Singularity

Bootstrap: docker
From: nvidia/cuda:8.0-cudnn6-devel-ubuntu16.04

%environment

	#Environment variables

	#Use bash as default shell
	SHELL=/bin/bash

	#Add CUDA paths
	CPATH="/usr/local/cuda/include:$CPATH"
	PATH="/usr/local/cuda/bin:$PATH"
	LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"
	CUDA_HOME="/usr/local/cuda"
	#CUDA root needed for Theano
	CUDA_ROOT="/usr/local/cuda"

	#Python 3.5 paths
	CPATH="/usr/include/python3.5m:$CPATH"
	PYTHONPATH="/usr/local/lib/python3.5/dist-packages:$PYTHONPATH"

	export PATH LD_LIBRARY_PATH CPATH CUDA_HOME PYTHONPATH CUDA_ROOT


%setup
	#Runs on host
	#The path to the image is $SINGULARITY_ROOTFS


%post
	#Post setup script

  #Makes a root build directory
  mkdir /build

	#Load environment variables
	. /environment

	#Default mount paths
	mkdir /scratch /data /shared /fastdata

	echo "Updating ubuntu"
	apt-get -y update
	apt-get -y upgrade
	apt-get -y dist-upgrade
	apt-get -y autoremove

	echo "Installing essential packages"
	apt-get install -y wget git vim cmake cmake-curses-gui build-essential

	echo "Installing OpenCV Dependencies"

	## GUI (if you want to use GTK instead of Qt, replace 'qt5-default' with 'libgtkglext1-dev' and remove '-DWITH_QT=ON' option in CMake):
	apt-get install -y qt5-default libvtk6-dev

	## Media I/O:
	apt-get install -y zlib1g-dev libjpeg-dev libwebp-dev libpng-dev libtiff5-dev libjasper-dev libopenexr-dev libgdal-dev

	## Video I/O:
	apt-get install -y libdc1394-22-dev libavcodec-dev libavformat-dev libswscale-dev libtheora-dev libvorbis-dev libxvidcore-dev libx264-dev yasm libopencore-amrnb-dev libopencore-amrwb-dev libv4l-dev libxine2-dev

	## Parallelism and linear algebra libraries:
	apt-get install -y libtbb-dev libeigen3-dev

	## Python:
	apt-get install -y python3.5-dev python3.5-tk python3.5-numpy

	## Make python 3.5m the default
	cd /usr/bin
	rm python
	ln -s python3.5m python

	## Install pip for python 3
	cd /build
	wget https://bootstrap.pypa.io/get-pip.py
	python get-pip.py

	## Installed required global python packages
	pip install pandas scipy sklearn matplotlib NLTK

	## Java:
	apt-get install -y ant default-jdk

	## Documentation:
	apt-get install -y doxygen

	#Update libs links
	ldconfig

	# OpenCV - INSTALL (YOU CAN CHANGE '3.3.0' FOR THE LAST STABLE VERSION)
  echo "Installing OpenCV"
	cd /build
	apt-get install -y unzip wget
	wget https://github.com/opencv/opencv/archive/3.3.0.tar.gz
	tar -xf 3.3.0.tar.gz
	rm 3.3.0.tar.gz
	cd opencv-3.3.0
	mkdir build
	cd build
	cmake -DWITH_QT=ON -DWITH_OPENGL=ON -DFORCE_VTK=ON -DWITH_TBB=ON -DWITH_GDAL=ON -DWITH_XINE=ON -DBUILD_EXAMPLES=ON -DENABLE_PRECOMPILED_HEADERS=OFF -D CMAKE_BUILD_TYPE=RELEASE \
	-D CMAKE_INSTALL_PREFIX=/usr/local \
	-D BUILD_opencv_python3=yes \
	-D PYTHON_DEFAULT_EXECUTABLE="/usr/bin/python3.5m" \
	-D CUDA_ARCH_BIN="3.0 3.5 3.7 5.0 5.2 6.0 6.1" \
	-D CUDA_CUDA_LIBRARY="/usr/local/cuda/lib64/stubs/libcuda.so" \
	..
	make -j4
	make install
	ldconfig


  #echo "Installing SMILE" - Doesn't support python 3.5
	#cd /build
	#apt-get install -y python-pyo python-kivy
	#git clone https://github.com/compmem/smile.git
	cd smile
	#pip install .

	#Update libs links
	ldconfig


  echo "Installing Theano"
	pip install cython nose pydot-ng pycuda Theano
	#Install libgpuarray needed by theano
	cd /build
	wget https://github.com/Theano/libgpuarray/releases/download/v0.7.5/libgpuarray-0.7.5.tar.gz
	tar -xf libgpuarray-0.7.5.tar.gz
	cd libgpuarray-0.7.5
	mkdir Build
	cd Build
	cmake .. -DCMAKE_BUILD_TYPE=Release
	make
	make install
	cd ..
	python setup.py build
	python setup.py install


	echo "Installing Tensorflow"
	TF_PYTHON_URL="https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow_gpu-1.4.1-cp35-cp35m-linux_x86_64.whl"
	pip install --ignore-installed --upgrade $TF_PYTHON_URL

	echo "Installing Keras"
	pip install keras

  echo "Installing Pytorch"
	pip install http://download.pytorch.org/whl/cu80/torch-0.3.0.post4-cp35-cp35m-linux_x86_64.whl
	pip install torchvision

	#Remove the build directory
	rm -rf /build

%runscript
	#Executes with the singularity run command
	#delete this section to use existing docker ENTRYPOINT command


%test
	#Test that script is a success