kaiju/containers/gamera.def

#==============================================================================
# CGS GAMERA (Serial) Containerization
#
# This Singularity definition file allows one to create a build environment for
# the GAMERA model. The base image/layer is Intels OneAPI HPC Toolkit allowing
# for Intel-based compilers.
#
# Run:
#   singularity build --fakeroot gamera_serial.sif gamera_serial.def
#   singularity run -e gamera_serial.sif
#
# Note: The initial build will take longer as Docker will be retrieving the
#       base image (~5.5GB). This time will vary depending upon your network.
# Note: The base image may fail to build (known issue). If it does, that
#       means that Intels container repository is having network issues.
#       A work-around is in development.
#
# 2024, Brent Smith
#==============================================================================

Bootstrap: docker
From: intel/oneapi-hpckit:2023.2.1-devel-ubuntu22.04
# Intel OneAPI Docker Images:
#     https://github.com/intel/oneapi-containers/tree/master/images
#     https://hub.docker.com/r/intel/oneapi-hpckit

# create GAMERA source directory that is bound during build
# using the SINGULARITY_BIND environment variable and
# the container SINGULARITY_ROOTFS internal variable to specify
# in the setup section not to make a directory on the host system
# https://github.com/apptainer/singularity/issues/1549#issuecomment-411588888
%setup
    mkdir -p ${SINGULARITY_ROOTFS}/kaiju/

%files
    requirements.txt .

#------------------------------------------------------------------------------
# commands run in container after base OS installation
%post -c /bin/bash

    # Directory Structure
    mkdir -p /cdf /hdf5 /miniconda3 /kaiju/build

    #============================================
    # NASA CDF Library (version 3.9.0)
    export CDF_FILE=cdf39_0-dist-all.tar.gz
    export CDF_URL=https://spdf.gsfc.nasa.gov/pub/software/cdf/dist
    wget --no-check-certificate $CDF_URL/cdf39_0/linux/$CDF_FILE -P /cdf
    cd /cdf && tar zxf $CDF_FILE && cd cdf39_0-dist &&\
        make OS=linux ENV=gnu CURSES=no all &&\
        make INSTALLDIR=/cdf install &&\
        rm ../$CDF_FILE && cd /
    #--------------------------------------------

    #============================================
    # HDF5 Library
    export HDF_FILE=hdf5-1.14.1-2
    export HDF_URL=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.1/src
    wget --no-check-certificate $HDF_URL/$HDF_FILE.tar.gz -P /hdf5
    cd /hdf5 && tar zxf $HDF_FILE.tar.gz && cd $HDF_FILE &&\
        ./configure FC=ifort --prefix=/hdf5 --enable-fortran &&\
        make && make install &&\
        rm ../$HDF_FILE.tar.gz && cd /
    #--------------------------------------------

    #============================================
    # Update System
    # known GPG key issue: https://github.com/intel/oneapi-containers/issues/53
    export key=https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
    curl -fsSL $key | gpg --dearmor > /usr/share/keyrings/intel-oneapi-archive-keyring.gpg
    apt -y update && apt install --no-install-recommends -y \
        build-essential \
        cmake \
        git \
        git-lfs \
        libgeos-dev \
        pkg-config && \
        # vim \
        rm -rf /var/lib/apt/lists/*
    #--------------------------------------------

    #============================================
    # Python Environment
    export PY_FILE=Miniconda3-latest-Linux-x86_64.sh
    cp requirements.txt /miniconda3/
    wget --no-check-certificate https://repo.anaconda.com/miniconda/$PY_FILE -P /miniconda3/
    cd /miniconda3 && /bin/bash $PY_FILE -b -u -p /miniconda3 && \
        rm $PY_FILE && /miniconda3/bin/conda init bash && \
        source /miniconda3/etc/profile.d/conda.sh &&\
        export PATH=/miniconda3/bin:$PATH &&\
        export PYTHONPATH=/miniconda3/bin:$PATH &&\
        conda config --set ssl_verify false &&\
        conda config --set auto_activate_base false &&\
        conda update -y --all &&\
        conda create -n kaiju-3.8 python=3.8 -y &&\
        conda activate kaiju-3.8 &&\
        conda update -y --all &&\
        pip3 install --default-timeout=100 -r /miniconda3/requirements.txt &&\
        cd /
    #--------------------------------------------

    #============================================
    # Environment for Building GAMERA in Container (and running GAMERA)
    cat > ~/.bashrc <<EOL
. /cdf/bin/definitions.B

export PATH="/hdf5/bin":$PATH
export HDF5_DIR=/hdf5
export HDF5_INCLUDE_DIRS=/hdf5/include
export CPATH=$HDF5_INCLUDE_DIRS
export INCLUDE="-I$HDF5_INCLUDE_DIRS"
export LD_LIBRARY_PATH="/hdf5:$LD_LIBRARY_PATH"

source /miniconda3/etc/profile.d/conda.sh
export PATH=/miniconda3/bin:$PATH
export PYTHONPATH=/miniconda3/bin:$PATH
conda activate kaiju-3.8
EOL
    cp ~/.bashrc /kaiju/build/gamera.bash
    . /kaiju/build/gamera.bash
    #--------------------------------------------

    #============================================
    # CGS GAMERA Setup/Compilation
    export KAIJUHOME=/kaiju
    export FC=/hdf5/bin/h5fc

    cd $KAIJUHOME/build &&\
        cmake -DALLOW_INVALID_COMPILERS=ON .. &&\
        make all
    # add GAMERA setup scripts to env
    echo "export KAIJUHOME=/kaiju" >> ~/.bashrc
    echo "source $KAIJUHOME/scripts/setupEnvironment.sh" >> ~/.bashrc
    echo "export PATH=$KAIJUHOME/build/bin:$PATH" >> ~/.bashrc
    echo "export PATH=$KAIJUHOME/quickstart/loop2d:$PATH" >> ~/.bashrc
    cp ~/.bashrc /kaiju/build/gamera.bash
    #--------------------------------------------

    # You should now have GAMERA compiled within the container.
    # Note: If you run `singularity shell`, you will still
    #       need to source gamera.bash.

%runscript
    # this section defaults to a POSIX (sh) shell environment
    exec /bin/bash /kaiju/build/gamera.bash