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WRF 4.1.2 installation with netCDF4, HDF5 in ubuntu 18.04 LTS
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| #!/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:$LD_LIBRARY_PATH" >> ~/.bashrc |
Thank you, @jamal919 for saving my day!!! It worked perfectly for compiling WRFv4.6. =)
The only part that I modified is to allow for mismatched argument when using higher version of gfortran --
According to https://forum.mmm.ucar.edu/threads/how-to-fix-rank-mismatch-between-actual-argument-at-1-and-actual-argument-at-2-scalar-and-rank-1.18391/#post-44568. When using higher levels of gfortran (say 11.3) to compile MPICH and WRF-Chem, it will cause a rank mismatch as shown below:
checking whether gfortran allows mismatched arguments... no
configure: error: The Fortran compiler gfortran will not compile files that call
allowing for mismatched arguments and then re-configure MPICH:
export fallow_argument=-fallow-argument-mismatch
export boz_argument=-fallow-invalid-boz
export FFLAGS="$fallow_argument $boz_argument -m64"
export FCFLAGS="$fallow_argument $boz_argument -m64"
Author
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!
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I followed the same step as suggested by @jamal919 .. and installed the following WRF and WPS versions:
For WRF:
git clone --recurse-submodule https://github.com/wrf-model/WRF.gitFor WPS:
git clone --recurse-submodule https://github.com/wrf-model/WPS.git