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Commit b008aeca authored by Marty Kandes's avatar Marty Kandes
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naked-singularity-v0.2.9 :: updated neon-cpu.def for comet to neon

v2.6.0; also added cmake to all base ubuntu definition files for comet
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...@@ -29,8 +29,8 @@ AUTHOR ...@@ -29,8 +29,8 @@ AUTHOR
VERSION VERSION
0.2.8 0.2.9
LAST UPDATED LAST UPDATED
Friday, April 6th, 2018 Wednesday, April 10th, 2018
...@@ -7,13 +7,12 @@ OSVersion: xenial ...@@ -7,13 +7,12 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
APPLICATION_NAME neon APPLICATION_NAME neon
APPLICATION_VERSION 2.0.0+41e746a APPLICATION_VERSION 2.6.0
APPLICATION_URL http://neon.nervanasys.com/index.html/index.html APPLICATION_URL https://ai.intel.com/neon/
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.1 SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
VERSION 0.0.1 LAST_UPDATED 20180410
LAST_UPDATED 20170830
%setup %setup
...@@ -21,11 +20,14 @@ OSVersion: xenial ...@@ -21,11 +20,14 @@ OSVersion: xenial
%post -c /bin/bash %post -c /bin/bash
# Set system locale
export LC_ALL=C export LC_ALL=C
# Install system metapackages
apt-get -y install ubuntu-standard apt-get -y install ubuntu-standard
apt-get -y install ubuntu-server apt-get -y install ubuntu-server
# Add repositories
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
...@@ -46,128 +48,147 @@ OSVersion: xenial ...@@ -46,128 +48,147 @@ OSVersion: xenial
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
apt-get -y update && apt-get -y upgrade && apt-get -y dist-upgrade && apt-get -y autoremove # Upgrade all packages to their latest versions
apt-get -y update && apt-get -y upgrade
mkdir /cvmfs /oasis /projects /scratch
cd /opt
# 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 build-essential
apt-get -y install clang apt-get -y install cmake
apt-get -y install cmake apt-get -y install libtool
apt-get -y install g++
apt-get -y install git
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install qt5-default
apt-get -y install libvtk6-dev
apt-get -y install zlib1g-dev
apt-get -y install libjpeg-dev
apt-get -y install libwebp-dev
apt-get -y install libpng-dev
apt-get -y install libtiff5-dev
apt-get -y install libjasper-dev
apt-get -y install libopenexr-dev
apt-get -y install libgdal-dev
apt-get -y install libdc1394-22-dev
apt-get -y install libavcodec-dev
apt-get -y install libavdevice-dev
apt-get -y install libavformat-dev
apt-get -y install libavfilter-dev
apt-get -y install libavresample-dev
apt-get -y install libavutil-dev
apt-get -y install libswscale-dev
apt-get -y install libtheora-dev
apt-get -y install libvorbis-dev
apt-get -y install libxvidcore-dev
apt-get -y install libv4l-dev
apt-get -y install v4l-utils
apt-get -y isntall libgstreamer0.10-dev
apt-get -y install libgstreamer-plugins-base0.10-dev
apt-get -y install x264
apt-get -y install libx264-dev
apt-get -y install libxine2-dev
apt-get -y install libfaac-dev
apt-get -y install libmp3lame-dev
apt-get -y install libopencore-amrnb-dev
apt-get -y install libopencore-amrwb-dev
apt-get -y install libsox-dev
apt-get -y install ffmpeg
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install libtbb-dev apt-get -y install zip
apt-get -y install libeigen3-dev
apt-get -y install libatlas-base-dev # 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
# Install miniconda3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
# Install aeon and neon dependencies
apt-get -y install clang
apt-get -y install libcurl4-openssl-dev
apt-get -y install libopencv-dev
apt-get -y install libsox-dev
apt-get -y install libboost-filesystem-dev
apt-get -y install libboost-system-dev
apt-get -y install libssl-dev
apt-get -y install ffmpeg
# Install aeon and neon python dependencies
apt-get -y install python-dev apt-get -y install python-dev
apt-get -y install python-pip apt-get -y install python-pip
apt-get -y install python-tk
apt-get -y install python-numpy
apt-get -y install python-virtualenv apt-get -y install python-virtualenv
apt-get -y install python3-dev apt-get -y install python-numpy
apt-get -y install python3-pip apt-get -y install python-h5py
apt-get -y install python3-tk apt-get -y install python-yaml
apt-get -y install python3-numpy apt-get -y install python-opencv
apt-get -y install python3-virtualenv apt-get -y install python-future
apt-get -y install python-configargparse
pip install -y --upgrade setuptools
cd /opt
apt-get -y install ant # Download, build, and install aeon for python
apt-get -y install default-jdk git clone https://github.com/NervanaSystems/aeon.git
mkdir -p /opt/aeon/build
apt-get -y install doxygen cd /opt/aeon/build
cmake .. \
apt-get -y install libprotobuf-dev -DCMAKE_BUILD_TYPE='Release' \
apt-get -y install protobuf-compiler -DPYTHON_EXECUTABLE='/usr/bin/python' \
apt-get -y install libgoogle-glog-dev -DPYTHON_LIBRARIES='/usr/lib/python2.7' \
apt-get -y install libgflags-dev -DPYTHON_INCLUDE_DIRS='/usr/include/python2.7' \
apt-get -y install libgphoto2-dev -DENABLE_AEON_SERVICE='OFF' \
apt-get -y install libhdf5-dev -DENABLE_AEON_CLIENT='ON' \
apt-get -y install libyaml-dev -DENABLE_OPENFABRICS_CONNECTOR='OFF'
pip install .
wget https://github.com/opencv/opencv/archive/3.3.0.tar.gz -O opencv-3.3.0.tar.gz
wget https://github.com/opencv/opencv_contrib/archive/3.3.0.tar.gz -O opencv_contrib-3.3.0.tar.gz
tar -xzf opencv-3.3.0.tar.gz
tar -xzf opencv_contrib-3.3.0.tar.gz
cd opencv-3.3.0
mkdir build
cd build
cmake -D CMAKE_BUILD_TYPE=RELEASE \
-D CMAKE_INSTALL_PREFIX=/usr/local \
-D BUILD_EXAMPLES=ON \
-D BUILD_PERF_TESTS=OFF \
-D BUILD_TBB=ON \
-D BUILD_TESTS=OFF \
-D BUILD_TIFF=ON \
-D ENABLE_AVX=ON \
-D ENABLE_PRECOMPILED_HEADERS=OFF \
-D FORCE_VTK=ON \
-D INSTALL_C_EXAMPLES=ON \
-D INSTALL_PYTHON_EXAMPLES=ON \
-D OPENCV_EXTRA_MODULES_PATH=/opt/opencv_contrib-3.3.0/modules \
-D WITH_CUDA=OFF \
-D WITH_EIGEN=OFF \
-D WITH_GDAL=ON \
-D WITH_IPP=OFF \
-D WITH_OPENCL=OFF \
-D WITH_OPENGL=ON \
-D WITH_QT=ON \
-D WITH_TBB=ON \
-D WITH_V4L=ON \
-D WITH_VTK=ON \
-D WITH_XINE=ON ..
make
make install
ldconfig
cd /opt cd /opt
# Download, build, and install neon for python
git clone https://github.com/NervanaSystems/neon.git git clone https://github.com/NervanaSystems/neon.git
cd neon cd /opt/neon
make sysinstall git checkout latest
make neon_install
# Install aeon and neon python3 dependencies
apt-get -y install python3-dev
apt-get -y install python3-pip
apt-get -y install python3-virtualenv
apt-get -y install python3-numpy
apt-get -y install python3-h5py
apt-get -y install python3-yaml
apt-get -y install python3-opencv
apt-get -y install python3-future
apt-get -y install python3-configargparse
pip3 install -y --upgrade setuptools
# Download, build, and install aeon for python3
cd /opt/aeon/build
cmake .. \
-DCMAKE_BUILD_TYPE='Release' \
-DPYTHON_EXECUTABLE='/usr/bin/python' \
-DPYTHON_LIBRARIES='/usr/lib/python3.5' \
-DPYTHON_INCLUDE_DIRS='/usr/include/python3.5' \
-DENABLE_AEON_SERVICE='OFF' \
-DENABLE_AEON_CLIENT='ON' \
-DENABLE_OPENFABRICS_CONNECTOR='OFF'
pip3 install .
# Download, build, and install neon for python3
cd /opt/neon
sed -i 's/@python setup.py install/@python3 setup.py install/' Makefile
make neon_install
# 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
# 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
# Set container environment variables
cd /.singularity.d/env
# Update database for mlocate
updatedb
%files %files
...@@ -175,4 +196,5 @@ OSVersion: xenial ...@@ -175,4 +196,5 @@ OSVersion: xenial
%test %test
cd /tmp
python /opt/neon/examples/mnist_mlp.py python /opt/neon/examples/mnist_mlp.py
...@@ -55,6 +55,7 @@ OSVersion: xenial ...@@ -55,6 +55,7 @@ OSVersion: xenial
apt-get -y install autoconf apt-get -y install autoconf
apt-get -y install automake apt-get -y install automake
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
......
...@@ -55,6 +55,7 @@ OSVersion: xenial ...@@ -55,6 +55,7 @@ OSVersion: xenial
apt-get -y install autoconf apt-get -y install autoconf
apt-get -y install automake apt-get -y install automake
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
......
...@@ -55,6 +55,7 @@ OSVersion: xenial ...@@ -55,6 +55,7 @@ OSVersion: xenial
apt-get -y install autoconf apt-get -y install autoconf
apt-get -y install automake apt-get -y install automake
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
......
...@@ -55,6 +55,7 @@ OSVersion: xenial ...@@ -55,6 +55,7 @@ OSVersion: xenial
apt-get -y install autoconf apt-get -y install autoconf
apt-get -y install automake apt-get -y install automake
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
......
...@@ -55,6 +55,7 @@ OSVersion: xenial ...@@ -55,6 +55,7 @@ OSVersion: xenial
apt-get -y install autoconf apt-get -y install autoconf
apt-get -y install automake apt-get -y install automake
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
......
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