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skyply.def
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357
skyply.def
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###########################################################################
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###########################################################################
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##
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## Apptainer Build File: Skyply
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## Function: Fully-integrated Simulation stack for WRF, CMAQ, & SCICHEM
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##
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## Documentation:
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##
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###########################################################################
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###########################################################################
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Bootstrap: docker
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From: rockylinux:9
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%labels
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Author HPCStack
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Version 1.0
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Description "Rocky 9 base with development tools for WRF/CMAQ"
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%environment
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############################################################
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## Compiler Settings
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############################################################
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# Intel Compiler
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#export CC=icc
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#export CXX=icpc
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#export FC=ifort
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#export F77=ifort
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# GNU Compiler
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export CC=gcc
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export CXX=g++
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export FC=gfortran
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export F77=gfortran
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############################################################
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## General
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############################################################
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export HPC_PATH=/opt/hpc
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export MODEL_PATH=/opt/models
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############################################################
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## OpenMPI Settings
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############################################################
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export MPI=/opt/hpc/mpi
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############################################################
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## OpenMP Settings
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############################################################
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export OMP_NUM_THREADS=1
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export OMP_PROC_BIND=spread
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export OMP_PLACES=cores
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############################################################
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## HDF5 Settings
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############################################################
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export HDF5=$HPC_PATH/hdf5
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export PHDF5=$HDF5
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############################################################
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## NetCDF Settings
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############################################################
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export NETCDF_INCDIR
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export NETCDF_LIBDIR
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export NETCDF=$HPC_PATH/netcdf
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export NETCDF=$NETCDF
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############################################################
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## IO/API Settings
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############################################################
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export MPI_HOME=$HPC_PATH/mpi
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export IOAPI=$HPC_PATH/ioapi
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############################################################
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## WRF Settings
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############################################################
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export WRF_DIR=$MODEL_PATH/wrf
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export PATH=$MPI_HOME/bin:$NETCDF/bin:$PATH
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export LD_LIBRARY_PATH=$MPI_HOME/lib:$HDF5/lib:$NETCDF/lib:$IOAPI/lib:$LD_LIBRARY_PATH
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############################################################
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## WPS Settings
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############################################################
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export WPS_DIR=$MODEL_PATH/wps
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############################################################
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## CMAQ Settings
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############################################################
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export CMAQ_DIR=$MODEL_PATH/cmaq
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export JASPERLIB=/usr/lib64
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export JASPERINC=/usr/include
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%post
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# Update system and enable CRB repository
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dnf -y install epel-release
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dnf config-manager --set-enabled crb
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dnf -y update
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# Install development packages
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dnf -y install \
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gcc gcc-gfortran gcc-c++ \
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python3 python3-pip \
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R R-devel \
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git wget which file time \
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make cmake automake autoconf libtool \
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libcurl-devel \
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tar bzip2 bzip2-devel \
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perl tcsh csh m4 \
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jasper jasper-devel \
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libpng libpng-devel \
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zlib zlib-devel \
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libxml2 libxml2-devel \
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xz xz-devel \
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zstd \
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sudo \
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unzip \
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diffutils \
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patch \
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--allowerasing \
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&& dnf clean all
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mkdir -p /opt/src /opt/hpc /opt/models
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# -------------------------------------------------
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# Create non-root user
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# -------------------------------------------------
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USERNAME="hpcuser"
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USER_UID=1000
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USER_GID=1000
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# Create group and user
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groupadd -g ${USER_GID} ${USERNAME}
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useradd -m -u ${USER_UID} -g ${USER_GID} -s /bin/bash ${USERNAME}
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# Set password (optional; often not needed for batch jobs)
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echo "${USERNAME}:password" | chpasswd
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# Give ownership of relevant directories
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chown -R ${USERNAME}:${USERNAME} /opt/src
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%post
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# -------------------------------------------------
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# Define package URLs
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# -------------------------------------------------
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OPENMPI_URL="https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz"
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HDF5_URL="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/downloads/hdf5-1.14.6.tar.gz"
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NETCDF_C_URL="https://downloads.unidata.ucar.edu/netcdf-c/4.10.0/netcdf-c-4.10.0.tar.gz"
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NETCDF_FORTRAN_URL="https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.2.tar.gz"
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IOAPI_URL="https://www.cmascenter.org/ioapi/download/ioapi-3.2.tar.gz"
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WRF_URL="https://github.com/wrf-model/WRF/releases/download/v4.6.0/v4.6.0.tar.gz"
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WPS_URL="https://github.com/wrf-model/WPS/archive/refs/tags/v4.6.0.tar.gz"
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SRC_DIR="/opt/src"
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mkdir -p ${SRC_DIR}
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# -------------------------------------------------
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# Package list (name + URL)
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# -------------------------------------------------
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packages=(
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"openmpi:${OPENMPI_URL}"
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"hdf5:${HDF5_URL}"
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"netcdf-c:${NETCDF_C_URL}"
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"netcdf-fortran:${NETCDF_FORTRAN_URL}"
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"ioapi:${IOAPI_URL}"
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"wrf:${WRF_URL}"
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"wps:${WPS_URL}"
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)
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# -------------------------------------------------
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# Download loop
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# -------------------------------------------------
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for pkg in "${packages[@]}"; do
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NAME="${pkg%%:*}"
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URL="${pkg#*:}"
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echo "Downloading ${NAME}..."
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mkdir -p ${SRC_DIR}/${NAME}
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cd ${SRC_DIR}/${NAME}
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wget ${URL}
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done
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%post
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export HPC_PATH=/opt/hpc
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export MODEL_PATH=/opt/models
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export MPI_HOME=$HPC_PATH/mpi
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export HDF5=$HPC_PATH/hdf5
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export NETCDF=$HPC_PATH/netcdf
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export IOAPI=$HPC_PATH/ioapi
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export PATH=$MPI_HOME/bin:$NETCDF/bin:$PATH
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export LD_LIBRARY_PATH=$MPI_HOME/lib:$HDF5/lib:$NETCDF/lib:$LD_LIBRARY_PATH
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# -------------------------------------------------
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# Build HDF5 (parallel)
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# -------------------------------------------------
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cd /opt/src
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tar -xzf hdf5-1.14.6.tar.gz
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cd hdf5-1.14.6
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CC=mpicc FC=mpif90 ./configure --prefix=$HDF5 --enable-parallel --enable-fortran
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make -j$(nproc)
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make install
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# -------------------------------------------------
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# Build NetCDF-C
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# -------------------------------------------------
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cd /opt/src
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export CC=/opt/hpc/mpi/bin/mpicc
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export CXX=/opt/hpc/mpi/bin/mpicxx
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export CPPFLAGS="-I/opt/hpc/hdf5/include"
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export LDFLAGS="-L/opt/hpc/hdf5/lib"
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export LD_LIBRARY_PATH=/opt/hpc/hdf5/lib:$LD_LIBRARY_PATH
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tar -xzf netcdf-c-4.10.0.tar.gz
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cd netcdf-c-4.10.0
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./configure --prefix=/opt/hpc/netcdf --enable-parallel-tests
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make -j$(nproc)
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make install
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# -------------------------------------------------
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# Build NetCDF-Fortran
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# -------------------------------------------------
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cd /opt/src
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tar -xzf v4.6.2.tar.gz
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cd netcdf-fortran-4.6.2
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CPPFLAGS="-I$NETCDF/include" \
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LDFLAGS="-L$NETCDF/lib" \
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./configure --prefix=$NETCDF --enable-large-files
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make -j$(nproc)
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make install
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# -------------------------------------------------
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# Build OpenMPI
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# -------------------------------------------------
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cd /opt/src
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tar -xzf openmpi-4.1.6.tar.gz
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cd openmpi-4.1.6
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./configure --prefix=$MPI_HOME
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make -j$(nproc)
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make install
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# -------------------------------------------------
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# Install WRF
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# -------------------------------------------------
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cd /opt/src
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tar -xzf v4.6.0.tar.gz
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mv WRFV4.6.0 /opt/models/wrf
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cd /opt/models/wrf
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printf "34\n1\n" | ./configure
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ulimit -s unlimited
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./compile em_real -j $(nproc) 2>&1 | tee compile.log || true
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ls -lh main || true
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ls -lh run || true
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# -------------------------------------------------
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# Install WPS
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# -------------------------------------------------
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cd /opt/src
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wget https://github.com/wrf-model/WPS/archive/refs/tags/v4.6.0.tar.gz
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# Extract WPS source
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tar -xzf v4.6.0.tar.gz
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mv WPS-4.6.0 /opt/models/wps
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cd /opt/models/wps
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# Tell WPS where WRF is installed
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export WRF_DIR=/opt/models/wrf
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# Configure automatically (choose Linux + gfortran)
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printf "1\n" | ./configure
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# Compile WPS
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./compile 2>&1 | tee compile.log || true
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# Verify binaries
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ls -lh geogrid/src/geogrid.exe || true
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ls -lh ungrib/src/ungrib.exe || true
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ls -lh metgrid/src/metgrid.exe || true
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# -------------------------
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# Install I/O API
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# -------------------------
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git clone https://github.com/cjcoats/ioapi-3.2.git
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cd ioapi-3.2
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export FC=gfortran
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export CC=gcc
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export NETCDF=/usr
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# Configure (Linux2_x86_64gfort is typical)
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make config
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# Choose: Linux2_x86_64gfort
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make -j$(nproc)
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echo "export IOAPI=/opt/ioapi-3.2" >> /environment
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# -------------------------
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# Install CMAQ
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# -------------------------
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cd /opt
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git clone https://github.com/USEPA/CMAQ.git
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cd CMAQ
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# Checkout stable release (optional)
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# git checkout 5.3.3
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echo "export CMAQ_HOME=/opt/CMAQ" >> /environment
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# CMAQ build scripts expect tcsh
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echo "CMAQ installed. Build manually via bldit scripts." > /opt/README
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