docker run -it nessie-py_notebook-server conda info --envs
# conda environments:
#
nessie-py /home/al-khawarizmi/.conda/envs/nessie-py
base * /opt/conda
Here是一个包含docker-compose.yml
文件的项目示例,该文件是一个指定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,并创建一个新的conda环境,而不是更新默认的base
conda环境。
2条答案
按热度按时间dgiusagp1#
所发生的情况是以下情况的后果:
1.在
docker-compose.yml
中,您在ip=0.0.0.0
中有一处排印错误,应为--ip=0.0.0.0
1.将主机的文件夹绑定到容器将覆盖
.bashrc
。1.您需要在交互模式(
-i
)下运行bash,以便正确读取.bashrc
例如,在
docker-compose.yml
中反映的这些点上的更改:o7jaxewo2#
根据这个article,有一个更简单的方法来完成这个任务,如果你把
SHELL ["conda", "run", "-n", "<venv>", "/bin/bash", "-c"]
放在你的 Dockerfile 中,并在你的 docker-compose.yml 中使用conda run --no-capture-output -n <venv> <your awesome command>
。例如,您的 Dockerfile 可能如下所示:
您的 docker-compose.yml 可能类似于以下内容: