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Dockerfile
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Dockerfile
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FROM nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04
MAINTAINER Yasuhiro Matsunaga <ymatsunaga@mail.saitama-u.ac.jp>
ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"
USER root
# Install all OS dependencies for notebook server that starts but lacks all
# features (e.g., download as all possible file formats)
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update \
&& apt-get install -yq --no-install-recommends \
csh \
wget \
bzip2 \
ca-certificates \
sudo \
locales \
fonts-liberation \
run-one \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
locale-gen
# Configure environment
ENV CONDA_DIR=/opt/conda \
SHELL=/bin/bash \
NB_USER=$NB_USER \
NB_UID=$NB_UID \
NB_GID=$NB_GID \
LC_ALL=en_US.UTF-8 \
LANG=en_US.UTF-8 \
LANGUAGE=en_US.UTF-8
ENV PATH=$CONDA_DIR/bin:$PATH \
HOME=/home/$NB_USER
# Copy a script that we will use to correct permissions after running certain commands
COPY fix-permissions /usr/local/bin/fix-permissions
RUN chmod a+rx /usr/local/bin/fix-permissions
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group
# and make sure these dirs are writable by the `users` group.
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
mkdir -p $CONDA_DIR && \
chown $NB_USER:$NB_GID $CONDA_DIR && \
chmod g+w /etc/passwd && \
fix-permissions $HOME && \
fix-permissions $CONDA_DIR
USER $NB_UID
WORKDIR $HOME
ARG PYTHON_VERSION=default
# Setup work directory for backward-compatibility
RUN mkdir /home/$NB_USER/work && \
fix-permissions /home/$NB_USER
# Install conda as jovyan and check the md5 sum provided on the download site
ENV MINICONDA_VERSION=4.8.2 \
MINICONDA_MD5=87e77f097f6ebb5127c77662dfc3165e \
CONDA_VERSION=4.8.2
RUN cd /tmp && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
echo "${MINICONDA_MD5} *Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
/bin/bash Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
rm Miniconda3-py37_${MINICONDA_VERSION}-Linux-x86_64.sh && \
echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
conda config --system --prepend channels conda-forge && \
conda config --system --prepend channels omnia && \
conda config --system --set auto_update_conda false && \
conda config --system --set show_channel_urls true && \
conda config --system --set channel_priority strict && \
if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \
conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
conda install --quiet --yes conda && \
conda install --quiet --yes pip && \
conda update --all --quiet --yes && \
conda clean --all -f -y && \
rm -rf /home/$NB_USER/.cache/yarn && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
##########################################
USER root
#RUN conda install --yes -c omnia -c conda-forge openmm openmmtools matplotlib && \
#RUN conda install --yes openmm openmmforcefields matplotlib && \
RUN conda install --yes openmm=7.4.1 matplotlib && \
rm -rf /home/$NB_USER/.cache/yarn && \
rm -rf /home/$NB_USER/.node-gyp && \
pip install nglview && \
pip install tables && \
pip install mdtraj && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
#RUN conda install pytorch torchvision cudatoolkit=10.2 -c pytorch
#RUN conda install -c conda-forge rdkit
#RUN conda install -c conda-forge nglview
#RUN jupyter labextension install nglview-js-widgets
RUN conda install --yes pytorch torchvision cudatoolkit=10.2 -c pytorch && \
rm -rf /home/$NB_USER/.cache/yarn && \
rm -rf /home/$NB_USER/.node-gyp && \
pip install pyro-ppl && \
pip install gpytorch && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
##########################################
# Install Tini
RUN conda install --quiet --yes tini && \
conda list tini | grep tini | tr -s ' ' | cut -d ' ' -f 1,2 >> $CONDA_DIR/conda-meta/pinned && \
conda clean --all -f -y && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
# Install Jupyter Notebook, Lab, and Hub
# Generate a notebook server config
# Cleanup temporary files
# Correct permissions
# Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change
RUN conda install --quiet --yes \
notebook \
jupyterhub \
jupyterlab && \
conda clean --all -f -y && \
npm cache clean --force && \
jupyter notebook --generate-config && \
rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
rm -rf /home/$NB_USER/.cache/yarn && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
EXPOSE 8888
# Configure container startup
ENTRYPOINT ["tini", "-g", "--"]
CMD ["start-notebook.sh"]
# Copy local files as late as possible to avoid cache busting
COPY start.sh start-notebook.sh start-singleuser.sh /usr/local/bin/
COPY jupyter_notebook_config.py /etc/jupyter/
# Fix permissions on /etc/jupyter as root
USER root
RUN fix-permissions /etc/jupyter/
# Install all OS dependencies for fully functional notebook server
RUN apt-get update && apt-get install -yq --no-install-recommends \
build-essential \
emacs-nox \
vim-tiny \
git \
jed \
libsm6 \
libxext-dev \
libxrender1 \
lmodern \
netcat \
python-dev \
# ---- nbconvert dependencies ----
texlive-xetex \
texlive-fonts-recommended \
texlive-generic-recommended \
# Optional dependency
texlive-fonts-extra \
# ----
tzdata \
unzip \
nano \
&& apt-get clean && rm -rf /var/lib/apt/lists/*
# ffmpeg for matplotlib anim & dvipng for latex labels
RUN apt-get update && \
apt-get install -y --no-install-recommends ffmpeg dvipng && \
rm -rf /var/lib/apt/lists/*
# Activate ipywidgets extension in the environment that runs the notebook server
RUN jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
# Also activate ipywidgets extension for JupyterLab
# Check this URL for most recent compatibilities
# https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build && \
jupyter labextension install jupyter-matplotlib --no-build && \
jupyter labextension install nglview-js-widgets --no-build && \
jupyter lab build -y && \
jupyter lab clean -y && \
npm cache clean --force && \
rm -rf /home/$NB_USER/.cache/yarn && \
rm -rf /home/$NB_USER/.node-gyp && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
# Import matplotlib the first time to build the font cache.
ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
fix-permissions /home/$NB_USER
#RUN apt-get update && apt-get install -y libsm6
#RUN pip install opencv-python==3.4.7.28
#RUN pip install tensorflow-gpu==1.13.1 --ignore-installed --user
#RUN pip install keras
#RUN pip install tqdm
#RUN pip install torchsummary
#RUN pip install progressbar
###########################################
USER root
RUN chmod -R go+rx $CONDA_DIR/share/jupyter && \
rm -rf $HOME/.local && \
fix-permissions $CONDA_DIR/share/jupyter
RUN mkdir -p /work && \
chown $NB_USER:$NB_GID /work && \
fix-permissions /work && \
chmod +x /usr/local/bin/* && \
chown $NB_USER:$NB_GID /usr/local/bin && \
fix-permissions /usr/local/bin && \
chown $NB_USER:$NB_GID $HOME && \
fix-permissions $HOME
USER $NB_USER
ENV NUM_OMP_THREADS 8
WORKDIR /work