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  • keras-tensorflow-cpu.def 13.38 KiB
    Bootstrap: debootstrap
    MirrorURL: http://us.archive.ubuntu.com/ubuntu
    OSVersion: xenial
    
    %labels
    
        APPLICATION_NAME keras + tensorflow
        APPLICATION_VERSION 2.2.0 + 1.8
        APPLICATION_URL https://keras.io/
    
        SYSTEM_NAME comet
        SYSTEM_SINGULARITY_VERSION 2.5.1
        SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
    
        SINGULARITY_IMAGE_SIZE 16384
    
        AUTHOR_NAME Marty Kandes
        AUTHOR_EMAIL mkandes@sdsc.edu
    
        LAST_UPDATED 20180712
    
    %setup
    
    %environment
    
        # Set system locale
        export LC_ALL=C
    
    %post -c /bin/bash
    
        # Set system locale
        export LC_ALL=C
    
        # Install system metapackages
        apt-get -y install ubuntu-standard
        apt-get -y install ubuntu-server
    
        # Add repositories
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
    
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
    
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
    
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
        add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
    
        # Upgrade all packages to their latest versions
        apt-get -y update && apt-get -y upgrade
    
        # Install common packages from 'main'
        apt-get -y install autoconf
        apt-get -y install automake
        apt-get -y install build-essential
        apt-get -y install libtool
        apt-get -y install pkg-config
        apt-get -y install gfortran
        apt-get -y install zip
    
        # Install expect to automate responses for interactive build questions
        apt-get -y install expect
    
        # Make filesystem mount points
        mkdir /cvmfs /oasis /projects /scratch
    
        # Use /tmp to store temporary files within the container during the
        # bootstraping process
        cd /tmp
    
        # Install Bazel from Debian Package
        apt-get -y install openjdk-8-jdk
        apt-get -y install zlib1g-dev
        wget https://github.com/bazelbuild/bazel/releases/download/0.13.1/bazel_0.13.1-linux-x86_64.deb
        dpkg -i bazel_0.13.1-linux-x86_64.deb
    
        # Install TensorFlow python(2) dependencies
        apt-get -y install python
        apt-get -y install python-dev
        apt-get -y install python-pip
        apt-get -y install python-wheel
        apt-get -y install python-enum34
        apt-get -y install python-mock
        apt-get -y install python-numpy
        
        # Download TensorFlow source
        cd /opt
        git clone https://github.com/tensorflow/tensorflow
        cd tensorflow
        git checkout r1.8
    
        # Build and install TensorFlow for python(2)
        echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
        echo 'spawn ./configure' >> install-tensorflow-python.exp
        echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
        echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
        echo 'expect "Please input the desired Python library path to use.  Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
        echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python.exp
        echo 'send "Y\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
        echo 'send " -march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=generic\r"' >> install-tensorflow-python.exp
        echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
        echo 'send "N\r"' >> install-tensorflow-python.exp
        echo 'expect "> "' >> install-tensorflow-python.exp
    
        chmod +x install-tensorflow-python.exp
        ./install-tensorflow-python.exp
    
        # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
        rm -rf /home/root/.cache
    
        bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
        bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
    
        pip install tensorflow_pkg/tensorflow-1.8.0-cp27-cp27mu-linux_x86_64.whl
    
        # Install common python packages for data science and machine learning applications
        apt-get -y install python-scipy
        apt-get -y install python-pandas
        apt-get -y install python-matplotlib
        apt-get -y install ipython
        apt-get -y install ipython-notebook
        apt-get -y install python-sympy
        apt-get -y install python-nose
        apt-get -y install python-sklearn
        apt-get -y install python-mlpy
        apt-get -y install python-nltk
        apt-get -y install python-statsmodels
        apt-get -y install libopencv-dev
        apt-get -y install python-opencv
    
        # Install common python packages for the biological and biomedical sciences
        apt-get -y install python-biopython
        apt-get -y install python-biopython-sql
    
        # Install other common python packages
        apt-get -y install python-h5py
    
        # Install TensorFlow python3 dependencies
        apt-get -y install python3-numpy
        apt-get -y install python3-dev
        apt-get -y install python3-pip
        apt-get -y install python3-wheel
        apt-get -y install python3-mock
    
        # Build and install TensorFlow for python3
        echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
        echo 'spawn ./configure' >> install-tensorflow-python3.exp
        echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
        echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
        echo 'expect "Please input the desired Python library path to use.  Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> install-tensorflow-python3.exp
        echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python3.exp
        echo 'send "Y\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
        echo 'send " -march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=generic\r"' >> install-tensorflow-python3.exp
        echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
        echo 'send "N\r"' >> install-tensorflow-python3.exp
        echo 'expect "> "' >> install-tensorflow-python3.exp
    
        chmod +x install-tensorflow-python3.exp
        ./install-tensorflow-python3.exp
    
        bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
        bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
    
        pip3 install tensorflow_pkg/tensorflow-1.8.0-cp35-cp35m-linux_x86_64.whl
    
        # Install common python3 packages for data science and machine learning applications
        apt-get -y install python3-scipy
        apt-get -y install python3-pandas
        apt-get -y install python3-matplotlib
        apt-get -y install ipython3
        apt-get -y install ipython3-notebook
        apt-get -y install python3-sympy
        apt-get -y install python3-nose
        apt-get -y install python3-sklearn
        apt-get -y install python3-nltk
    
        # Install common python3 packages for the biological and biomedical sciences
        apt-get -y install python3-biopython
        apt-get -y install python3-biopython-sql
    
        # Install other common python3 packages
        apt-get -y install python3-h5py
    
        # Install Keras dependencies for python(2) and python3
        apt-get -y install python-yaml
        apt-get -y install python3-yaml
    
        cd /opt
     
        # Download, build, and install Keras
        wget https://github.com/keras-team/keras/archive/2.2.0.tar.gz
        tar -xzvf 2.2.0.tar.gz
        cd /opt/keras-2.2.0
        python setup.py install
        python3 setup.py install
    
        # Set container environment variables
        cd /.singularity.d/env
    
        # Update database for mlocate
        updatedb
    
    %files
    
    %runscript
    
    %test