arezaii/pf_singularity_demo:latest

$ singularity pull shub://arezaii/pf_singularity_demo:latest

Singularity Recipe

Bootstrap: docker
From: centos:7.4.1708
%labels
    # A base OS image to use for building ParFlow 
%post    

    # update OS

    yum -y update

    #-----------------------------------------------------------------------------
    #  Package dependencies
    #-----------------------------------------------------------------------------
    yum -y  install  epel-release
    yum  install -y  \
    autoconf \
    automake \
    binutils \
    cmake3 \
    file \
    gcc  \
    gcc-c++  \
    gcc-gfortran \
    git \
    libtool \
    lsof \
    make \
    tcl-devel \
    tcsh \
    time \
    tk-devel \
    wget \
    which \
    zlib \
    zlib-devells

    export CORE_COUNT=$(nproc)
    HOME_DIR=/home/parflow
    export PARFLOW_LIB_DIR=${HOME_DIR}/pflib
    export DOWNLOAD_DIR=${HOME_DIR}/downloads
    mkdir -p ${PARFLOW_LIB_DIR}
    cd ${HOME_DIR}   

    #-----------------------------------------------------------------------------
    # Build libraries
    #-----------------------------------------------------------------------------
    
    #
    # OMPI
    # 
    echo "Installing Open MPI"
    export OMPI_DIR=${PARFLOW_LIB_DIR}/ompi
    export OMPI_VERSION=4.0.1
    export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-$OMPI_VERSION.tar.gz"
    mkdir -p ${DOWNLOAD_DIR}/ompi    
    mkdir -p $OMPI_DIR
    # Download
    cd ${DOWNLOAD_DIR}/ompi && wget -O openmpi-$OMPI_VERSION.tar.gz $OMPI_URL && tar -xf openmpi-$OMPI_VERSION.tar.gz
    # Compile and install
    cd ${DOWNLOAD_DIR}/ompi/openmpi-$OMPI_VERSION && ./configure --prefix=$OMPI_DIR && make install -j${CORE_COUNT}
    cd ../..
    rm -fr ompi openmpi-$OMPI_VERSION.tar.gz
    # Set env variables so we can
    # compile our application
    export PATH=$OMPI_DIR/bin:$PATH
    export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH

        #
    # HDF5
    #
    echo "Installing HDF5"
    export HDF5_DIR=${PARFLOW_LIB_DIR}/hdf5
    export HDF5_VERSION=1.10.5
    export HDF5_URL="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz"
    mkdir -p $HDF5_DIR
    mkdir -p ${DOWNLOAD_DIR}/hdf5
    cd ${DOWNLOAD_DIR}/hdf5 && \
    wget ${HDF5_URL} && \
    tar -xf hdf5-${HDF5_VERSION}.tar.gz && \
    cd hdf5-${HDF5_VERSION} && \
    CC=mpicc CXX=mpicxx ./configure \
      --prefix=$HDF5_DIR \
      --enable-parallel && \
    make -j${CORE_COUNT} && make install -j${CORE_COUNT} && \
    cd .. && \
    rm -fr hdf5-${HDF5_VERSION} hdf5-${HDF5_VERSION}.tar.gz
    export LD_LIBRARY_PATH=$HDF5_DIR/lib:$LD_LIBRARY_PATH


    #
    # SILO 
    #
    echo "Installing SILO"
    export SILO_DIR=${PARFLOW_LIB_DIR}/silo
    export SILO_VERSION=4.10.2    
    mkdir -p $SILO_DIR
    mkdir -p ${DOWNLOAD_DIR}/silo
    cd ${DOWNLOAD_DIR}/silo

    wget -O silo-${SILO_VERSION}.tar.gz \
        https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-${SILO_VERSION}/silo-${SILO_VERSION}.tar.gz && \
    tar -xf silo-${SILO_VERSION}.tar.gz && \
    cd silo-${SILO_VERSION} && \
    ./configure  --prefix=$SILO_DIR --disable-silex --disable-hzip --disable-fpzip FC=gfortran F90=gfortran --with-hdf5=${PARFLOW_LIB_DIR}/hdf5/include,${PARFLOW_LIB_DIR}/hdf5/lib && \
    make install -j${CORE_COUNT} && \
    cd .. && \
    rm -fr silo-${SILO_VERSION} silo-${SILO_VERSION}.tar.gz


    #
    # Hypre
    #
    echo "Installing Hypre"
    export HYPRE_DIR=${PARFLOW_LIB_DIR}/hypre
    export HYPRE_VERSION=2.18.2
    mkdir -p ${DOWNLOAD_DIR}/hypre
    cd ${DOWNLOAD_DIR}/hypre
    wget https://github.com/hypre-space/hypre/archive/v${HYPRE_VERSION}.tar.gz && \
    tar xf v${HYPRE_VERSION}.tar.gz && \
    cd hypre-${HYPRE_VERSION}/src && \
    CC=mpicc cxx=mpicxx && \
    ./configure --prefix=${HYPRE_DIR} && \
    make install -j${CORE_COUNT} && \
    cd .. && \
    rm -fr hypre-${HYPRE_VERSION} v${HYPRE_VERSION}.tar.gz

%labels
    A ParFlow container to be used with ompi base

%environment
    export PARFLOW_MPIEXEC_EXTRA_FLAGS="--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"
    

##############################

# SequentialIO=TRUE

##############################


%apprun seq

    exec tclsh "$@"

%applabels seq

    Parflow with sequentialIO set to true, so no need to distribute inputs or undistribute outputs

%appinstall seq

    cd /home/parflow
    
    export CORE_COUNT=1
    export PARFLOW_DIR=/home/parflow/pfdir_seq
    export MPI_DIR=/home/parflow/pflib/ompi
    export HDF5_DIR=/home/parflow/pflib/hdf5
    export NETCDF_DIR=/home/parflow/pflib/netcdf
    export SILO_DIR=/home/parflow/pflib/silo
    export HYPRE_DIR=/home/parflow/pflib/hypre
    export PATH=${MPI_DIR}/bin:$PATH
    export LD_LIBRARY_PATH=${HDF5_DIR}/lib:${MPI_DIR}/lib:$LD_LIBRARY_PATH
    
    #-----------------------------------------------------------------------------
    # Parflow configure and build
    #-----------------------------------------------------------------------------
    
    
        
    git clone -b master --single-branch https://github.com/parflow/parflow.git parflow_seq && \
    cd parflow_seq && \
    git checkout b1c408fcb99f1f242a3c0830517eda80515b6201 && \
    cd .. && \
    mkdir -p build_seq && \
    cd build_seq && \
    cmake3 ../parflow_seq \
    -DPARFLOW_AMPS_LAYER=mpi1 \
    -DPARFLOW_AMPS_SEQUENTIAL_IO=TRUE \
    -DHYPRE_ROOT=${HYPRE_DIR} \
    -DSILO_ROOT=${SILO_DIR} \
    -DHDF5_ROOT=${HDF5_DIR} \
    -DPARFLOW_ENABLE_TIMING=TRUE \
    -DPARFLOW_HAVE_CLM=ON \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX=${PARFLOW_DIR} && \
    make install -j${CORE_COUNT}
    #cd .. && \
    #rm -fr parflow build


%appenv seq

    export PARFLOW_DIR=/home/parflow/pfdir_seq
    export PARFLOW_MPIEXEC_EXTRA_FLAGS="--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"


%apphelp seq

    This is the help for seq. This app runs parflow compiled with SequentialIO=TRUE
    To run: $ singularity run --app seq <path_to_singularity_container> <tcl_file> [optional arguments passed to tcl_file]

%apptest seq
    # These tests can't be run inside the immutable container because of how parflow requires to write to disk
    export PARFLOW_DIR=/home/parflow/pfdir_seq
    export PARFLOW_MPIEXEC_EXTRA_FLAGS="--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"
    cd /home/parflow/build_seq
    make test    


##############################

# SequentialIO=False

##############################


%apphelp par

    This is the help for par.


%appinstall par

    cd /home/parflow    
    
    export CORE_COUNT=1
    export PARFLOW_DIR=/home/parflow/pfdir_par
    export MPI_DIR=/home/parflow/pflib/ompi
    export HDF5_DIR=/home/parflow/pflib/hdf5
    export NETCDF_DIR=/home/parflow/pflib/netcdf
    export SILO_DIR=/home/parflow/pflib/silo
    export HYPRE_DIR=/home/parflow/pflib/hypre
    export PATH=${MPI_DIR}/bin:$PATH
    export LD_LIBRARY_PATH=${HDF5_DIR}/lib:${MPI_DIR}/lib:$LD_LIBRARY_PATH
    
    #-----------------------------------------------------------------------------
    # Parflow configure and build
    #-----------------------------------------------------------------------------
    
    #PARFLOW_MPIEXEC_EXTRA_FLAGS="--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"
        
    git clone -b master --single-branch https://github.com/parflow/parflow.git parflow_par && \
    cd parflow_par && \
    git checkout b1c408fcb99f1f242a3c0830517eda80515b6201 && \
    cd .. && \
    mkdir -p build_par && \
    cd build_par && \
    cmake3 ../parflow_par \
    -DPARFLOW_AMPS_LAYER=mpi1 \
    -DPARFLOW_AMPS_SEQUENTIAL_IO=FALSE \
    -DHYPRE_ROOT=${HYPRE_DIR} \
    -DSILO_ROOT=${SILO_DIR} \
    -DHDF5_ROOT=${HDF5_DIR} \
    -DPARFLOW_ENABLE_TIMING=TRUE \
    -DPARFLOW_HAVE_CLM=ON \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX=${PARFLOW_DIR} && \
    make install -j${CORE_COUNT} 
    # cd .. && \
    # rm -fr build


%appenv par

    export PARFLOW_DIR=/home/parflow/pfdir_par
    export PARFLOW_MPIEXEC_EXTRA_FLAGS="--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"

%apprun par

    exec tclsh "$@"

%apptest par
    # These tests can't be run inside the immutable container because of how parflow requires to write to disk
    export PARFLOW_DIR=/home/parflow/pfdir_par
    export PARFLOW_MPIEXEC_EXTRA_FLAGS="--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"
    cd /home/parflow/build_par
    make test

Collection

• Name: arezaii/pf_singularity_demo
• License: None

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