Compile & Install WRF4.1.2 On CentOS 8.2

2020-06-08 | 阅读：次

Weather Research and Forcast Model

Install "GNU Tools" and "gfortran"

run commands in bash terminal

dnf -y install gcc  
dnf -y install cpp gcc-c++  
dnf -y install gcc-gfortran  
dnf -y install unzip bzip2 time nfs-utils perl tcsh wget git m4 mlocate.x86_64 libX11-devel.x86_64 libXext-devel.x86_64 libXrender-devel.x86_64 fontconfig-devel.x86_64 curl-devel cmake cairo-devel pixman-devel bzip2-devel byacc flex libXmu-devel libXt-devel libXaw libXaw-devel  

Directory Structure

Build_WRF       (Main Directory)  
|--LIBRARIES    (Library Directory)  
|--geos         (Geography Data and mount to /data/geos)  
|--DATA         (Directory for Real-time Data)  
|--src          (Directory for Source Code)  

Notes:

You can create folder(“Build_WRF”) wherever you want as long as you are authorized

In this tutotial, the folder(“Build_WRF”) was build in /root/

Tests:

Make a new Directory as “tests” and download “Fortran_C_tests.tar” into it. Follow the online tutotial to finish it.(https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php)

cd /root/Build_WRF/src  
mkdir TESTS  
cd TESTS  
wget http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_tests.tar --no-check-certificate  
tar -xf Fortran_C_tests.tar  

Test #1: Fixed Format Fortran Test: TEST_1_fortran_only_fixed.f

gfortran TEST_1_fortran_only_fixed.f  
./a.out  

The following should print out to the screen:

SUCCESS test 1 fortran only fixed format

Test #2: Free Format Fortran: TEST_2_fortran_only_free.f90

gfortran TEST_2_fortran_only_free.f90  
./a.out

The following should print out to the screen:

Assume Fortran 2003: has FLUSH, ALLOCATABLE, derived type, and ISO C Binding  
SUCCESS test 2 fortran only free format  

Test #3: C: TEST_3_c_only.c

gcc TEST_3_c_only.c  
./a.out 

The following should print out to the screen:

SUCCESS test 3 c only

Test #4: Fortran Calling a C Function (our gcc and gfortran have different defaults, so we force both to always use 64 bit [-m64] when combining them): TEST_4_fortran+c_c.c, and TEST_4_fortran+x_f.f90

gcc -c -m64 TEST_4_fortran+c_c.c  
gfortran -c -m64 TEST_4_fortran+c_f.f90  
gfortran -m64 TEST_4_fortran+c_f.o TEST_4_fortran+c_c.o  
./a.out  

The following should print out to the screen:

C function called by Fortran  
Values are xx = 2.00 and ii = 1  
SUCCESS test 4 fortran calling c  

Test #5: csh In the command line, type:

./TEST_csh.csh

The result should be:

SUCCESS csh test

Test #6: perl In the command line, type:

./TEST_perl.pl

The result should be:

SUCCESS perl test

Test #7: sh In the command line, type:

./TEST_sh.sh

The result should be:

SUCCESS sh test

Environments

Set Environments

###DIR  
export DIR=/root/Build_WRF/LIBRARIES  
###MPICH  
export PATH=${DIR}/mpich/bin:$PATH  
export LD_LIBRARY_PATH=${DIR}/mpich/lib:$LD_LIBRARY_PATH  
###HDF5
export HDF5=${DIR}/hdf5  
export PATH=${DIR}/hdf5/bin:$PATH  
export LD_LIBRARY_PATH=${DIR}/hdf5/lib:$LD_LIBRARY_PATH
###NETCDF  
export PATH=${DIR}/netcdf/bin:$PATH  
export NETCDF=${DIR}/netcdf  
export LD_LIBRARY_PATH=${DIR}/netcdf/lib:$LD_LIBRARY_PATH  
###LIBPNG  
export LD_LIBRARY_PATH=${DIR}/libpng/lib:$LD_LIBRARY_PATH  
###JASPER  
export PATH=${DIR}/jasper/bin:$PATH  
export LD_LIBRARY_PATH=${DIR}/jasper/lib:$LD_LIBRARY_PATH  
export JASPERLIB=${DIR}/jasper/lib  
export JASPERINC=${DIR}/jasper/include  
###WRF  
ulimit -s unlimited  
export MALLOC_CHECK_=0  
export WRF_EM_CORE=1  
export WRFIO_NCD_LARGE_FILE_SUPPORT=1  
###WPS  
export WRF_DIR=/root/Build_WRF/src/WRF-4.1.2  

Notes:

Variables export above will write to ~/.bash_profile, remember source .bash_profile after modify it.

If you do this module, please do not any changes about “.bash_profile” file in moudle 4(“4. Dependencies”).

LIBRARIES

cd /root/Build_WRF/src

To locate to “/root/Build_WRF/LIBRARIES” faster, we export a variable as “DIR”:

nano ~/.bash_profile

### DIR  
export DIR=/root/Build_WRF/LIBRARIES  

Update PATH variable

source ~/.bash_profile

MPI

wget https://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz  
tar -xzf mpich-3.3  
cd mpich-3.3  
./configure --prefix=${DIR}/mpich  
make -j2  
make install  
cd ..  

Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### MPICH  
export PATH=${DIR}/mpich/bin:$PATH  
export LD_LIBRARY_PATH=${DIR}/mpich/lib:$LD_LIBRARY_PATH  

Update PATH variable

source ~/.bash_profile

ZLIB

wget https://zlib.net/zlib-1.2.11.tar.gz  
tar -xzf zlib-1.2.11.tar.gz  
cd zlib-1.2.11  
./configure --prefix=${DIR}/zlib  
make -j2  
make install  
cd ..  

HDF5

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz  
tar xzf hdf5-1.10.5.tar.gz  
cd hdf5-1.10.5  
CC=gcc  
FC=gfortran  
CXX=g++  
./configure --with-zlib=${DIR}/zlib --prefix=${DIR}/hdf5 --enable-fortran --enable-fortran2003 --enable-cxx  
make -j2  
make install  
cd ..  

Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### HDF5
export HDF5=${DIR}/hdf5
export PATH=${DIR}/hdf5/bin:$PATH
export LD_LIBRARY_PATH=${DIR}/hdf5/lib:$LD_LIBRARY_PATH

Update PATH variable.

source ~/.bash_profile

PnetCDF

NetCDF-C

export CC=gcc  
export CFLAGS="-fPIC"  
export CPP=cpp  
export CPPFLAGS="-I${DIR}/hdf5/include"  
export LDFLAGS="-L${DIR}/hdf5/lib"  
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.0.tar.gz  
tar xzf netcdf-c-4.7.0.tar.gz  
cd netcdf-c-4.7.0  
./configure --prefix=${DIR}/netcdf  
make -j2  
make install  
cd ..  

NetCDF-Fortran

export LD_LIBRARY_PATH=${NCDIR}/lib:${LD_LIBRARY_PATH}  
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.5.tar.gz  
tar xzf netcdf-fortran-4.4.5.tar.gz  
cd netcdf-fortran-4.4.5  
export CC=gcc  
export F77=gfortran  
export FC=gfortran  
export FCFLAGS="-m64"  
export CPP=cpp  
export CPPFLAGS="-I${DIR}/netcdf/include"  
export LDFLAGS="-L${DIR}/netcdf/lib"  
./configure --prefix=${DIR}/netcdf  
make -j2  
make install  
cd ..  

Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### NETCDF  
export PATH=${DIR}/netcdf/bin:$PATH  
export NETCDF=${DIR}/netcdf  
export LD_LIBRARY_PATH=${DIR}/netcdf/lib:$LD_LIBRARY_PATH  

Update PATH variable.

source ~/.bash_profile

Notes:
Chect whether the file(“netcdf.inc”) exists， do >1. or >2.:

1. ```
  find / -name netcdf.inc
```
the terminal will show the find information of netcdf.inc, like below:
```
  [root@localhost netcdf-fortran-4.4.5]# find / -name netcdf.inc  
  /root/Build_WRF/src/netcdf-fortran-4.4.5/fortran/netcdf.inc  
  /root/Build_WRF/LIBRARIES/netcdf/include/netcdf.inc  
```
If you see “/root/Build_WRF/LIBRARIES/netcdf/include/netcdf.inc”,
this mean “netcdf.inc” has been successfully generated, go to the next install module. Else, retry this module again(begain at “export CC=gcc”).

```
  ls $DIR/netcdf/include/
```

the terminal will show the find information of netcdf.inc, like below:

  [root@localhost netcdf-fortran-4.4.5]# ls $DIR/netcdf/include/  
  netcdf_aux.h     netcdf.h      netcdf_meta.h       netcdf_nc_interfaces.mod  typesizes.mod  
  netcdf_f03.mod   netcdf.inc    netcdf.mod          netcdf_nf_data.mod  
  netcdf_filter.h  netcdf_mem.h  netcdf_nc_data.mod  netcdf_nf_interfaces.mod  

If you see “netcdf.inc”, this mean “netcdf.inc” has been successfully generated, go to the next install module. Else, retry this module again(begain at “export CC=gcc”).

LIBPNG

wget ftp://ftp.simplesystems.org/pub/libpng/png/src/libpng16/libpng-1.6.37.tar.gz  
tar xzf libpng-1.6.37.tar.gz  
cd libpng-1.6.37/  
export CC=gcc  
export F77=gfortran  
export FC=gfortran  
export FCFLAGS="-m64"  
export CPP=cpp  
export CPPFLAGS="-I${DIR}/netcdf/include"  
export LDFLAGS="-L${DIR}/netcdf/lib"  
./configure --prefix=${DIR}/libpng  
make -j2  
make install  
cd ..  

Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### libpng  
export LD_LIBRARY_PATH=${DIR}/libpng/lib:$LD_LIBRARY_PATH  

Update PATH variable.

source ~/.bash_profile

JASPER

wget https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.19.tar.gz  
tar xzf jasper-1.900.19.tar.gz  
cd jasper-1.900.19  
./configure --prefix=${DIR}/jasper  
make -j2  
make install  
cd ..  

Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### jasper  
export PATH=${DIR}/jasper/bin:$PATH  
export LD_LIBRARY_PATH=${DIR}/jasper/lib:$LD_LIBRARY_PATH  

Update PATH variable.

source ~/.bash_profile

Tests

Download this tar file and place it in the TESTS directory, and then “cd” into the TESTS directory:

wget http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_NETCDF_MPI_tests.tar --no-check-certificate  
tar -xf Fortran_C_NETCDF_MPI_tests.tar  

Test #1: Fortran + C + NetCDF

cp ${DIR}/netcdf/include/netcdf.inc .  
gfortran -c 01_fortran+c+netcdf_f.f  
gcc -c 01_fortran+c+netcdf_c.c  
gfortran 01_fortran+c+netcdf_f.o 01_fortran+c+netcdf_c.o -L${NETCDF}/lib -lnetcdff -lnetcdf  
./a.out  

The following should be displayed on your screen:

C function called by Fortran  
Values are xx = 2.00 and ii = 1  
SUCCESS test 1 fortran + c + netcdf  

Test #2: Fortran + C + NetCDF + MPI

cp ${NETCDF}/include/netcdf.inc .  
mpif90 -c 02_fortran+c+netcdf+mpi_f.f  
mpicc -c 02_fortran+c+netcdf+mpi_c.c  
mpif90 02_fortran+c+netcdf+mpi_f.o 02_fortran+c+netcdf+mpi_c.o -L${NETCDF}/lib -lnetcdff -lnetcdf
mpirun ./a.out  

The following should be displayed on your screen:

C function called by Fortran  
Values are xx = 2.00 and ii = 1  
status = 2  
SUCCESS test 2 fortran + c + netcdf + mpi  

Building WRF

wget https://github.com/wrf-model/WRF/archive/v4.1.2.tar.gz  
mv v4.1.2.tar.gz WRFv4.1.2.tar.gz  

Parameters of building WRF. Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### WRF  
ulimit -s unlimited  
export MALLOC_CHECK_=0  
export WRF_EM_CORE=1  
export WRFIO_NCD_LARGE_FILE_SUPPORT=1  

Update PATH variable.

source ~/.bash_profile

tar -xzf WRFv4.1.2.tar.gz  
cd WRF-4.1.2/  

Edit the default config to eneable Jasper. It’s a option, not required. As below:

nano arch/Config.pl

I_really_want_to_output_grib2_from_WRF = "TRUE" ;

Notes: “JASPERLIB” and “JASPERINC” must be set in ~/.bash_profile.
Create PATH variable in file .bash_profile:

nano ~/.bash_profile

export JASPERLIB=${DIR}/jasper/lib  
export JASPERINC=${DIR}/jasper/include  

Update PATH variable.

source ~/.bash_profile

Configure

./configure  
34  
1  

./compile em_real >& log.compile & tail -f log.compile  
ls -lah main/*.exe  

If you see real.exe and wrf.exe then correct. Else check Error in log.compile file.

cd ..

Buinding WPS

wget https://github.com/wrf-model/WPS/archive/v4.1.tar.gz  
tar xvzf v4.1.tar.gz  
cd WPS-4.1  

Setting the directory of WRF installed, Not required. But setting it if you change the name or location of WRF install directory instand of default directory.
Create PATH variable in file .bash_profile:

nano ~/.bash_profile

### WPS  
export WRF_DIR=/root/Build_WRF/src/WRF-4.1.2  

Update PATH variable.

source ~/.bash_profile

Configure

./configure  
3  

Edit configure.wps file
Change DM_FC to mpif90 and Append -lgomp in WRF_LIB.

nano configure.wps

DM_FC = mpif90  
WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \  
          -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \  
          -L$(WRF_DIR)/external/io_int -lwrfio_int \  
          -L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \  
          -L$(NETCDF)/lib -lnetcdff -lnetcdf -lgomp  

./compile >& log.compile & tail -f log.compile  
ls -lah *.exe  

If you see geogrid.exe metgrid.exe and ungrib.exe then correct.
Else check Error in log.compile file.

cd ..

Run a Case

=========================================================
Notes:
This case referenfe from “How to Install WRF Model On CentOS Version 7”.

Create Directory for Geography Data

cd /root/Build_WRF/
wget http://www2.mmm.ucar.edu/wrf/src/wps_files/geog_complete.tar.bz2
tar -xvjf geog_complete.tar.bz2

If above link is invaild, do as below:

wget https://www2.mmm.ucar.edu/wrf/src/wps_files/geog_complete.tar.gz  
wget https://www2.mmm.ucar.edu/wrf/src/wps_files/albedo_modis.tar.bz2  
wget https://www2.mmm.ucar.edu/wrf/src/wps_files/maxsnowalb_modis.tar.bz2  
tar -xzf geog_complete.tar.gz  
tar -xjf albedo_modis.tar.bz2  
tar -xjf maxsnowalb_modis.tar.bz2  
mv albedo_modis geog/  
mv maxsnowalb_modis geog/  

Create directory for Real-time Data

mkdir -p /root/Build_WRF/DATA  
cd /root/Build_WRF/DATA  
wget http://hydro.haii.or.th/tmp/WRF/gfs.t00z.pgrb2.0p50.f000  
wget http://hydro.haii.or.th/tmp/WRF/gfs.t00z.pgrb2.0p50.f006  

Or retrieve Real-time update data from gfs web site

Running WPS

cd /root/Build_WRF/WPS-4.1  
rm namelist.wps  
wget http://hydro.haii.or.th/tmp/WRF/namelist.wps  

Edit namelist.wps section max_dom, start_date, end_date base on Real-time Data. Setting geog_data_path to Geography Data.

nano namelist.wps

&share  
max_dom = 1,  
start_date = '2017-05-17_00:00:00','2006-08-16_12:00:00',  
end_date = '2017-05-17_06:00:00','2006-08-16_12:00:00',  
geog_data_path = '/root/Build_WRF/geog/'

Pay attention to the first colmun of start_date、end_date. make it shape base on max_dom(here is 1).

Create Geography Data

./geogrid.exe  
ls -lah geo_em.d01.nc  

The progress is correct if you see geo_em.d01.nc.

Link Real-time Data top WPS

./link_grib.csh /root/Build_WRF/DATA/gfs.t00z.pgrb2.0p50.f0*

Link Vtable

ln -sf ungrib/Variable_Tables/Vtable.GFS Vtable

Create grib file
```
./ungrib.exe  
ls -lah FILE*  
```

The progress is run success if you see FILE*.

Create met file
```
./metgrid.exe  
ls -lah met_em.*  
```
The progress is run success if you see met_em.*.

Run WRF

cd /root/Build_WRF/WRFV3/test/em_real/

Link met file from WPS to WRF
```
ln -sf /root/Build_WRF/WPS/met_em* .  
```

Edit namelist.input

rm namelist.input  
wget http://hydro.haii.or.th/tmp/WRF/namelist.input  

Edit namelist.input in section run_hours, start_year, start_month, start_day, start_hour, end_year, end_month, end_day, end_hour and num_metgrid_levels.

nano namelist.input

&time_control  
    run_days = 0,  
    run_hours = 6,  
    run_minutes = 0,  
    run_seconds = 0,  
    start_year = 2017, 2000, 2000,  
    start_month = 05, 01, 01,  
    start_day = 17, 24, 24,  
    start_hour = 00, 12, 12,  
    start_minute = 00, 00, 00,  
    start_second = 00, 00, 00,  
    end_year = 2017, 2000, 2000,  
    end_month = 05, 01, 01,  
    end_day = 17, 25, 25,  
    end_hour = 06, 12, 12,  
    end_minute = 00, 00, 00,  
    end_second = 00, 00, 00,  
    interval_seconds = 10800  
&domains  
    time_step = 150,  
    time_step_fract_num = 0,  
    time_step_fract_den = 1,  
    max_dom = 1,  
    e_we = 74, 112, 94,  
    e_sn = 61, 97, 91,  
    e_vert = 30, 30, 30,  
    p_top_requested = 5000,  
    num_metgrid_levels = 32,  

Pay attention to the first colmun of start_date、end_date、et.al. make it shape base on max_dom(here is 1).