#!/bin/sh
#$ -N WRF
#$ -pe p28*full 28
#$ -cwd

cd /home/user/input_dir

module load WRF/3.8.1-openmpi-intel

mpirun -np $NSLOTS $FLAGS wrf.exe

mkdir dependencies
cd dependencies/

wget https://support.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.10.5.tar.gz
export CC=mpicc
export CXX=mpic++
export FC=mpif90
export F90=mpif90
tar xzvf hdf5-1.10.5.tar.gz
cd hdf5-1.10.5
./configure --prefix=/apps/WRF/dependencies/ --enable-parallel --enable-shared --enable-fortran
make -j 8 install

wget http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/pnetcdf-1.12.0.tar.gz
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif90
export F90=mpif90
export OMPI_MPICC=icc
export OMPI_MPICXX=icpc
export OMPI_MPIFC=ifort
export OMPI_MPIF77=ifort
export OMPI_MPIF90=ifort
export CFLAGS="-g -O2 -fPIC"
export CXXFLAGS="-g -O2 -fPIC"
export FFLAGS="-g -fPIC"
export FCFLAGS="-g -fPIC"
export FLDFLAGS="-fPIC"
export F90LDFLAGS="-fPIC"
export LDFLAGS="-fPIC"
tar xzvf pnetcdf-1.12.0.tar.gz
cd pnetcdf-1.12.0
./configure --prefix=/apps/WRF/dependencies/ --enable-fortran --enable-large-file-test
make -j 8 install

wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.2.tar.gz
HDF5=/apps/WRF/dependencies
PNET=/apps/WRF/dependencies/export 
CPPFLAGS="-I$HDF5/include -I$PNET/include"
export CFLAGS="-I$HDF5/include -I$PNET/include"
export CXXFLAGS="-I$HDF5/include -I$PNET/include"
export FCFLAGS="-I$HDF5/include -I$PNET/include"
export FFLAGS="-I$HDF5/include -I$PNET/include"
export LDFLAGS="-I$HDF5/include -I$PNET/include -L$PNET/lib -L$HDF5/lib"
export WRFIO_NCD_LARGE_FILE_SUPPORT=1
tar xzvf netcdf-c-4.7.2.tar.gz
cd netcdf-c-4.7.2
./configure --prefix=/apps/WRF/dependencies/ --disable-static --enable-shared --with-pic --enable-parallel-tests -enable-pnetcdf --enable-largefile
make
make install

wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.2.tar.gz
NCDIR=/apps/WRF/dependencies
export LD_LIBRARY_PATH=${NCDIR}/lib:${LD_LIBRARY_PATH}
export CPPFLAGS="-I$HDF5/include -I$NCDIR/include"
export CFLAGS="-I$HDF5/include -I$NCDIR/include"
export CXXFLAGS="-I$HDF5/include -I$NCDIR/include"
export FCFLAGS="-I$HDF5/include -I$NCDIR/include"
export FFLAGS="-I$HDF5/include -I$NCDIR/include"
export LDFLAGS="-I$HDF5/include -I$NCDIR/include -L$NCDIR/lib"
tar xzvf netcdf-fortran-4.5.2.tar.gz 
cd netcdf-fortran-4.5.2
./configure --prefix=$NCDIR --disable-static --enable-shared --with-pic --enable-parallel-tests --enable-large-file-tests --enable-largefile
make
make install

#Download
wget http://www2.mmm.ucar.edu/wrf/src/WRFV3.8.1.TAR.gz
tar -xvzf WRFV3.8.1.TAR.gz
mv WRFV3/* .
rm -rf WRFV3

#install WRF-a
export PHDF5=/apps/WRF/dependencies/
export NETCDF=/apps/WRF/dependencies/
export PNETCDF=/apps/WRF/dependencies/
./clean -a
./configure (#67)
vi configure.wrf (-openmp u -qopenmp)
./compile -j 8 wrf