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Commit 7377f020 authored by Michael Blaschek's avatar Michael Blaschek :bicyclist:
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update to imgw

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archive/comet/keras/keras-theano-gpu.def deleted 100644 → 0
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Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu
OSVersion: xenial
%labels
APPLICATION_NAME keras + theano
APPLICATION_VERSION 2.2.0 + 1.0.3
APPLICATION_URL https://keras.io/
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.2
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 20181203
%setup
%environment
# Set system locale
export LC_ALL=C
# Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Set other environment variables
export PATH="/opt/miniconda2/bin:${PATH}"
export MKL_THREADING_LAYER='GNU'
export KERAS_BACKEND='theano'
%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} ${OSVERSION}-security restricted"
# Upgrade all packages to their latest versions
apt-get -y update && apt-get -y upgrade
# Install common packages from 'main'
apt-get -y install autoconf
apt-get -y install automake
apt-get -y install build-essential
apt-get -y install cmake
apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran
apt-get -y install zip
# Install expect to automate responses for interactive build questions
apt-get -y install expect
# Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
# Use /tmp to store temporary files within the container during the
# bootstraping process
cd /tmp
# Install miniconda2
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod +x Miniconda2-latest-Linux-x86_64.sh
./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
# Location of NVIDIA repositories
declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
# Install NVIDIA package dependencies
apt-get -y install x11-common
apt-get -y install xserver-xorg-core
apt-get -y install xserver-xorg-legacy
apt-get -y install cmake
apt-get -y install make
apt-get -y install dkms
apt-get -y install linux-libc-dev
apt-get -y install libc6-dev
apt-get -y install lib32gcc1
apt-get -y install libc6-i386
apt-get -y install libgl1
apt-get -y install libwayland-client0
apt-get -y install libwayland-server0
apt-get -y install pkg-config
apt-get -y install screen-resolution-extra
apt-get -y install libvdpau1
apt-get -y install libatk1.0-0
apt-get -y install libcairo-gobject2
apt-get -y install libcairo2
apt-get -y install libfontconfig1
apt-get -y install libgdk-pixbuf2.0-0
apt-get -y install libgtk-3-0
apt-get -y install libgtk2.0-0
apt-get -y install libjansson4
apt-get -y install freeglut3-dev
apt-get -y install libx11-dev
apt-get -y install libxmu-dev
apt-get -y install libxi-dev
apt-get -y install libglu1-mesa
apt-get -y install libglu1-mesa-dev
apt-get -y install default-jre
# Download NVIDIA drivers, libraries, and packages
wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb"
wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb"
wget --wait=10 "${ML_REPO_URL}/libnccl2_2.3.4-1+cuda9.2_amd64.deb"
wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.3.4-1+cuda9.2_amd64.deb"
# Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
mkdir -p /usr/lib/nvidia
# Install NVIDIA drivers, libraries, and packages
dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
dpkg -i cuda-drivers_396.26-1_amd64.deb
dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
dpkg -i libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb
dpkg -i libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb
dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb
dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb
# Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Install python(2) dependencies for Theano
export PATH="/opt/miniconda2/bin:${PATH}"
conda install -y numpy
conda install -y scipy
conda install -y mkl
conda install -y nose
conda install -y sphinx
conda install -y pydot-ng
# Install Theano for python(2)
conda install -y theano
# Install common python packages for data science and machine
# learning applications
conda install -y pandas
conda install -y matplotlib
conda install -y ipython
conda install -y ipython-notebook
conda install -y sympy
conda install -y scikit-learn
conda install -y scikit-image
conda install -y nltk
conda install -y statsmodels
conda install -y opencv
# Install Keras dependencies for python(2)
conda install -y yaml
conda install -y pyyaml
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
# Update database for mlocate
updatedb
%files
%runscript
%test
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