Run Python scripts on command line running Docker images

Question

I built a docker image using Dockerfile with Python and some libraries inside (no my project code inside). In my local work dir, there are some scripts to be run on the docker. So, here what I did

$ cd /path/to/my_workdir
$ docker run -it --name test -v `pwd`:`pwd` -w `pwd` my/code:test python src/main.py --config=test --results-dir=/home/me/Results

The command python src/main.py --config=test --results-dir=/home/me/Results is what I want to run inside the Docker container.

However, it returns,

/home/docker/miniconda3/bin/python: /home/docker/miniconda3/bin/python: cannot execute binary file

How can I fix it and run my code?

Here is my Dockerfile

FROM nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04

MAINTAINER Me <[email protected]>

RUN apt update -yq && \
    apt install -yq curl wget unzip git vim cmake sudo

RUN adduser --disabled-password --gecos '' docker && \
    adduser docker sudo && \
    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers

USER docker

WORKDIR /home/docker/

RUN chmod a+rwx /home/docker/ && \
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
    bash Miniconda3-latest-Linux-x86_64.sh -b && rm Miniconda3-latest-Linux-x86_64.sh 

ENV PATH /home/docker/miniconda3/bin:$PATH

Run pip install absl-py==0.5.0 atomicwrites==1.2.1 attrs==18.2.0 certifi==2018.8.24 chardet==3.0.4 cycler==0.10.0 docopt==0.6.2 enum34==1.1.6 future==0.16.0 idna==2.7 imageio==2.4.1 jsonpickle==1.2 kiwisolver==1.0.1 matplotlib==3.0.0 mock==2.0.0 more-itertools==4.3.0 mpyq==0.2.5 munch==2.3.2 numpy==1.15.2 pathlib2==2.3.2 pbr==4.3.0 Pillow==5.3.0 pluggy==0.7.1 portpicker==1.2.0 probscale==0.2.3 protobuf==3.6.1 py==1.6.0 pygame==1.9.4 pyparsing==2.2.2 pysc2==3.0.0 pytest==3.8.2 python-dateutil==2.7.3 PyYAML==3.13 requests==2.19.1 s2clientprotocol==4.10.1.75800.0 sacred==0.8.1 scipy==1.1.0 six==1.11.0 sk-video==1.1.10 snakeviz==1.0.0 tensorboard-logger==0.1.0 torch==0.4.1 torchvision==0.2.1 tornado==5.1.1 urllib3==1.23

USER docker
ENTRYPOINT ["/bin/bash"]

It seems like you'd get an equivalent and simpler setup by creating an ordinary Python virtual environment and running the pip install line to set it up; you can put that list of packages into a requirements.txt file to make it repeatable. What are you gaining by using Docker here? — David Maze
– David Maze, Commented Jul 6, 2020 at 11:07
Yes, your comment is right. When running the command "docker run -it --name test -v pwd:pwd -w pwd my/code:test python src/main.py --config=test --results-dir=/home/me/Results", I got /home/docker/miniconda3/bin/python: /home/docker/miniconda3/bin/python: cannot execute binary file — GoingMyWay
– GoingMyWay, Commented Jul 6, 2020 at 11:13

lsd · Accepted Answer · 2020-07-06 09:54:46Z

1

Try making the file executable before running it.

as John mentioned to do in the dockerfile

FROM python:latest

COPY src/main.py /usr/local/share/

RUN chmod +x /usr/local/share/src/main.py      #<-**--- just add this also

# I have some doubts about the pathing 

CMD ["/usr/local/share/src/main.py", "--config=test --results-dir=/home/me/Results"]

answered Jul 6, 2020 at 9:54

lsd

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5 Comments

GoingMyWay Over a year ago

Thanks, there are many python files, and sometimes I need to change my python files, so I think cp all my files to images is not practical. Instead, I want to run the task in command line. How can I fix my current issue?

lsd Over a year ago

docker run -it --name test -v pwd:pwd -w pwd my/code:test python chmod +x "src/main.py && src/main.py --config=test --results-dir=/home/me/Results" Try running two commands sequentially like this.

GoingMyWay Over a year ago

Thanks, it is a bit weird, by replace the python commands with pwd, it also returns /bin/pwd: /bin/pwd: cannot execute binary file

GoingMyWay Over a year ago

Use your suggestion. I got /bin/bash: python: No such file or directory

GoingMyWay Over a year ago

I followed the code, github.com/oxwhirl/pymarl/blob/master/docker/Dockerfile and github.com/oxwhirl/pymarl/blob/master/run.sh

John Arnok · Accepted Answer · 2020-07-06 09:43:17Z

0

You can run a python script in docker by adding this to your docker file:

FROM python:latest

COPY src/main.py /usr/local/share/

CMD ["src/main.py", "--config=test --results-dir=/home/me/Results"]

answered Jul 6, 2020 at 9:43

John Arnok

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1 Comment

GoingMyWay Over a year ago

Thanks, this is a good method. But how can I fix my current issue? There are many command-line arguments to be passed to python, I prefer to run the code in the command line,

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