BootStrap: docker
From: ubuntu:20.04

%post
    export DEBIAN_FRONTEND=noninteractive
    apt-get update
    apt-get install --no-install-recommends -y software-properties-common
    add-apt-repository ppa:openkim/latest -y
    apt-get update
    apt-get upgrade --no-install-recommends -y
    apt-get install --no-install-recommends -y \
        gpg-agent \
        bc \
        build-essential \
        ccache \
        clang \
        curl \
        doxygen \
        enchant \
        g++ \
        gcc \
        gfortran \
        git \
        hdf5-tools \
        less \
        libblas-dev \
        libeigen3-dev \
        libenchant-dev \
        libfftw3-dev \
        libgsl-dev \
        libhdf5-serial-dev \
        libhwloc-dev \
        libjpeg-dev \
        liblapack-dev \
        libnetcdf-dev \
        libomp-dev \
        libopenblas-dev \
        libnuma-dev \
        libpng-dev \
        libproj-dev \
        libreadline-dev \
        libvtk6-dev \
        libyaml-dev \
        libzstd-dev \
        make \
        mpi-default-bin \
        mpi-default-dev \
        ninja-build \
        python3-dev \
        python3-pip \
        python3-pkg-resources \
        python3-setuptools \
        python3-virtualenv \
        python3-venv \
        python-is-python3 \
        rsync \
        ssh \
        texlive \
        texlive-latex-recommended \
        texlive-formats-extra \
        texlive-pictures \
        texlive-publishers \
        texlive-science \
        dvipng \
        latexmk \
        xindy \
        vim-nox \
        virtualenv \
        voro++-dev \
        wget \
        xxd \
        valgrind \
        gdb \
        zstd \
        libyaml-cpp-dev \
        libkim-api-dev \
        openkim-models

    ###########################################################################
    # Latest CMake (needed for OneAPI)
    ###########################################################################

    wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | tee /etc/apt/trusted.gpg.d/kitware.gpg >/dev/null
    apt-add-repository 'deb https://apt.kitware.com/ubuntu/ focal main'
    apt update
    apt install -y cmake

    ###########################################################################
    # OneAPI
    ###########################################################################

    cd /tmp
    wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
    # add to your apt sources keyring so that archives signed with this key will be trusted.
    apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
    # remove the public key
    rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
    echo "deb https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
    add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
    apt update
    apt install -y \
        intel-oneapi-compiler-dpcpp-cpp \
        intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic \
        intel-oneapi-compiler-fortran \
        intel-oneapi-dev-utilities \
        intel-oneapi-openmp \
        intel-oneapi-ipp-devel \
        intel-oneapi-mpi-devel \
        intel-oneapi-tbb-devel \
        intel-oneapi-ippcp-devel \
        intel-oneapi-ccl-devel \
        intel-oneapi-dnnl-devel \
        intel-oneapi-onevpl-devel \
        intel-oneapi-dal-devel \
        intel-oneapi-mkl-devel \
        intel-oneapi-libdpstd-devel

    ###########################################################################
    # KIM-API
    ###########################################################################

    # workaround for installing files in /usr/share/doc inside of a container
    sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
    apt-get install -y libkim-api-doc
    sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes

    # install KIM models
    KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
    gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
    gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz

    kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
    kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
    kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
    kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
    kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
    kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu


    ###########################################################################
    # Plumed
    ###########################################################################

    export PLUMED_PKG_VERSION=2.8.2

    mkdir plumed
    cd plumed
    curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz
    tar -xzf plumed.tar.gz
    cd plumed-${PLUMED_PKG_VERSION}
    ./configure --disable-doc --prefix=/usr
    make
    make install
    cd ../../
    rm -rvf plumed

    ###########################################################################
    # Customizations
    ###########################################################################

    # set custom prompt indicating the container name
    CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
    cat >$CUSTOM_PROMPT_ENV <<EOF
#!/bin/bash
PS1="[ubuntu20.04_oneapi:\u@\h] \W> "
EOF
    chmod 755 $CUSTOM_PROMPT_ENV


    ###########################################################################
    # Cleanup
    ###########################################################################
    # clean cache
    rm -rf /var/lib/apt/lists/*

%environment
    LC_ALL=C
    export LC_ALL
    export PATH=/usr/lib/ccache:$PATH
    # tell OpenMPI to not try using Infiniband
    OMPI_MCA_btl="^openib"
    # do not warn about unused components as this messes up testing
    OMPI_MCA_btl_base_warn_component_unused="0"
    export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused

%labels
    Author akohlmey, rbberger