Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
OSVersion: bionic
Include: apt wget sudo vim build-essential git sudo software-properties-common dirmngr gpg-agent curl


%labels
MAINTAINER_NAME Jafaruddin Lie
MAINTAINER_EMAIL jafar.lie@monash.edu

APPLICATION_NAME Simul-atrophy



%environment
CUDABINPATH=/usr/local/cuda/bin
CUDALIBPATH=/usr/local/cuda/lib64/stubs:/usr/local/cuda/lib64/:/usr/local/cuda/lib
export LD_LIBRARY_PATH=$CUDALIBPATH:$LD_LIBRARY_PATH
export DEBIAN_FRONTEND=noninteractive
export CC=/usr/bin/gcc-6
export CXX=/usr/bin/g++-6
export PETSC_VERSION=3.6.3
export PETSC_DIR=/petsc
export PETSC_ARCH=arch-linux2-cxx-debug
export ITK_VERSION=4.9.1
export ITK_DIR=/opt/itk/${ITK_VERSION}
export SIMUL_ATROPHY_DIR=/simul-atrophy/build/src
export PATH=$SIMUL_ATROPHY_DIR:$PATH:$CUDABINPATH


%post
echo "*********************************************************"
echo "Setup and display environment"
echo "*********************************************************"
export LC_ALL=en_AU.UTF-8
export LANGUAGE=en_AU.UTF-8
export DEBIAN_FRONTEND=noninteractive
echo $LC_ALL
echo $LANGUAGE
echo $DEBIAN_FRONTEND
echo "*********************************************************"
echo "Install repositories"
echo "*********************************************************"
apt-get install -y software-properties-common
apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic main restricted'
apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic-updates main restricted'
apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic universe'
apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic-updates universe'
echo "*********************************************************"
echo "Update repositories and install desktop"
echo "*********************************************************"
apt update
apt upgrade -y
apt install -y locales
locale-gen en_AU.UTF-8
apt install -y wget ubuntu-desktop vim software-properties-common git cmake
echo "*********************************************************"
echo "Installing CUDA"
echo "*********************************************************"
#apt install -y cuda-9-0
#apt-get install -y g++ freeglut3-dev build-essential libx11-dev libxmu-dev libxi-dev libglu1-mesa libglu1-mesa-dev
apt-get install -y gcc-6 g++-6
mkdir -p /mnt/cuda10
cd /mnt/cuda10
#wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/cuda_10.0.130_410.48_linux.run
#wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/cudnn-10.0-linux-x64-v7.6.1.34.tgz
#chmod +x cuda_10.0.130_410.48_linux.run
#./cuda_10.0.130_410.48_linux.run --tmpdir=/mnt/cuda10/ --toolkitpath=/usr/local/cuda10/ --toolkit --samples --samplespath=/usr/local/cuda9/ --silent --override
#ln -s /usr/local/cuda10 /usr/local/cuda
#ln -s /usr/bin/gcc-6 /usr/local/cuda/bin/gcc
#ln -s /usr/bin/g++-6 /usr/local/cuda/bin/g++
#tar -xzvf cudnn-10.0-linux-x64-v7.6.1.34.tgz
#cp cuda/include/cudnn.h /usr/local/cuda/include
#cp cuda/lib64/libcudnn* /usr/local/cuda/lib64
#chmod a+r /usr/local/cuda/include/cudnn.h /usr/local/cuda/lib64/libcudnn*
#echo "*********************************************************"
echo "Installing python dependencies"
echo "*********************************************************"
apt install -y python-pip python-pyqt5 pyqt5-dev python-tk
echo "*********************************************************"
echo "Installing vglrun and TurboVNC"
echo "*********************************************************"
#wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.1.2_amd64.deb
#dpkg -i turbovnc_2.1.2_amd64.deb
#wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.2_amd64.deb
#dpkg -i virtualgl_2.6.2_amd64.deb
apt update
apt -y upgrade
export LC_ALL=en_AU.UTF-8
export LANGUAGE=en_AU.UTF-8
export DEBIAN_FRONTEND=noninteractive
apt update
apt -y upgrade


echo "install gfortran"
apt-get install -y gfortran

echo "*********************************************************"
echo "dependency setup"
echo "*********************************************************"
export CC=$(which gcc-6)
export CXX=$(which g++-6)
export PETSC_VERSION=3.6.3
export PETSC_DIR=/petsc
export PETSC_ARCH=arch-linux2-cxx-debug
export ITK_VERSION=4.9.1
export ITK_DIR=/opt/itk/${ITK_VERSION}
apt-get install -y libboost-all-dev
apt-get install -y cmake

echo "*********************************************************"
echo "Installing PETSC"
echo "*********************************************************"
cd /
# require 3.6.3.1, but this is the closest i can find
git clone https://gitlab.com/petsc/petsc.git
cd petsc
# comment this line out to use petsc master.
git checkout tags/v${PETSC_VERSION}
./configure --with-cc=gcc-6 --with-cxx=g++-6 --with-fc=gfortran --with-64-bit-indicies=yes --download-mpich=yes --download-fblaslapack --with-clanguage=cxx --prefix=/opt/petsc/${PETSC_VERSION}
make all


# ITK install
echo "*********************************************************"
echo "Installing ITK"
echo "*********************************************************"
cd /
wget http://sourceforge.net/projects/itk/files/itk/4.9/InsightToolkit-${ITK_VERSION}.tar.gz/download -O InsightToolkit-${ITK_VERSION}.tar.gz
tar -xf InsightToolkit-${ITK_VERSION}.tar.gz
cd InsightToolkit-${ITK_VERSION}
mkdir bin && cd bin
cmake .. -DCMAKE_INSTALL_PREFIX=/opt/itk/${ITK_VERSION}
make
make install

echo "*********************************************************"
echo "Installing Simul-atrophy"
echo "*********************************************************"
cd /
git clone https://github.com/Inria-Asclepios/simul-atrophy.git
cd simul-atrophy
mkdir build && cd build
cmake ..
make


%runscript
$*