Bootstrap: localimage
From: pnetcdf_openmpi-4.0.2_gcc-9_ubuntu-18.sif

%post
    # Paths to the compiled netcdf, pnetcdf file
    BUILDDIR=/tmp
    PREFIX=/usr/local

    # env variables from specific compiler
    export CXX=/usr/bin/g++-9
    export CC=/usr/bin/gcc-9
    export FC=/usr/bin/gfortran-9

    # env variables from openmpi for runtime
    export OMPI_DIR=/opt/ompi
    export SINGULARITY_OMPI_DIR=$OMPI_DIR
    export SINGULARITYENV_APPEND_PATH=$OMPI_DIR/bin
    export SINGULARITYENV_APPEND_LD_LIBRARY_PATH=$OMPI_DIR/lib

    # Set env variables for build 
    export PATH=$OMPI_DIR/bin:$PATH
    export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
    export MANPATH=$OMPI_DIR/share/man:$MANPATH

    # 
    export LANG=C.UTF-8
    export LC_ALL=C.UTF-8

    ## for apt to be noninteractive
    export DEBIAN_FRONTEND=noninteractive
    export DEBCONF_NONINTERACTIVE_SEEN=true
    export MPI4PY_VERSION=3.0.3 
    export HDF5_VERSION=1.10.6 
    export PNETCDF_VERSION=1.12.1 
    export NETCDF4_VERSION=4.7.3 
    export NETCDF4_PYTHON_VERSION=1.5.3

   
    # Install Python packages
    python3 -m pip install --upgrade pip
    python3 -m pip install pytest
    python3 -m pip install NuMPI
    python3 -m pip install ase matscipy
    python3 -m pip install Cython
        
    # Bison, Flex and  dh-autoreconf. Needed for PTscotch in 
    apt-get -qq update
    apt-get -y -qq install flex bison dh-autoreconf

    # Download Petsc and Slepc
    export PETSC_DIRECTORY=/opt
    git clone -b release https://gitlab.com/petsc/petsc.git $PETSC_DIRECTORY/petsc

    # Install Petsc: 
    cd $PETSC_DIRECTORY/petsc
    ./configure --with-64-bit-indices=0 --with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native -mtune=native" --download-fblaslapack=1 --download-mumps --download-scalapack --download-parmetis --download-metis --download-ptscotch --download-petsc4py=yes
    make all check
    export PETSC_DIR=$PETSC_DIRECTORY/petsc
    export PETSC_ARCH=arch-linux-c-opt
    export PYTHONPATH="/opt/petsc/arch-linux-c-opt/lib"
    
    # Install Slepc
    export SLEPC_DIRECTORY=/opt 
    export SLEPC_DIR=$SLEPC_DIRECTORY/slepc
    git clone -b release https://gitlab.com/slepc/slepc $SLEPC_DIRECTORY/slepc
    cd $SLEPC_DIRECTORY/slepc
    ./configure --with-scalapack=1 --download-arpack --download-elpa --download-slepc4py
    make SLEPC_DIR=$SLEPC_DIRECTORY/slepc PETSC_DIR=$PETSC_DIRECTORY/petsc PETSC_ARCH=arch-linux-c-opt
    # make SLEPC_DIR=$SLEPC_DIRECTORY/slepc PETSC_DIR=$PETSC_DIRECTORY/petsc check
    export PYTHONPATH="/opt/slepc/arch-linux-c-opt/lib"

%environment
    # Variables to be used at runtime 
    export LANG=C.UTF-8
    export LC_ALL=C.UTF-8
    export OMPI_DIR=/opt/ompi
    export SINGULARITY_OMPI_DIR=$OMPI_DIR
    export SINGULARITYENV_APPEND_PATH=$OMPI_DIR/bin
    export SINGULARITYENV_APPEND_LD_LIBARY_PATH=$OMPI_DIR/lib
    export SINGULARITYENV_APPEND_LD_LIBARY_PATH=/usr/local/lib
    export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
    export PETSC_DIR=/opt/petsc
    export PETSC_ARCH=arch-linux-c-opt
    export SLEPC_DIR=$SLEPC_DIRECTORY/slepc
    export PYTHONPATH="/opt/petsc/arch-linux-c-opt/lib"
    export PYTHONPATH="/opt/slepc/arch-linux-c-opt/lib" 

%runscript ‚