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 <me#me.com>
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"]
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"]
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"]
Related
I have built a Docker image which calls a bash file and processes some files in a specific folder, but I can't manage to make it run/work. I have tried different approaches but cannot find where the issue is. Building an image with
docker build -t user/mycontainer .
works, but the bash script doesn't run when I
docker run mycontainer `pwd`:/app
Instead it produces an error:
docker: Error response from daemon: OCI runtime create failed: container_linux.go:380: starting container process caused: exec: "/path/c/to/where/i/run/teh/docker:/app": stat /path/c/to/where/i/run/teh/docker:/app: no such file or directory: unknown.
When I run docker ps there aren't any containers, but if I docker ps -a the container just built appears.
I try running
docker exec -it <container id build> bash
and I get a different error response from daemon:
Container <container id build> is not running
The docker image seems to build all the dependencies and the bash code works when run it separately in my local within the folder.
My dockerfile looks:
FROM alpine:latest
# Create directory in container image for app code
RUN mkdir -p /app
# Copy app code (.) to /app in container image
COPY . /app
# Set working directory context
ARG TIPPECANOE_RELEASE="1.36.0"
RUN apk add --no-cache sudo git g++ make libgcc libstdc++ sqlite-libs sqlite-dev zlib-dev bash \
&& addgroup sudo && adduser -G sudo -D -H tippecanoe && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers \
&& cd /root \
&& git clone https://github.com/mapbox/tippecanoe.git tippecanoe \
&& cd tippecanoe \
&& git checkout tags/$TIPPECANOE_RELEASE \
&& cd /root/tippecanoe \
&& make \
&& make install \
&& cd /root \
&& rm -rf /root/tippecanoe \
&& apk del git g++ make sqlite-dev
RUN chmod +x ./app/bash.sh
USER tippecanoe
WORKDIR /app
CMD ["./bash.sh"]
I am struggling with permissions on docker volume, I get access denied for writing.
This is a small part of my docker file
FROM ubuntu:18.04
RUN apt-get update && \
apt-get install -y \
apt-transport-https \
build-essential \
ca-certificates \
curl \
vim && \............
RUN curl -sL https://deb.nodesource.com/setup_8.x | bash - && apt-get install -y nodejs
# Add non-root user
ARG USER=user01
RUN useradd -Um -d /home/$USER -s /bin/bash $USER && \
apt install -y python3-pip && \
pip3 install qrcode[pil]
#Copy that startup.sh into the scripts folder
COPY /scripts/startup.sh /scripts/startup.sh
#Making the startup.sh executable
RUN chmod -v +x /scripts/startup.sh
#Copy node API files
COPY --chown=user1 /node_api/* /home/user1/
USER $USER
WORKDIR /home/$USER
# Expose needed ports
EXPOSE 3000
VOLUME /data_storage
ENTRYPOINT [ "/scripts/startup.sh" ]
Also a small part of my startup.sh
#!/bin/bash
/usr/share/lib/provision.py --enterprise-seed $ENTERPRISE_SEED > config.json
Then my docker builds command:
sudo docker build -t mycontainer .
And the docker run command:
sudo docker run -v data_storage:/home/user01/.client -p 3008:3000 -itd mycontainer
The problem I have is that the Python script will create the folder: /home/user01/.client and it will copy some files in there. That always worked fine. But now I want those files, which are data files, in a volume for backup porpuses. And as I am mapping with my volume I get permissions denied, so the python script is not able to write anymore.
So at the end of my dockerfile this instructions combined with the mapping in the docker run command give me the permission denied:
VOLUME /data_storage
Any suggestions on how to resolve this? some more permissions needed for the "user01"?
Thanks
I was able to resolve my issue by removing the "volume" command from the dockerfile and just doing the mapping at the moment of executing the docker run:
sudo docker run -v data_storage:/home/user01/.client -p 3008:3000 -itd mycontainer
I'm experimenting for the first time to try to create a docker container to run ROS. I am getting a confusing error and I cant figure out how to trouble
bash-3.2$ docker run -ti --name turtlebot3 rosdocker To run a command
as administrator (user "root"), use "sudo <command>". See "man
sudo_root" for details.
bash: /home/ros/catkin_ws/devel/setup.bash: No such file or directory
I am creating rosdocker with this dockerfile, from inside vscode. I am using the Docker plugin and using the "Build Image" command. Here's the Dockerfile:
FROM ros:kinetic-robot-xenial
RUN apt-get update && apt-get install --assume-yes \sudo \
python-pip \
ros-kinetic-desktop-full \
ros-kinetic-turtlebot3 \
ros-kinetic-turtlebot3-bringup \
ros-kinetic-turtlebot3-description \
ros-kinetic-turtlebot3-fake \
ros-kinetic-turtlebot3-gazebo \
ros-kinetic-turtlebot3-msgs \
ros-kinetic-turtlebot3-navigation \
ros-kinetic-turtlebot3-simulations \
ros-kinetic-turtlebot3-slam \
ros-kinetic-turtlebot3-teleop
# install python packages
RUN pip install -U scikit-learn numpy scipy
RUN pip install --upgrade pip
# create non-root user
ENV USERNAME ros
RUN adduser --ingroup sudo --disabled-password --gecos "" --shell /bin/bash --home /home/$USERNAME $USERNAME
RUN bash -c 'echo $USERNAME:ros | chpasswd'
ENV HOME /home/$USERNAME
USER $USERNAME
# create catkin_ws
RUN mkdir /home/$USERNAME/catkin_ws
WORKDIR /home/$USERNAME/catkin_ws
# add catkin env
RUN echo 'source /opt/ros/kinetic/setup.bash' >> /home/$USERNAME/.bashrc
RUN echo 'source /home/$USERNAME/catkin_ws/devel/setup.bash' >> /home/$USERNAME/.bashrc
I am not sure where the error is coming from and I don't know how to debug or troubleshoot it. I would appreciate any pointers!
You are creating an user ros and then in the last line doing this:
RUN echo 'source /home/$USERNAME/catkin_ws/devel/setup.bash' >> /home/$USERNAME/.bashrc
So obviously, system will look for "/home/ros/catkin_ws/devel/setup.bash" which is not created any where inside docker file.
Either create this file or if you are planning to mount from host to docker, then run with
docker run -ti --name turtlebot3 rosdocker -v sourcevolume:destinationvolume
I want to create a docker image with oracle client and cx_oracle of python. I am using multi stage docker to build the image but I am missing an env variable due to which cx_oracle is not able to find an oracle client library.
FROM oraclelinux:7-slim
RUN curl -o /etc/yum.repos.d/public-yum-ol7.repo https://yum.oracle.com/public-yum-ol7.repo && \
yum-config-manager --enable ol7_oracle_instantclient && \
yum -y install oracle-instantclient18.3-basic oracle-instantclient18.3-devel oracle-instantclient18.3-sqlplus && \
rm -rf /var/cache/yum && \
echo /usr/lib/oracle/18.3/client64/lib > /etc/ld.so.conf.d/oracle-instantclient18.3.conf && \
ldconfig
ENV PATH=$PATH:/usr/lib/oracle/18.3/client64/bin
FROM python:slim
COPY ./requirement.txt ./requirement.txt
RUN pip install -r ./requirement.txt
COPY --from=0 /usr/lib/oracle/18.3/client64/lib /root/usr/lib/oracle/18.3/client64/lib
COPY --from=0 /usr/lib/oracle/18.3/client64/bin /root/usr/lib/oracle/18.3/client64/bin
ENV PATH=$PATH:/root/usr/lib/oracle/18.3/client64/bin:/root/usr/lib/oracle/18.3/client64/lib
ENV ORACLE_HOME=/root/usr/lib/oracle/18.3/client64/:$ORACLE_HOME
ENV LD_LIBRARY_PATH=/root/usr/lib/oracle/18.3/client64/:$LD_LIBRARY_PATH
RUN echo $PATH
RUN echo $ORACLE_HOME
RUN chmod 755 /root/usr/lib/oracle/18.3/client64/lib/*
RUN ls -l /root/usr/lib/oracle/18.3/client64/lib
CMD ["chmod","755","/root/usr/lib/oracle/18.3/client64/lib/*"]
CMD ["ls", "-l" ,"/root/usr/lib/oracle/18.3/client64/lib"]
CMD ["python","test.py"]
Below is the error
DPI-1047: 64-bit Oracle Client library cannot be loaded: "libclntsh.so: cannot open shared object file: No such file or directory". See https://oracle.github.io/odpi/doc/installation.html#linux
Oracle has Python Dockerfiles at https://github.com/oracle/docker-images/tree/main/OracleLinuxDevelopers
Also see https://blogs.oracle.com/opal/docker-for-oracle-database-applications-in-nodejs-and-python-part-1
I'm trying to learn Synatxnet. I have it running through Docker. But I really dont know much about either program Synatxnet or Docker. On the Github Sytaxnet page it says
The SyntaxNet models are configured via a combination of run-time
flags (which are easy to change) and a text format TaskSpec protocol
buffer. The spec file used in the demo is in
syntaxnet/models/parsey_mcparseface/context.pbtxt.
How exactly do I find the spec file to edit it?
I compiled SyntaxNet in a Docker container using these Instructions.
FROM java:8
ENV SYNTAXNETDIR=/opt/tensorflow PATH=$PATH:/root/bin
RUN mkdir -p $SYNTAXNETDIR \
&& cd $SYNTAXNETDIR \
&& apt-get update \
&& apt-get install git zlib1g-dev file swig python2.7 python-dev python-pip -y \
&& pip install --upgrade pip \
&& pip install -U protobuf==3.0.0b2 \
&& pip install asciitree \
&& pip install numpy \
&& wget https://github.com/bazelbuild/bazel/releases/download/0.2.2b/bazel-0.2.2b-installer-linux-x86_64.sh \
&& chmod +x bazel-0.2.2b-installer-linux-x86_64.sh \
&& ./bazel-0.2.2b-installer-linux-x86_64.sh --user \
&& git clone --recursive https://github.com/tensorflow/models.git \
&& cd $SYNTAXNETDIR/models/syntaxnet/tensorflow \
&& echo "\n\n\n" | ./configure \
&& apt-get autoremove -y \
&& apt-get clean
RUN cd $SYNTAXNETDIR/models/syntaxnet \
&& bazel test --genrule_strategy=standalone syntaxnet/... util/utf8/...
WORKDIR $SYNTAXNETDIR/models/syntaxnet
CMD [ "sh", "-c", "echo 'Bob brought the pizza to Alice.' | syntaxnet/demo.sh" ]
# COMMANDS to build and run
# ===============================
# mkdir build && cp Dockerfile build/ && cd build
# docker build -t syntaxnet .
# docker run syntaxnet
First, comment out the command line in the dockerfile, then create and cd into an empty directory on your host machine. You can then create a container from the image, mounting a directory in the container to your hard-drive:
docker run -it --rm -v /pwd:/tmp bash
You'll now have a bash session in the container. Copy the spec file into /tmp from /opt/tensorflow/syntaxnet/models/parsey_mcparseface/context.pbtxt (I'm guessing that's where it is given the info you've provided above -- I can't get your dockerfile to build an image so I can't confirm it; you can always run find . -name context.pbtxt from root to find it), and exit the container (ctrl-d or exit).
You now have the file on your host's hd ready to edit, but you really want it in a running container. If the directory it comes from contains only that file, then you can simply mount your host directory at that path in the container. If it contains other things, then you can use a, so called, bootstrap script to move the file from your mounted directory (in the example above, that's tmp) to its home location. Alternatively, you may be able to tell the software where to find the spec file with a flag, but that will take more research.