wrf_install

#!/bin/bash
#########################################################
#		      WRF Install Script     			        #
# This Script was based on the framework provided by    #
# https://github.com/bakamotokatas/WRF-Install-Script,  #
# rewritten by uho-33.                                  #
# To execute this script "bash wrf_install"	            #
#########################################################
type="ARW"
#########################################################
#     WRF and WPS compile configure                     #
#########################################################
# In default, this script will choose 'dmpar' mode of WRF and basic type of nesting. 
# For WPS, this script will choose 'serial' mode in defult.
# For more information, see https://www2.mmm.ucar.edu/wrf/OnLineTutorial/Compile/wrf_compile2.php 
# and https://www2.mmm.ucar.edu/wrf/OnLineTutorial/Compile/wps_compile2.php.
# If you have specific requirements, change the value below:

WRF_config1=34 # WRF mode for compiling in parallel
WRF_config2=1 # WRF type of nesting
WPS_config=1 # WPS mode

##########################################################
if [ -n "$1" ]; then
    if [ "$1" = "-chem" ]; then
        type="Chem"
    elif [ "$1" = "-arw" ]; then
        type="ARW"
    elif [ "$1" = "-hydro" ]; then
        type="Hydro"
    else
        echo "Unrecognized option, please run as"
        echo "For WRF-ARW \"bash WRF${WRFversion}_Install.bash -arw\""
        echo "For WRF-Chem \"bash WRF${WRFversion}_Install.bash -chem\""
	echo "For WRF-Hydro \"bash WRF${WRFversion}_Install.bash -hydro\""
        exit
    fi
fi
echo "############################################################"
echo "Welcome! This Script will install the WRF${WRFversion}-${type}"
echo "Installation may take several hours and it takes 52 GB storage. Be sure that you have enough time and storage."
echo "Please run this script in the place where you want to install WRF and WPS."
echo "############################################################"
#########################################################
#	Controls					                        #
#########################################################

if [ "$EUID" -eq 0 ]
  then echo "ERROR: Running this script as root or sudo, is not suggested"
  exit
fi
osbit=$(uname -m)
if [ "$osbit" = "x86_64" ]; then
        echo "64 bit operating system is used"
else
        echo "Sorry! This script was written for 64 bit operating systems."
exit
fi
local_language=$(locale | grep LANG | grep tr_TR)
if [ -n "$local_language" ]; then
 echo "Merhaba, WRF modelinin kodundaki hatadan dolayı, WRF kurulumu işletim sistemi dili Türkçe olduğunda, Türkçedeki i ve ı harflerinin farklı olması sebebiyle hata vermektedir. Lütfen işletim sisteminizin dilini başka bir dile çevirip yeniden çalıştırınız. Kurulum bittikten sonra işletim sistemi dilini tekrar Türkçe'ye çevirebilirsiniz."
 exit
fi
wget_path=$(which wget)
if [ -z "$wget_path" ]; then
    echo "ERROR: Can not find wget. Please install it, then try again."
    exit 1
fi

csh_status=$(which csh)
if [ -z "$csh_status" ]; then
 echo "ERROR: Can not find csh. Please install it, then try again."
 exit 1
fi
#########################################################
#   Test and install conda                              #
#########################################################
# Ensure input is not empty
get_non_empty_input() {
    local input=""
    while [ -z "$input" ]; do
        read -p "$1" -e input
    done
    echo "$input"
}

check_input() {
    local input_var_name=$1
    local input_value
    input_value=$(eval echo \$${input_var_name})
    if [ "$input_value" != "n" ] && [ "$input_value" != "y" ]; then
        while [ "$input_value" != "n" ] && [ "$input_value" != "y" ]; do
            echo "Unrecognizable input, please enter again:"
            read input_value
        done
        eval "$input_var_name=\"$input_value\""
    fi
}


# Check whether conda exists
eval "$(cat ~/.bashrc | tail -n +10)"
conda_status=$(which conda)

# Set conda path
if [ -n "$conda_status" ]; then
    echo "Found conda in $(which conda). It will be used to install packages."
    env_exist=$(conda env list | grep '^WRF')
    echo "In default, necessary package will install in environment 'WRF'"
    if [ -n "$env_exist" ]; then
        env_status=$(get_non_empty_input "The environment 'WRF' has exited. Do you want to install in it? [y/n] ")
        if [ "$env_status" = "y" ]; then
            env_name=WRF
        fi
    else 
        env_status=$(get_non_empty_input "Do you want to use this name? [y/n] ")
        check_input env_status
        if [ "$env_status" = "y" ]; then
            env_name=WRF
        fi
    fi
else
    conda_loc_status=$(get_non_empty_input "Conda is not installed. In default, it will be installed in ${HOME}/miniconda3. [y/n] ")
    check_input conda_loc_status
    if [ "$conda_loc_status" = "n" ]; then
        while [ "$conda_loc_status" = "n" ]; do
            conda_path=$(get_non_empty_input "Please enter the path where the Miniconda will be installed: ")
            conda_path=$(eval echo "$conda_path/miniconda3")
            conda_loc_status=$(get_non_empty_input "Miniconda will be installed in ${conda_path}. [y/n] ")
            check_input conda_loc_status
        done
    elif [ "$conda_loc_status" = "y" ]; then
        conda_path=$(eval echo "${HOME}/miniconda3")
    fi
    env_exist=""
    echo "In default, necessary package will install in environment 'WRF'."
    env_status=$(get_non_empty_input "Do you want to use this name? [y/n] ")
    check_input env_status
    if [ "$env_status" = "y" ]; then
        env_name=WRF
    fi
fi

# Set environment name
if [ "$env_status" = "n" ]; then
    while [ "$env_status" = "n" ]; do
        env_name=$(get_non_empty_input "Please enter your environment's name: ")
        env_status=$(get_non_empty_input "Your environment's name is ${env_name}. [y/n] ")
        check_input env_status
        if [ -n "$conda_status" ]; then
            env_exist=$(conda env list | grep ^${env_name})
            if [ -n "$env_exist" ]; then
                env_status=$(get_non_empty_input "The environment has exited. Do you want to install in it? [y/n] ")
                check_input env_status
                if [ "$env_status" = "y" ]; then
                    conda activate $env_name
                fi
            fi
        fi
    done
fi

# Install conda
if [ -z "$conda_status" ]; then
    mkdir -p $conda_path
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $conda_path/miniconda.sh
    if [ $? -ne 0 ]; then
        echo "Failed to download Miniconda. Exiting the script."
        exit 1
    fi
    bash $conda_path/miniconda.sh -b -u -p $conda_path
    rm -rf $conda_path/miniconda.sh
    $conda_path/bin/conda init bash
    eval "$(cat ~/.bashrc | tail -n +10)"
    conda_status=$(which conda)
    if [ -z "$conda_status" ]; then
        echo "failed to install conda. Please try again or install matually."
        exit 1
    else
        echo "Successfully install Miniconda!"
    fi
fi


#########################################################
#   Installing necessary packages                       #
#########################################################

# By Conda #
######################

if [ "$type" = "Chem" ]; then
 extra_packages="flex bison"
fi

###
packagelist="git make cmake gfortran gcc=12.2.0 m4 curl perl libpng netcdf4 libnetcdf netcdf-fortran jasper=1.900.1 zlib mpich ${extra_packages}"
package4checks="git make cmake gfortran gcc m4 curl perl libpng netcdf4 libnetcdf netcdf-fortran jasper zlib mpich ${extra_packages}"
packagesnotinstalled=no

if [ -z "$env_exist" ]; then
    conda create -n $env_name $packagelist -c conda-forge -y
    conda activate $env_name
else
    conda activate ${env_name}
    for packagecheck in $package4checks; do
    packagechecked=$(conda list | grep -w $packagecheck)
    if [ -z "$packagechecked" ]; then
        packagesnotinstalled=yes
        break
    fi
    done
    if [ "$packagesnotinstalled" = "yes" ]; then
        conda install $packagelist -c conda-forge -y
    fi
fi

packagesnotinstalled="no"

for packagecheck in $package4checks; do
    packagechecked=$(conda list | grep -w $packagecheck)
    if [ -z "$packagechecked" ]; then
        echo "$packagecheck not installed"
        packagesnotinstalled=yes
    fi
done

if [ "$packagesnotinstalled" = "yes" ]; then
    echo "Some packages were not installed, please install the missing packages and re-run the script."
    exit 1
fi
echo "All required packages are installed."
#########################################
echo "" >> ~/.bashrc
bashrc_exports=("#WRF Variables" "export PATH=${MPICH_DIR}/bin:$PATH" "export CC=gcc" "export CXX=g++" "export FC=gfortran" "export FCFLAGS=-m64" "export F77=gfortran" "export FFLAGS=-m64"
		"export NETCDF=${CONDA_PREFIX}" "export HDF5=${CONDA_PREFIX}" "export LDFLAGS=-L${CONDA_PREFIX}/lib"
		"export CPPFLAGS=-I${CONDA_PREFIX}/include" "export MPICH_DIR=${CONDA_PREFIX}" "export LD_LIBRARY_PATH=${MPICH_DIR}/lib:${CONDA_PREFIX}/lib" "export MPI_LIB=${MPICH_DIR}/lib" "export JASPERLIB=${CONDA_PREFIX}/lib" "export JASPERINC=${CONDA_PREFIX}/include")
for bashrc_export in "${bashrc_exports[@]}" ; do
[[ -z $(grep "${bashrc_export}" ~/.bashrc) ]] && echo "${bashrc_export}" >> ~/.bashrc
done
export CC=gcc
export CXX=g++
export FC=gfortran
export FCFLAGS=-m64
export F77=gfortran
export FFLAGS=-m64
export NETCDF=${CONDA_PREFIX}
export HDF5=${CONDA_PREFIX}
export LDFLAGS=-L${CONDA_PREFIX}/lib
export CPPFLAGS=-I${CONDA_PREFIX}/include
export LD_LIBRARY_PATH=${MPICH_DIR}/lib:${CONDA_PREFIX}/lib:$LD_LIBRARY_PATH
export MPICH_DIR=${CONDA_PREFIX}
export MPI_LIB=-L${MPICH_DIR}/lib
export MPI_INCLUDE_DIR=${MPICH_DIR}/include
export JASPERLIB=${CONDA_PREFIX}/lib
export JASPERINC=${CONDA_PREFIX}/include
if [ "$type" = "Chem" ]; then
[[ -z $(grep "export FLEX_LIB_DIR=${CONDA_PREFIX}/lib" ~/.bashrc) ]] && echo "export FLEX_LIB_DIR=${CONDA_PREFIX}/lib" >> ~/.bashrc
[[ -z $(grep "export YACC='yacc -d'" ~/.bashrc) ]] && echo "export YACC='yacc -d'" >> ~/.bashrc
export FLEX_LIB_DIR=${CONDA_PREFIX}/lib
export YACC='yacc -d'
fi
#########################################
#	WRF Installation		            #
#########################################
DIR=$(pwd)
skip_wrf_status="n"
if [ -d "WRF" ]; then
    skip_wrf_status=$(get_non_empty_input "WARNING: WRF has existed. Do you want to skip install it? [y/n] ")
    check_input skip_wrf_status
fi  
if [ "$skip_wrf_status" = "n" ]; then
    install_WRF_by_prec_status="n"
    [ -d "WRF" ] && install_WRF_by_prec_status=$(get_non_empty_input "Do you want to install using the pre-cloned repository? [y/n] ")
    if [ "$install_WRF_by_prec_status" = "n" ]; then
        [ -d "WRF" ] && mv WRF WRF-old
        git clone --recurse-submodules https://github.com/wrf-model/WRF
        # Ensure download successfully
        if [ $? -ne 0 ]; then
            echo "Failed to clone the repository. Exiting the script."
            exit 1
        fi
    fi

    if [ "$type" = "Hydro" ]; then
        export WRF_HYDRO=1
        mkdir Build_WRF
        cd Build_WRF/packages
        [ -f "v5.2.0.tar.gz" ] && mv v5.2.0.tar.gz v5.2.0.tar.gz-old
        wget https://github.com/NCAR/wrf_hydro_nwm_public/archive/refs/tags/v5.2.0.tar.gz -O v5.2.0.tar.gz
        tar -zxvf v5.2.0.tar.gz
        /bin/cp -rf wrf_hydro_nwm_public-5.2.0/trunk/NDHMS/* $DIR/WRF/hydro/
        rm v5.2.0.tar.gz
        rm -r wrf_hydro_nwm_public-5.2.0
        cd $DIR
    fi
    cd WRF
    ./clean -a
    if [ "$type" = "Chem" ]; then
    export WRF_CHEM=1
    export WRF_KPP=1
    fi

    ( echo ${WRF_config1} ; echo ${WRF_config2} ) | ./configure
    sed -i 's#-L/usr/lib -lnetcdff -lnetcdf#-L${NETCDF}/lib -lnetcdff -lnetcdf#g' configure.wrf
    gfortversion=$(gfortran -dumpversion | cut -d '.' -f 1)
    if [ "$gfortversion" -lt 8 ] && [ "$gfortversion" -ge 6 ]; then
    sed -i '/-DBUILD_RRTMG_FAST=1/d' configure.wrf
    fi

    logsave log.compile ./compile em_real

    if [ -n "$(grep "Problems building executables, look for errors in the build log" log.compile)" ]; then
            echo "Sorry, There were some errors while installing WRF."
            echo "Please create new issue for the problem, https://github.com/uho-33/script-for-instal-WRF/issues"
            exit
    fi
    cd ..
fi
# [ -d "WRF-${WRFversion}-${type}" ] && mv WRF-${WRFversion}-${type} WRF-${WRFversion}-${type}-old
# mv WRFV${WRFversion} WRF-${WRFversion}-${type}
#########################################
#	WPS Installation		            #
#########################################
skip_wps_status="n"
if [ -d "WPS" ]; then
    skip_wps_status=$(get_non_empty_input "WARNING: WPS has existed. Do you want to skip install it? [y/n] ")
    check_input skip_wps_status
fi  
if [ "$skip_wps_status" = "n" ]; then
    install_WPS_by_prec_status="n"
    [ -d "WPS" ] && install_WPS_by_prec_status=$(get_non_empty_input "Do you want to install using the pre-cloned repository? [y/n] ")
    if [ "$install_WRF_by_prec_status" = "n" ]; then
        git clone https://github.com/wrf-model/WPS
        if [ $? -ne 0 ]; then
            echo "Failed to clone the repository. Exiting the script."
            exit 1
        fi
    fi
    cd WPS
    ./clean -a
    sed -i '163s/.*/    NETCDFF="-lnetcdff"/' configure
    echo ${WPS_config} | ./configure
    logsave log.compile ./compile
    sed -i "s# geog_data_path.*# geog_data_path = '../WPS_GEOG/'#" namelist.wps
    cd ..
fi
#########################################
#	Opening Geog Data Files 	#
#########################################
if [ -d "WPS_GEOG" ]; then
  echo "WRF and WPS are installed successfully"
  echo "Directory WPS_GEOG is already exists."
  echo "Do you want WPS_GEOG files to be redownloaded and reexracted?"
  while [ -z "$GEOG_validation" ]; do
    GEOG_validation=$(get_non_empty_input "please enter [y/n]")
    if [ ${GEOG_validation} = "y" ]; then
        wget https://www2.mmm.ucar.edu/wrf/src/wps_files/geog_high_res_mandatory.tar.gz -O geog_high_res_mandatory.tar.gz
        tar -zxvf geog_high_res_mandatory.tar.gz
    elif [ ${GEOG_validation} = "n" ]; then
        echo "You can download it later from http://www2.mmm.ucar.edu/wrf/src/wps_files/geog_high_res_mandatory.tar.gz and extract it"
    else
        echo "Unrecognizable input, please enter again."
        GEOG_validation=""
    fi
  done
else
wget https://www2.mmm.ucar.edu/wrf/src/wps_files/geog_high_res_mandatory.tar.gz -O geog_high_res_mandatory.tar.gz
tar -zxvf geog_high_res_mandatory.tar.gz
fi
if [ "$type" = "Chem" ]; then
 cd WPS_GEOG
 Chem_Geog="modis_landuse_21class_30s soiltype_top_2m soiltype_bot_2m albedo_ncep maxsnowalb erod clayfrac_5m sandfrac_5m"
 for i in ${Chem_Geog}; do
  if [ ! -d $i ]; then
   echo $i
   wget https://www2.mmm.ucar.edu/wrf/src/wps_files/${i}.tar.bz2 -O ${i}.tar.bz2
   tar -xvf ${i}.tar.bz2
   rm ${i}.tar.bz2
  fi
 done
 cd ..
fi
#######################################
#       PREP_CHEM_SRC                 #
#######################################
if [ "$type" = "Chem" ]; then
 echo "Do you want the PREP-CHEM-SRC program to be installed? PREP-CHEM-SRC is a widely used emission preparation program for WRF-Chem."
 echo "please type yes or no"
 read prep_chem_validation
  if [ ${prep_chem_validation} = "yes" ]; then
  echo "firstly starting to compile convert_emiss.exe. convert_emiss.exe is needed for convert emissions which are created from PREP-CHEM-SRC." 
  cd WRF-${WRFversion}-${type}
  logsave convert_emi.log ./compile emi_conv
  cd ..
  echo "Compilation of convert_emiss.exe is finished, now PREP-CHEM-SRC download and compilation has started."
  [ -d "PREP-CHEM-SRC-1.5" ] && mv PREP-CHEM-SRC-1.5 PREP-CHEM-SRC-1.5-old
  [ -f "prep_chem_sources_v1.5_24aug2015.tar.gz" ] && mv prep_chem_sources_v1.5_24aug2015.tar.gz prep_chem_sources_v1.5_24aug2015.tar.gz-old
  wget ftp://aftp.fsl.noaa.gov/divisions/taq/global_emissions/prep_chem_sources_v1.5_24aug2015.tar.gz -O prep_chem_sources_v1.5_24aug2015.tar.gz
  tar -zxvf prep_chem_sources_v1.5_24aug2015.tar.gz
  cd PREP-CHEM-SRC-1.5/bin/build
  sed -i "s#NETCDF=.*#NETCDF=/usr#" include.mk.gfortran.wrf
  sed -i 's#-L$(NETCDF)/lib#-L/usr/lib/x86_64-linux-gnu#' include.mk.gfortran.wrf
  sed -i "s#HDF5=.*#HDF5=/usr/lib/x86_64-linux-gnu/hdf5/serial#" include.mk.gfortran.wrf
  sed -i "s#HDF5_INC=.*#HDF5_INC=-I/usr/include/hdf5/serial#" include.mk.gfortran.wrf
  sed -i 's#-L$(HDF5)/lib#-L/usr/lib/x86_64-linux-gnu/hdf5/serial#' include.mk.gfortran.wrf
  gfortversion=$(gfortran -dumpversion | cut -d '.' -f 1)
  if [ "$gfortversion" -ge 10 ]; then
  sed -i 's#F_OPTS=.*#F_OPTS=  -Xpreprocessor -D$(CHEM) -O2 -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch#' include.mk.gfortran.wrf
  fi
  sed -i "s#-L/scratchin/grupos/catt-brams/shared/libs/gfortran/zlib-1.2.8/lib#-L/usr/lib#" include.mk.gfortran.wrf
  sed -i "842s#.*#    'ENERGY     ',\&#" ../../src/edgar_emissions.f90
  sed -i "843s#.*#    'INDUSTRY   ',\&#" ../../src/edgar_emissions.f90
  sed -i "845s#.*#    'TRANSPORT  '/)#" ../../src/edgar_emissions.f90
  make OPT=gfortran.wrf CHEM=RADM_WRF_FIM
  cd ..
  mkdir datain
  cd datain
  wget ftp://aftp.fsl.noaa.gov/divisions/taq/global_emissions/global_emissions_v3_24aug2015.tar.gz -O global_emissions_v3_24aug2015.tar.gz
  tar -zxvf global_emissions_v3_24aug2015.tar.gz
  mv Global_emissions_v3/* .
  rm -r Global_emissions_v3
  mv Emission_data/ EMISSION_DATA
  mv surface_data/ SURFACE_DATA
  cd ../../..
  echo "PREP-CHEM-SRC compilation has finished."
  fi
fi
##########################################################
#	End						#
##########################################################
echo "Installation has completed"
exec bash
exit