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Dockerfile
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# Shared arguments
ARG USERNAME="vscode"
ARG USER_UID=1000
ARG USER_GID=$USER_UID
FROM ubuntu:20.04 AS gadgetron_baseimage
LABEL org.opencontainers.image.source=https://github.com/gadgetron/gadgetron
ARG USERNAME
ARG USER_UID
ARG USER_GID
ARG HOME=/home/$USERNAME
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get install -y sudo wget git-core rsync curl net-tools libxml2 \
&& apt-get clean
# Create the user
RUN groupadd --gid $USER_GID $USERNAME \
&& useradd --uid $USER_UID --gid $USER_GID -m $USERNAME -s /bin/bash \
#
# [Optional] Add sudo support. Omit if you don't need to install software after connecting.
&& echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \
&& chmod 0440 /etc/sudoers.d/$USERNAME
# The version of conda to use
ARG CONDA_VERSION=22.11.1
# Based on https://github.com/ContinuumIO/docker-images/blob/master/miniconda3/debian/Dockerfile.
# We also install conda-lock.
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
&& mkdir -p /opt \
&& sh miniconda.sh -b -p /opt/conda \
&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
&& find /opt/conda/ -follow -type f -name '*.a' -delete \
&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
&& [ -z "$CONDA_VERSION" ] || /opt/conda/bin/conda install -n base conda=$CONDA_VERSION \
&& /opt/conda/bin/conda install -c conda-forge -n base conda-lock \
&& /opt/conda/bin/conda clean -afy \
&& groupadd -r conda --gid 900 \
&& usermod -aG conda ${USERNAME} \
&& chown -R :conda /opt/conda \
&& chmod -R g+w /opt/conda \
&& find /opt -type d | xargs -n 1 chmod g+s
# Copy environment, which will be filtered for later staged
COPY --chown=$USER_UID:conda environment.yml /tmp/build/
# Create mount points for tests
RUN mkdir -p /test && chown ${USER_UID}:${USER_GID} /test
VOLUME /test
# Add a section to /etc/bash.bashrc that ensures that a section is present at the end of ~/.bashrc.
# We can't just write to .bashrc from here because it will be overwritten if the vscode user has
# opted to use their own dotfiles repo. The dotfiles repo is cloned after the postCreateCommand
# in the devcontainer.json file is executed.
RUN echo "\n\
if ! grep -q \"^source /opt/conda/etc/profile.d/conda.sh\" ${HOME}/.bashrc; then\n\
echo \"source /opt/conda/etc/profile.d/conda.sh\" >> ${HOME}/.bashrc\n\
echo \"conda activate $(grep 'name:' /tmp/build/environment.yml | awk '{print $2}')\" >> ${HOME}/.bashrc\n\
fi\n" >> /etc/bash.bashrc
ENV TINI_VERSION v0.19.0
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
RUN chmod +x /tini
FROM gadgetron_baseimage AS gadgetron_dev_cuda
ARG USER_UID
ARG HOME
USER ${USER_UID}
RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
RUN grep -v "#.*\<NOFILTER\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
USER root
FROM gadgetron_baseimage AS gadgetron_dev_nocuda
ARG USER_UID
ARG HOME
USER ${USER_UID}
RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
RUN grep -v "#.*\<cuda\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
USER root
FROM gadgetron_dev_cuda AS gadgetron_cudabuild
ARG USER_UID
USER ${USER_UID}
WORKDIR /opt
RUN sudo chown $USER_UID:$USER_GID /opt && mkdir -p /opt/code/gadgetron && mkdir -p /opt/package
COPY --chown=$USER_UID:conda . /opt/code/gadgetron/
SHELL ["/bin/bash", "-c"]
RUN . /opt/conda/etc/profile.d/conda.sh && umask 0002 && conda activate gadgetron && sh -x && \
cd /opt/code/gadgetron && \
mkdir build && \
cd build && \
cmake ../ -GNinja -DUSE_MKL=ON -DCMAKE_INSTALL_PREFIX=/opt/package && \
ninja && \
ninja install
FROM gadgetron_dev_nocuda AS gadgetron_nocudabuild
ARG USER_UID
USER ${USER_UID}
WORKDIR /opt
RUN sudo chown $USER_UID:$USER_GID /opt && mkdir -p /opt/code/gadgetron && mkdir -p /opt/package
COPY --chown=$USER_UID:conda . /opt/code/gadgetron/
SHELL ["/bin/bash", "-c"]
RUN . /opt/conda/etc/profile.d/conda.sh && umask 0002 && conda activate gadgetron && sh -x && \
cd /opt/code/gadgetron && \
mkdir build && \
cd build && \
cmake ../ -GNinja -DUSE_MKL=ON -DCMAKE_INSTALL_PREFIX=/opt/package && \
ninja && \
ninja install
FROM gadgetron_baseimage AS gadgetron_rt_cuda
ARG USER_UID
ARG HOME
USER ${USER_UID}
RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
RUN grep -v "#.*\<dev\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
COPY --from=gadgetron_cudabuild --chown=$USER_UID:conda /opt/package /opt/conda/envs/gadgetron/
COPY --from=gadgetron_cudabuild --chown=$USER_UID:conda /opt/code/gadgetron/docker/entrypoint.sh /opt/
RUN chmod +x /opt/entrypoint.sh
RUN sudo mkdir -p /opt/integration-test && sudo chown ${USER_GID}:${USER_UID} /opt/integration-test
COPY --from=gadgetron_cudabuild --chown=$USER_UID:conda /opt/code/gadgetron/test/integration /opt/integration-test/
ENTRYPOINT [ "/tini", "--", "/opt/entrypoint.sh" ]
FROM gadgetron_baseimage AS gadgetron_rt_nocuda
ARG USER_UID
ARG HOME
USER ${USER_UID}
RUN mkdir -p ${HOME}/.cache/conda/notices && sudo chown -R ${USER_UID}:conda ${HOME}/.cache/conda/notices
RUN grep -v "#.*\<cuda\|dev\>" /tmp/build/environment.yml > /tmp/build/filtered_environment.yml
RUN umask 0002 && /opt/conda/bin/conda env create -f /tmp/build/filtered_environment.yml && /opt/conda/bin/conda clean -afy && sudo chown -R :conda /opt/conda
COPY --from=gadgetron_nocudabuild --chown=$USER_UID:conda /opt/package /opt/conda/envs/gadgetron/
COPY --from=gadgetron_nocudabuild --chown=$USER_UID:conda /opt/code/gadgetron/docker/entrypoint.sh /opt/
RUN chmod +x /opt/entrypoint.sh
RUN sudo mkdir -p /opt/integration-test && sudo chown ${USER_GID}:${USER_UID} /opt/integration-test
COPY --from=gadgetron_nocudabuild --chown=$USER_UID:conda /opt/code/gadgetron/test/integration /opt/integration-test/
ENTRYPOINT [ "/tini", "--", "/opt/entrypoint.sh" ]