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Merge pull request #33 from the-virtual-brain/deploy_hbp
Config files for deploy at OpenShift
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| # | ||
| # TVB & NEST simulations environment | ||
| # | ||
| # Prepare conda env, install NEST, then tvb-library from Pypi | ||
| # Finally link tvb-scripts and tvb-nest from Github sources | ||
| # | ||
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| FROM jupyter/minimal-notebook | ||
| MAINTAINER [email protected] | ||
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| ENV DEBIAN_FRONTEND noninteractive | ||
| ENV LANG=C.UTF-8 | ||
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| USER root | ||
| RUN apt-get update; apt-get install -y automake libtool build-essential git vim octave \ | ||
| wget python3.7 libpython3.7 libpython3-dev libncurses5-dev libreadline-dev libgsl0-dev cython3 \ | ||
| python3.7-dev python3-pip python3-numpy python3-scipy python3-matplotlib python3-nose \ | ||
| ipython3 python3-venv python-virtualenv python3-pyqt5 python3-dev libgsl-dev libncurses-dev \ | ||
| subversion cmake zip unzip; \ | ||
| apt-get clean | ||
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| RUN wget -q http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz \ | ||
| && tar xf mpich-3.1.4.tar.gz \ | ||
| && cd mpich-3.1.4 \ | ||
| && ./configure --disable-fortran --enable-fast=all,O3 --prefix=/usr \ | ||
| && make -j$(nproc) \ | ||
| && make install \ | ||
| && ldconfig \ | ||
| && cd .. \ | ||
| && rm -rf mpich-3.1.4 \ | ||
| && rm mpich-3.1.4.tar.gz | ||
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| RUN mkdir -m777 $HOME/env; mkdir -m777 $HOME/packages | ||
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| USER $NB_UID | ||
| # Create a dedicated Python env for working in it | ||
| ENV VENV=$HOME/env/neurosci | ||
| ENV CONDAENV_NAME nestenv | ||
| ENV CONDAENV /opt/conda/envs/nestenv | ||
| ENV CONDAENV_PYTHON /opt/conda/envs/nestenv/bin/python | ||
| ENV CONDAENV_PIP /opt/conda/envs/nestenv/bin/pip | ||
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| RUN conda create -n $CONDAENV_NAME python=3 | ||
| RUN conda install --name $CONDAENV_NAME cython setuptools | ||
| RUN $CONDAENV_PIP install parameters quantities neo "django<1.9" django-tagging future hgapi gitpython sumatra nixio | ||
| RUN $CONDAENV_PIP install --upgrade nose ipython | ||
| # django<1.9 is needed for pynest - september 2019 - NEST 2.18 | ||
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| # Install from sources libneurosim (NEST boost dependency) | ||
| WORKDIR $HOME/packages | ||
| RUN git clone --depth 1 https://github.com/INCF/libneurosim.git; \ | ||
| cd libneurosim; ./autogen.sh; \ | ||
| mkdir $VENV/build | ||
| WORKDIR $VENV/build | ||
| RUN mkdir libneurosim; \ | ||
| cd libneurosim; \ | ||
| PYTHON=$CONDAENV_PYTHON $HOME/packages/libneurosim/configure --prefix=$VENV; \ | ||
| make; make install; ls $VENV/lib $VENV/include; \ | ||
| ln -s /usr/lib/python3.7/config-x86_64-linux-gnu/libpython3.7.so $VENV/lib/ | ||
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| # Install NEST, latest stable version (July 2019) | ||
| ENV NEST_VER=2.20.0 | ||
| ENV NEST=nest-simulator-$NEST_VER | ||
| ENV NEST_SRC=$HOME/packages/$NEST | ||
| ENV NEST_INSTALL_DIR=$VENV/nest_build | ||
| ENV NEST_PYTHON_PREFIX=${NEST_INSTALL_DIR}/lib/python3.7/site-packages | ||
| ENV NEST_MODULE_PATH=${NEST_INSTALL_DIR}/lib/nest | ||
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| WORKDIR $HOME/packages | ||
| RUN wget https://github.com/nest/nest-simulator/archive/v2.20.0.tar.gz -O $HOME/packages/$NEST.tar.gz; \ | ||
| tar xzf $NEST.tar.gz; rm $NEST.tar.gz; \ | ||
| cd $NEST; \ | ||
| cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL_DIR \ | ||
| -Dwith-python=3 \ | ||
| -Dwith-libneurosim=$VENV \ | ||
| -DPYTHON_EXECUTABLE=$CONDAENV/bin/python3 \ | ||
| -DPYTHON_LIBRARY=$CONDAENV/lib \ | ||
| -DPYTHON_INCLUDE_DIR=$CONDAENV/include/python3.8 \ | ||
| $NEST_SRC; \ | ||
| make; make install | ||
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| # Install nestml | ||
| RUN git clone --depth 1 https://github.com/nest/nestml.git; \ | ||
| cd nestml; \ | ||
| $CONDAENV_PYTHON setup.py install | ||
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| # Install TVB specific packages | ||
| WORKDIR $HOME/packages | ||
| RUN $CONDAENV_PIP install pandas xarray pytest pytest-cov pytest-benchmark oct2py scikit-learn scipy; \ | ||
| $CONDAENV_PIP install --ignore-installed entrypoints | ||
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| RUN wget https://zenodo.org/record/3688773/files/tvb-data.zip?download=1 -O tvb_data.zip; \ | ||
| mkdir tvb_data; unzip tvb_data.zip -d tvb_data; rm tvb_data.zip; \ | ||
| cd tvb_data; \ | ||
| $CONDAENV_PYTHON setup.py develop | ||
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| RUN git clone --depth 1 --branch tvb-multiscale-cosim https://github.com/the-virtual-brain/tvb-root.git | ||
| ARG LAST_SHA_ROOT=LATEST | ||
| RUN cd tvb-root; \ | ||
| git pull origin tvb-multiscale-cosim --allow-unrelated-histories; \ | ||
| cd scientific_library; \ | ||
| $CONDAENV_PYTHON setup.py develop; | ||
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| RUN git clone --depth 1 https://github.com/the-virtual-brain/tvb-multiscale.git | ||
| ARG LAST_SHA_MULTISCALE=LATEST | ||
| RUN cd tvb-multiscale; \ | ||
| git pull; \ | ||
| $CONDAENV_PYTHON setup.py develop --no-deps; | ||
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| RUN mkdir -m777 /home/jovyan/.tvb-temp /home/jovyan/.local | ||
| RUN mkdir -m777 /home/jovyan/.local/share | ||
| RUN mkdir -m777 /home/jovyan/.local/share/jupyter | ||
| RUN mkdir -m777 /home/jovyan/.local/share/jupyter/runtime | ||
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| # Register conda env python as jupyerhub kernel | ||
| RUN $CONDAENV_PIP install --user ipykernel | ||
| RUN $CONDAENV_PYTHON -m ipykernel install --user | ||
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| WORKDIR $HOME | ||
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| ENV NEST_INSTALL_DIR=${NEST_INSTALL_DIR} | ||
| ENV NEST_PYTHON_PREFIX=${NEST_INSTALL_DIR}/lib/python3.8/site-packages | ||
| ENV PYTHONPATH=$PYTHONPATH:$VENV:${NEST_PYTHON_PREFIX} | ||
| # Note that the following are automatically reset if NEST is imported | ||
| # via a call to tvb_nest.simulator_nest.nest_factory.load_nest() | ||
| ENV NEST_DATA_DIR=${NEST_INSTALL_DIR}/share/nest | ||
| ENV SLI_PATH=${NEST_INSTALL_DIR}/share/nest/sli | ||
| ENV NEST_MODULE_PATH=${NEST_MODULE_PATH} | ||
| ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${NEST_MODULE_PATH} | ||
| ENV NEST_DOC_DIR=${NEST_INSTALL_DIR}/share/doc/nest | ||
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| ## Install local tvb-multiscale: | ||
| ENV MYMODULES_DIR=$HOME/packages/tvb-multiscale/tvb_nest/nest/modules | ||
| ENV MYMODULES_BLD_DIR=$HOME/packages/nest_modules_builds | ||
| RUN cp -r ${MYMODULES_DIR} ${MYMODULES_BLD_DIR} | ||
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| ARG WORK_DIR=/home/jovyan/packages/notebooks | ||
| ARG TVB_NEST_Examples=/home/jovyan/packages/notebooks/TVB-NEST-Examples | ||
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| RUN mkdir -m777 $WORK_DIR | ||
| RUN mkdir -m777 $TVB_NEST_Examples | ||
| RUN cp -r /home/jovyan/packages/tvb-multiscale/docs/documented_example_notebook/* $TVB_NEST_Examples | ||
| RUN chmod -R 777 $WORK_DIR | ||
| RUN chmod -R 777 $TVB_NEST_Examples | ||
| RUN chmod -R 777 /home/jovyan/packages/tvb-multiscale/tvb_nest/examples | ||
| RUN chown -R jovyan: $TVB_NEST_Examples | ||
| RUN chown -R jovyan: /home/jovyan/packages/tvb-multiscale/tvb_nest/examples | ||
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| WORKDIR $WORK_DIR | ||
| # CMD is defined in the base image: jupyter/minimal-notebook |
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