Dockerfile

FROM jupyter/tensorflow-notebook:2ce7c06a61a1
LABEL maintainer="Luca Ghiringhelli <ghiringhelli@fhi-berlin.mpg.de>"

# ================================================================================
# Linux applications and libraries
# ================================================================================


USER root
RUN apt-get update \
 && apt-get install -y -q --no-install-recommends \
        gcc \
        gfortran \
        liblapack-dev \
        libblas-dev \
        libnetcdf-dev \
        netcdf-bin \
        libxpm-dev \
        libgsl-dev \
        lsof \
        vim \
        git-lfs\
        openjdk-8-jdk \
        xvfb \
        cmake \
        mpi \
        openmpi-bin \
        openmpi-common \
        openssh-server \
        openssh-client \
        libopenmpi-dev \
        graphviz \
 && apt-get clean \
 && rm -rf /var/lib/apt/lists/*
USER $NB_UID

# Dependecies:
# - quippy: gcc gfortran liblapack-dev libblas-dev libnetcdf-dev netcdf-bin libxpm-dev libgsl-dev

# ================================================================================
# Python environment
# ================================================================================

# This part contains the installation of all the common/basic python packages.
# All the other package will be installed by the tutorial's own setup scripts.
# Add any additional packages you want available for use in a Python 3 notebook
# to the first line here (e.g., nglview, jupyter_contrib_nbextensions, etc.)
# https://github.com/ipython-contrib/jupyter_contrib_nbextensions

RUN pip install --upgrade pip
RUN conda install --quiet --yes \
    'pytorch::pytorch-cpu==1.1.0' \
    'pytorch::torchvision-cpu==0.3.0' \
    'nglview==2.7.0' \
    'jupyter_contrib_nbextensions==0.5.1' \
    'jupyter_nbextensions_configurator==0.4.1' \
    'ase' \
    'asap3' \
    'dscribe' \
    'pytest' \
    'mpi4py' \
    'orjson' \
    'hdbscan' \
    'pyyaml==6' \
    'pynndescent' \
 && conda install -c plotly plotly-orca \
 && conda install -c conda-forge umap-learn \
 && conda clean -tipsy \
 && jupyter nbextensions_configurator enable --user \
 && jupyter nbextension install nglview --py --sys-prefix \
 && jupyter nbextension enable nglview --py --sys-prefix \
 && jupyter nbextension enable execute_time/ExecuteTime \
 && jupyter nbextension enable init_cell/main \
 && jupyter nbextension enable collapsible_headings/main \
 && fix-permissions $CONDA_DIR \
 && fix-permissions /home/$NB_USER 


# Dependecies:
# - ase: many
# - nglview: many
# - asap3: grain-boundaries

# fixing pip installation issue of nomad-lab dependency: orjson

# ================================================================================
#  QMMLPACK
# ================================================================================

# for the test TMPDIR has to be defined
ENV TMPDIR "/tmp/"

WORKDIR /opt/qmmlpack
COPY 3rdparty/qmmlpack .

USER root

RUN ./make --debug --verbose cpp --include-path /usr/include/gsl/ --library-path /usr/lib/
RUN ./make --debug --verbose python --include-path /usr/include/gsl/ --library-path /usr/lib/

RUN chown -R $NB_USER:$NB_GID $PWD
USER $NB_USER


#RUN make -v install
ENV PYTHONPATH "/opt/qmmlpack/python":$PYTHONPATH

# The CML_PLUGINS environment variable tells cmlkit to register the cscribe plugin, which provides the dscribe interface.
ENV CML_PLUGINS "cscribe"
ENV CML_DATASET_PATH $HOME/tutorials/data/cmlkit/

# Dependecies:
# - ase: many
# - nglview: many
# - asap3: grain-boundaries

# ================================================================================
#  QUIP + GAP + quippy
# ================================================================================

# All the QUIPs go here; added to path in the end.
WORKDIR /opt/quip

# QUIP for general use is the OpenMP version.
ENV QUIP_ARCH linux_x86_64_gfortran_openmp
ENV QUIP_INSTALLDIR /opt/quip/bin

COPY 3rdparty/quip .
COPY 3rdparty/gap src/GAP
COPY files/Makefile.inc build/$QUIP_ARCH/
# COPY files/GIT_VERSION .
# COPY files/GAP_VERSION src/GAP/

USER root
RUN chown -R $NB_USER:$NB_GID $PWD
USER $NB_USER

# Installs with no suffix, e.g. quip
RUN make \
 && make install

# Installs quippy
RUN pip install src/f90wrap \
 && make install-quippy

# Make quippy executable available from terminal
ENV PATH /opt/quip/bin:$PATH

# ================================================================================
#  SISSO++
# ================================================================================

WORKDIR /opt/cpp_sisso

COPY 3rdparty/cpp_sisso .
WORKDIR /opt/cpp_sisso/build
USER root
RUN cmake -C ../cmake/toolchains/gnu_py.cmake -DEXTERNAL_BOOST=OFF ../ \
&& make install

# ================================================================================
#  KERAS-VIS
# ================================================================================

WORKDIR /opt/keras-vis

COPY 3rdparty/keras-vis .
RUN pip install .

# ================================================================================
#  ATOMIC FEATURES
# ================================================================================

WORKDIR /opt/atomic_features

COPY 3rdparty/atomic-features-package ./atomic-features-package
USER root
RUN pip install ./atomic-features-package

# ================================================================================
# Install all of the package dependencies of the tutorials
# ================================================================================

RUN conda install pynndescent

WORKDIR /opt/tutorials
COPY tutorials/ .

RUN pip install ./analytics-arise \ 
&& pip install 'git+https://github.com/AndreasLeitherer/ARISE.git'   
RUN pip install ./analytics-atomic-features
RUN pip install ./analytics-clustering-tutorial
RUN pip install ./analytics-cmlkit
RUN pip install ./analytics-co2-sgd-tutorial
RUN pip install ./analytics-compressed-sensing
RUN pip install ./analytics-convolutional-nn 
RUN pip install ./analytics-decision-tree
RUN pip install ./analytics-descriptor-role
RUN pip install ./analytics-domain-of-applicability
RUN pip install ./analytics-error-estimates
RUN pip install ./analytics-exploratory-analysis
RUN pip install ./analytics-gap-si-surface
RUN pip install ./analytics-grain-boundaries
RUN pip install ./analytics-kaggle-competition
RUN pip install ./analytics-krr4mat
RUN pip install ./analytics-nn-regression
RUN pip install ./analytics-perovskites-tolerance-factor
RUN pip install ./analytics-query-nomad-archive
RUN pip install ./analytics-sgd-alloys-oxygen-reduction-evolution
RUN pip install ./analytics-soap-atomic-charges
RUN pip install ./analytics-tcmi
RUN pip install ./analytics-tetradymite-PRM2020

RUN pip install nomad-lab
# Temporary fix numpy version
RUN pip install numpy==1.17

USER root

# Trick to stop caching
ARG CACHE_DATE=2021-1-26

# Create headers for all tutorials
COPY generate_headers.py .
COPY files files
RUN pip install Pillow
RUN python generate_headers.py

# Customize jupyter 
WORKDIR $HOME
COPY files/custom.css custom.css
COPY files/logo.png logo.png
COPY files/Titillium Titillium
RUN mkdir .jupyter/custom 
RUN mv custom.css .jupyter/custom \
 && mv logo.png .jupyter/custom \
 && mv Titillium .jupyter/custom
ARG TUTORIALS_HOME=$HOME/tutorials


RUN fix-permissions /opt/tutorials \
 && fix-permissions $CONDA_DIR

# Linking all the notebooks of the tutorials
WORKDIR $TUTORIALS_HOME
RUN ln -s /opt/tutorials/*/*.ipynb . \
 && jupyter-trust -y *.ipynb

# Linking images or other assets may required by the tutorials
WORKDIR $TUTORIALS_HOME/assets
RUN ln -s /opt/tutorials/*/assets/*  .

# Linking data may be required by the tutorials
WORKDIR $TUTORIALS_HOME/data
RUN mkdir data && ln -s /opt/tutorials/*/data/* .

# Testing tutorials 
RUN  cp -r tutorials test_tutorials
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/ARISE.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/atomic_features.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/clustering_tutorial.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/cmlkit.ipynb" 
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/CO2_SGD.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/compressed_sensing.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/convolutional_nn.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/decision_tree.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/descriptor_role.ipynb" 
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/error_estimates.ipynb" 
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/exploratory_analysis.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/gap_si_surface.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/grain_boundaries.ipynb" 
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/kaggle_competition.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/krr4mat.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/nn_regression.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/perovskites_tolerance_factor.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=5000 --to notebook --execute "test_tutorials/query_nomad_archive.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/sgd_alloys_oxygen_reduction_evolution.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/soap_atomic_charges.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/tcmi.ipynb" 
RUN jupyter nbconvert --ExecutePreprocessor.timeout=1000 --to notebook --execute "test_tutorials/tetradymite_PRM2020.ipynb" 
# Remove following tutorial because test is too long
# RUN jupyter nbconvert --ExecutePreprocessor.timeout=20000 --to notebook --execute "test_tutorials/domain_of_applicability.ipynb" 

RUN rm -r test_tutorials    

# ================================================================================
# Switch back to jovyan to avoid accidental container runs as root
# ================================================================================

WORKDIR $HOME

RUN fix-permissions $TUTORIALS_HOME \
 && fix-permissions $HOME/.local/share/jupyter \
 && fix-permissions $CONDA_DIR

USER $NB_UID