Base Kernel 20.09

Author: hephaex

commons/Dockerfile.base

@@ -0,0 +1,369 @@
+FROM ubuntu:18.04
+
+ENV NUMPY_VERSION 1.18.5
+ENV SCIPY_VERSION 1.5.2
+
+# Python 2.7 or 3.6 is supported by Ubuntu Bionic out of the box
+ARG python=3.6
+ENV PYTHON_VERSION=${python}
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    MPLBACKEND=Svg \
+    PYTHONUNBUFFERED=1 \
+    LD_LIBRARY_PATH="/usr/include/x86_64-linux-gnu:/opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/lib/intel64:/opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/include:/usr/local/lib:$LD_LIBRARY_PATH" \
+    PATH="/usr/local/sbin:/usr/bin/cmake/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/src/lightgbm/LightGBM:/usr/local/bin/mecab" \
+    LIBRARY_PATH="/opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/lib/intel64" \
+    mecab_dicdir=/usr/local/lib/mecab/dic/mecab-ko-dic \
+    LANG=C.UTF-8
+
+# Set default shell to /bin/bash
+SHELL ["/bin/bash", "-cu"]
+
+WORKDIR /tmp
+RUN apt-get update -y && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+        build-essential \
+        gcc g++ make \
+	automake \
+	gfortran \
+        wget zip unzip \
+        software-properties-common 
+
+RUN apt update -y && \
+    add-apt-repository -y "deb http://security.ubuntu.com/ubuntu xenial-security main" && \
+    wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && \
+    apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && \
+    rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && \
+    wget https://apt.repos.intel.com/setup/intelproducts.list -O /etc/apt/sources.list.d/intelproducts.list && \
+    apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+	ca-certificates \
+	dkms \
+        git \
+        curl \
+        vim \
+	yasm \
+  	openssh-client openssh-server \
+        libssl-dev \
+        libmpdec2 \
+	pdsh curl net-tools \
+	iputils-ping \
+        libcurl3-dev \
+        libfreetype6-dev \
+        libhdf5-serial-dev \
+        libzmq3-dev \
+        libjpeg-dev \
+        libpng-dev \
+	libsm6 \
+	libxext6 \
+	libxrender-dev \
+	libcairo2-dev libgirepository1.0-dev pkg-config gir1.2-gtk-3.0 \
+        libgeos-dev libgeos++-dev \
+    	openjdk-8-jdk \
+        pkg-config \
+        zlib1g-dev \
+	mime-support \
+	proj-bin libproj-dev libgeos-dev libgeos++-dev graphviz \
+        python${PYTHON_VERSION} \
+        python${PYTHON_VERSION}-dev \
+	intel-mkl-2020.3-111 intel-ipp-2020.2-108 intel-tbb-2020.3-108 intel-daal-2020.2-108 intel-mpi-2019.8-108 \
+	libxml2-dev \
+	libxslt1-dev \
+	libasound2-dev \
+	libnuma-dev \
+	libjasper-dev \
+        libtiff-dev \
+	libavcodec-dev \
+        libavformat-dev \
+	libswscale-dev \
+	libxine2-dev \
+	libv4l-dev \
+	libboost-dev \
+	libboost-system-dev \
+	libboost-filesystem-dev \
+	libopenblas-dev liblapack-dev \
+	xvfb \
+	fonts-nanum \
+	fonts-nanum-coding \
+	fonts-nanum-extra \
+	&& \
+    rm -fr /var/lib/apt/lists/* && \
+    echo "/opt/intel/daal/lib/intel64" >> /etc/ls.so.conf && \
+    echo "/opt/intel/ipp/lib/intel64" >> /etc/ls.so.conf && \
+    echo "/opt/intel/lib/intel64" >> /etc/ls.so.conf && \
+    echo "/opt/intel/mkl/lib/intel64" >> /etc/ls.so.conf && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* && \
+    ldconfig 
+
+RUN curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
+    apt-get update -y && \
+    apt-get install -y --no-install-recommends nodejs && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# OFED
+ENV STAGE_DIR=/tmp
+RUN mkdir -p ${STAGE_DIR}
+ENV MLNX_OFED_VERSION=4.6-1.0.1.1
+RUN cd ${STAGE_DIR} && \
+    wget -q -O - http://www.mellanox.com/downloads/ofed/MLNX_OFED-${MLNX_OFED_VERSION}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu18.04-x86_64.tgz | tar xzf -
+RUN cd ${STAGE_DIR}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu18.04-x86_64 && \
+    ./mlnxofedinstall --user-space-only --without-fw-update --all -q && \
+    cd ${STAGE_DIR} && \
+    rm -rf ${STAGE_DIR}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-ubuntu18.04-x86_64*
+    
+RUN if [[ "${PYTHON_VERSION}" == "3.6" ]]; then \
+        apt-get install -y python${PYTHON_VERSION}-distutils python-apt ; \
+    fi
+
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 2
+
+WORKDIR /tmp
+RUN curl https://bootstrap.pypa.io/get-pip.py | python3 && \
+    python3 -m pip install --no-cache-dir -U setuptools pip 
+
+RUN python3 -m pip install --no-cache-dir --upgrade -Iv \
+    	    Cython==0.29.21 \
+	    tornado==6.0.4 \
+	    pystan==2.19.1.1 \
+	    pycairo==1.19.0 \
+	    python-language-server[all] \	    
+	    matplotlib==3.1.1 
+
+WORKDIR /tmp
+RUN git clone -q --branch=master git://github.com/xianyi/OpenBLAS.git && \
+    cd OpenBLAS && \
+    make DYNAMIC_ARCH=1 NO_AFFINITY=1 NUM_THREADS=48 FC=gfortran NO_CBLAS=1 NO_LAPACK=1 NO_LAPACKE=1 && \
+    make install
+
+RUN git clone --recursive https://github.com/bodono/scs-python.git  && \
+    cd /tmp/scs-python && \
+    python setup.py install --scs 
+
+RUN cd /tmp && \
+    git clone --branch=v${NUMPY_VERSION} --depth=1 https://github.com/numpy/numpy.git numpy && \
+    cd numpy && \
+    git checkout -b v${NUMPY_VERSION} && \
+    cp site.cfg.example site.cfg && \
+    echo "[mkl]" >> site.cfg && \
+    echo "include_dirs = /opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/include/" >> site.cfg && \
+    echo "library_dirs = /opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/lib/intel64" >> site.cfg && \
+    echo "mkl_libs = mkl_rt" >> site.cfg && \
+    echo "lapack_libs =" >> site.cfg && \
+    python3 setup.py bdist_wheel -d /tmp 
+
+# Install scipy
+RUN cd /tmp && \
+    git clone --branch=v${SCIPY_VERSION} --depth=1 https://github.com/scipy/scipy.git scipy && \
+    cd scipy && \
+    git checkout -b v${SCIPY_VERSION} && \  
+    cp site.cfg.example site.cfg && \
+    echo "[mkl]" >> site.cfg && \
+    echo "include_dirs = /opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/include/" >> site.cfg && \
+    echo "library_dirs = /opt/intel/compilers_and_libraries_2020.3.279/linux/mkl/lib/intel64" >> site.cfg && \
+    echo "mkl_libs = mkl_rt" >> site.cfg && \
+    echo "lapack_libs =" >> site.cfg && \
+    python3 -m pip install -U --no-cache-dir /tmp/numpy-{NUMPY_VERSION}-cp36-cp36m-linux_x86_64.whl && \
+    python3 setup.py install 
+
+RUN python3 -m pip install pip --no-cache-dir \
+    	    Cartopy==0.18.0 \
+	    notebook==6.0.3 
+
+WORKDIR /tmp
+COPY ./requirements.txt /tmp
+RUN python3 -m pip install --no-cache-dir --upgrade -r requirements.txt && \
+    python3 -m pip install --no-cache-dir tensorflow_model_analysis && \
+    python3 -m pip uninstall -y \
+        tensorboard tensorboard-plugin-wit tensorflow \
+        tensorflow-estimator tensorflow-addons tensorflow-datasets \
+	tensorflow-gan tensorflow-hub tensorflow-metadata \
+	tensorflow-probability 	tensorflow-text \
+	tensorflow-model-analysis tensorflow-serving-api \
+	torch && \
+    rm -f /tmp/requirements.txt
+
+# install NLP packages *mecab-ko & khai*
+WORKDIR /tmp
+RUN curl -LO https://bitbucket.org/eunjeon/mecab-ko/downloads/mecab-0.996-ko-0.9.2.tar.gz && \
+    tar zxfv mecab-0.996-ko-0.9.2.tar.gz && \
+    cd mecab-0.996-ko-0.9.2 && \
+    ./configure && \
+    make -j$(nproc) && \
+    make check && \
+    make install
+
+# Install mecab-ko-dic" 
+WORKDIR /tmp
+RUN curl -LO https://bitbucket.org/eunjeon/mecab-ko-dic/downloads/mecab-ko-dic-2.1.1-20180720.tar.gz && \
+    tar -zxvf mecab-ko-dic-2.1.1-20180720.tar.gz && \
+    cd mecab-ko-dic-2.1.1-20180720 && \
+    ./autogen.sh && \
+    ./configure && \
+    make -j$(nproc) && \
+    sh -c 'echo "dicdir=/usr/local/lib/mecab/dic/mecab-ko-dic" > /usr/local/etc/mecabrc' && \
+    make install && \
+    cd /tmp && \
+    git clone https://bitbucket.org/eunjeon/mecab-python-0.996.git && \
+    python3 -m pip install /tmp/mecab-python-0.996
+
+# OpenCV
+RUN ln -s /usr/include/libv4l1-videodev.h /usr/include/linux/videodev.h && \
+    apt-get install -y \
+	libgstreamer1.0-dev \
+	libgstreamer-plugins-base1.0-dev \
+	libgtk-3-dev \
+        libtbb-dev \
+	libatlas-base-dev \
+	libdc1394-22-dev \
+	libxvidcore-dev \
+	libfaac-dev \
+	libmp3lame-dev \
+	libtheora-dev \
+	libvorbis-dev \
+	libxvidcore-dev \
+	libopencore-amrnb-dev libopencore-amrwb-dev \
+	libavresample-dev \
+	x264 \
+	libx264-dev \
+	v4l-utils \	
+	libprotobuf-dev protobuf-compiler \
+	libgoogle-glog-dev libgflags-dev \
+	libgphoto2-dev \
+	libeigen3-dev \
+	libhdf5-dev \	
+    && \	
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN wget https://github.com/Kitware/CMake/releases/download/v3.18.1/cmake-3.18.1-Linux-x86_64.sh \
+         -q -O /tmp/cmake-install.sh && \
+    chmod u+x /tmp/cmake-install.sh && \
+    mkdir /usr/bin/cmake && \
+    /tmp/cmake-install.sh --skip-license --prefix=/usr/bin/cmake && \
+    rm /tmp/cmake-install.sh
+
+WORKDIR /tmp
+ENV OPENCV_VERSION="4.4.0"
+RUN wget https://github.com/opencv/opencv/archive/${OPENCV_VERSION}.zip && \
+    wget -O opencv-contrib.zip https://github.com/opencv/opencv_contrib/archive/${OPENCV_VERSION}.zip && \
+    unzip ${OPENCV_VERSION}.zip && \
+    unzip opencv-contrib.zip && \
+    mkdir opencv-${OPENCV_VERSION}/cmake_binary && \
+    cd opencv-${OPENCV_VERSION}/cmake_binary && \
+    cmake \
+      -DCMAKE_BUILD_TYPE=RELEASE \
+      -D BUILD_TIFF=ON \
+      -D BUILD_opencv_java=OFF \
+      -D ENABLE_FAST_MATH=1 \
+      -D WITH_IPP=ON \
+      -D WITH_TBB=ON \
+      -D WITH_EIGEN=ON \
+      -D WITH_V4L=ON \
+      -D BUILD_TESTS=OFF \
+      -D BUILD_PERF_TESTS=OFF \
+      -D OPENCV_EXTRA_MODULES_PATH="../../opencv_contrib-4.4.0/modules" \
+      -D CMAKE_BUILD_TYPE=RELEASE \
+      -D CMAKE_INSTALL_PREFIX=$(python3 -c "import sys; print(sys.prefix)") \
+      -D PYTHON_EXECUTABLE=$(which python3) \
+      -D PYTHON_INCLUDE_DIR=$(python3 -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())") \
+      -D PYTHON_PACKAGES_PATH=$(python3 -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())") \
+      .. 2>&1 | tee cmake_messages.txt && \
+    make -j$(nproc) && \
+    make install && \
+    cd /tmp && \
+    python3 -m pip install --no-cache-dir opencv-python && \
+    rm -fr opencv* 
+
+# XGBoost
+RUN git clone  --recursive https://github.com/dmlc/xgboost && \
+    cd xgboost && \
+    mkdir build && \
+    cd build && \
+    cmake .. && \
+    make -j$(nproc) && \
+    cd ../python-package && \
+    python3 setup.py install 
+
+# LightGBM
+RUN cd /usr/local/src && mkdir lightgbm && cd lightgbm && \
+    git clone --recursive --branch stable --depth 1 https://github.com/microsoft/LightGBM && \
+    cd LightGBM && mkdir build && cd build && \
+    cmake .. && \
+    make -j$(nproc) && \
+    cd /usr/local/src/lightgbm/LightGBM/python-package && \
+    python3 setup.py install --precompile
+
+# Install Open MPI
+RUN mkdir /tmp/openmpi && \
+    cd /tmp/openmpi && \
+    wget https://www.open-mpi.org/software/ompi/v4.0/downloads/openmpi-4.0.4.tar.gz && \
+    tar zxf openmpi-4.0.4.tar.gz && \
+    cd openmpi-4.0.4 && \
+    ./configure --enable-orterun-prefix-by-default && \
+    make -j $(nproc) all && \
+    make install && \
+    ldconfig && \
+    rm -rf /tmp/openmpi*
+
+# Install OpenSSH for MPI to communicate between containers
+RUN apt-get install -y --no-install-recommends openssh-client openssh-server && \
+    mkdir -p /var/run/sshd
+
+# Allow OpenSSH to talk to containers without asking for confirmation
+RUN cat /etc/ssh/ssh_config | grep -v StrictHostKeyChecking > /etc/ssh/ssh_config.new && \
+    echo "    StrictHostKeyChecking no" >> /etc/ssh/ssh_config.new && \
+    mv /etc/ssh/ssh_config.new /etc/ssh/ssh_config
+
+# Create a wrapper for OpenMPI to allow running as root by default
+RUN mv /usr/local/bin/mpirun /usr/local/bin/mpirun.real && \
+    echo '#!/bin/bash' > /usr/local/bin/mpirun && \
+    echo 'mpirun.real --allow-run-as-root "$@"' >> /usr/local/bin/mpirun && \
+    chmod a+x /usr/local/bin/mpirun
+
+# Configure OpenMPI to run good defaults:
+RUN echo "btl_tcp_if_exclude = lo,docker0" >> /usr/local/etc/openmpi-mca-params.conf
+
+# Install OpenSSH for MPI to communicate between containers
+RUN mkdir -p /var/run/sshd
+
+# Allow OpenSSH to talk to containers without asking for confirmation
+RUN cat /etc/ssh/ssh_config | grep -v StrictHostKeyChecking > /etc/ssh/ssh_config.new && \
+    echo "    StrictHostKeyChecking no" >> /etc/ssh/ssh_config.new && \
+    mv /etc/ssh/ssh_config.new /etc/ssh/ssh_config
+
+# install git-lfs
+WORKDIR /tmp
+RUN curl -sLO https://github.com/git-lfs/git-lfs/releases/download/v2.11.0/git-lfs-linux-amd64-v2.11.0.tar.gz && \
+    tar -zxf git-lfs-linux-amd64-v2.11.0.tar.gz && \
+    bash install.sh 
+
+COPY ./service-defs /etc/backend.ai/service-defs
+RUN curl -fL https://github.com/cdr/code-server/releases/download/v3.4.1/code-server-3.4.1-linux-amd64.tar.gz \
+  | tar -C /usr/local/lib -xz && \
+    mv /usr/local/lib/code-server-3.4.1-linux-amd64 /usr/local/lib/code-server-3.4.1 && \
+    ln -s /usr/local/lib/code-server-3.4.1/bin/code-server /usr/local/bin/code-server
+
+RUN jupyter nbextensions_configurator enable && \
+    jupyter contrib nbextension install && \
+    jupyter nbextension enable --py --sys-prefix widgetsnbextension && \
+    jupyter serverextension enable --py jupyterlab --sys-prefix && \
+    jupyter labextension install --no-build @jupyter-widgets/jupyterlab-manager && \
+    jupyter labextension install --no-build @krassowski/jupyterlab-lsp && \
+    jupyter serverextension enable --py jupyter_lsp && \
+    jupyter labextension install --no-build @jupyterlab/toc && \
+    jupyter nbextension enable execute_time/ExecuteTime && \
+    jupyter nbextension enable toc2/main && \
+    jupyter labextension install @pyviz/jupyterlab_pyviz && \
+    jupyter labextension install @bokeh/jupyter_bokeh && \
+    jupyter labextension install --no-build jupyterlab-nvdashboard && \
+    jupyter lab build
+
+RUN apt autoclean && \
+    rm -rf /var/lib/apt/lists/* && \	
+    rm -rf /root/.cache && \
+    rm -rf /tmp
+
+WORKDIR /home/work