WRF 4.1.2 installation with netCDF4, HDF5 in ubuntu 18.04 LTS

install_wrf41.sh

#!/bin/bash
## WRF installation with parallel process.
# Download and install required library and data files for WRF.
# License: LGPL
# Jamal Khan <[email protected]>
# Tested in Ubuntu 18.04 LTS

# basic package managment
sudo apt update
sudo apt upgrade
sudo apt install gcc gfortran g++ libtool automake autoconf make m4 grads default-jre csh

## Directory Listing
export HOME=`cd;pwd`
mkdir $HOME/WRF
cd $HOME/WRF
mkdir Downloads
mkdir Library

## Downloading Libraries
cd Downloads
wget -c https://www.zlib.net/zlib-1.2.13.tar.gz
wget -c https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz
wget -c https://downloads.unidata.ucar.edu/netcdf-c/4.9.0/netcdf-c-4.9.0.tar.gz
wget -c https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.0/netcdf-fortran-4.6.0.tar.gz
wget -c http://www.mpich.org/static/downloads/3.3.1/mpich-3.3.1.tar.gz
wget -c https://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz
wget -c https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip

# Compilers
export DIR=$HOME/WRF/Library
export CC=gcc
export CXX=g++
export FC=gfortran
export F77=gfortran

# zlib
cd $HOME/WRF/Downloads
tar -xvzf zlib-1.2.13.tar.gz
cd zlib-1.2.13/
./configure --prefix=$DIR
make
make install

# hdf5 library for netcdf4 functionality
cd $HOME/WRF/Downloads
tar -xvzf hdf5-1.10.5.tar.gz
cd hdf5-1.10.5
./configure --prefix=$DIR --with-zlib=$DIR --enable-hl --enable-fortran
make check
make install

export HDF5=$DIR
export LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH

## Install NETCDF C Library
cd $HOME/WRF/Downloads
tar -xvzf netcdf-c-4.9.0.tar.gz
cd netcdf-c-4.9.0/
export CPPFLAGS=-I$DIR/include 
export LDFLAGS=-L$DIR/lib
./configure --prefix=$DIR --disable-dap
make check
make install

export PATH=$DIR/bin:$PATH
export NETCDF=$DIR

## NetCDF fortran library
cd $HOME/WRF/Downloads
tar -xvzf netcdf-fortran-4.6.0.tar.gz
cd netcdf-fortran-4.6.0/
export LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH
export CPPFLAGS=-I$DIR/include 
export LDFLAGS=-L$DIR/lib
export LIBS="-lnetcdf -lhdf5_hl -lhdf5 -lz" 
./configure --prefix=$DIR --disable-shared
make check
make install

## MPICH
cd $HOME/WRF/Downloads
tar -xvzf mpich-3.3.1.tar.gz
cd mpich-3.3.1/
./configure --prefix=$DIR
make
make install

export PATH=$DIR/bin:$PATH

# libpng
cd $HOME/WRF/Downloads
export LDFLAGS=-L$DIR/lib
export CPPFLAGS=-I$DIR/include
tar -xvzf libpng-1.6.37.tar.gz
cd libpng-1.6.37/
./configure --prefix=$DIR
make
make install

# JasPer
cd $HOME/WRF/Downloads
unzip jasper-1.900.1.zip
cd jasper-1.900.1/
autoreconf -i
./configure --prefix=$DIR
make
make install
export JASPERLIB=$DIR/lib
export JASPERINC=$DIR/include

############################ WRF 4.1.2 #################################
## WRF v4.1.2
## Downloaded from git tagged releases
########################################################################
cd $HOME/WRF/Downloads
wget -c https://github.com/wrf-model/WRF/archive/v4.1.2.tar.gz
tar -xvzf v4.1.2.tar.gz -C $HOME/WRF
cd $HOME/WRF/WRF-4.1.2
./clean
./configure # 34, 1 for gfortran and distributed memory
./compile em_real

export WRF_DIR=$HOME/WRF/WRF-4.1.2

## WPSV4.1
cd $HOME/WRF/Downloads
wget -c https://github.com/wrf-model/WPS/archive/v4.1.tar.gz
tar -xvzf v4.1.tar.gz -C $HOME/WRF
cd $HOME/WRF/WPS-4.1
./configure #3
./compile

######################## Post-Processing Tools ####################
## ARWpost
cd $HOME/WRF/Downloads
wget -c http://www2.mmm.ucar.edu/wrf/src/ARWpost_V3.tar.gz
tar -xvzf ARWpost_V3.tar.gz -C $HOME/WRF
cd $HOME/WRF/ARWpost
./clean
sed -i -e 's/-lnetcdf/-lnetcdff -lnetcdf/g' $HOME/WRF/ARWpost/src/Makefile
./configure #3
sed -i -e 's/-C -P/-P/g' $HOME/WRF/ARWpost/configure.arwp
./compile

######################## Model Setup Tools ########################
## DomainWizard
cd $HOME/WRF/Downloads
wget -c http://esrl.noaa.gov/gsd/wrfportal/domainwizard/WRFDomainWizard.zip
mkdir $HOME/WRF/WRFDomainWizard
unzip WRFDomainWizard.zip -d $HOME/WRF/WRFDomainWizard
chmod +x $HOME/WRF/WRFDomainWizard/run_DomainWizard

######################## Static Geography Data ####################
# http://www2.mmm.ucar.edu/wrf/users/download/get_sources_wps_geog.html
cd $HOME/WRF/Downloads
wget -c https://www2.mmm.ucar.edu/wrf/src/wps_files/geog_high_res_mandatory.tar.gz
tar -xvzf geog_high_res_mandatory.tar.gz -C $HOME/WRF


## export PATH and LD_LIBRARY_PATH
echo "export PATH=$DIR/bin:$PATH" >> ~/.bashrc
echo "export LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH" >> ~/.bashrc

Hi @wde0924, I am glad that it helped, and thanks for documenting this argument-mismatch issue that was introduced in GCC 9/10.

@ everyone who found this helpful and commented, I thank you too. I am seeing quite a few comments about the problem faced, I am sorry that it did not work for you, and I could not be of help when you commented.

It has been a long time, and is in my to-do list to revise this guide - I should do that at some point. Particularly, there are some extra environment variable (cflags, libs) often needed with the latest version of netcdf-c and netcdf-fortran. I will update that too - hopefully sooner than later.

Cheers!