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7.5. WRF
Hua Xu edited this page Oct 6, 2023
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Create a Test folder
mkdir TESTS
cd TESTSDownload the test cases and start tests, the output of tests should include SUCCESS
wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_tests.tar
tar -xf Fortran_C_tests.tar
gfortran TEST_1_fortran_only_fixed.f
./a.out
gfortran TEST_2_fortran_only_free.f90
./a.out
gcc TEST_3_c_only.c
./a.out
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
./TEST_csh.csh
./TEST_perl.pl
./TEST_sh.shmkdir Build_WRF
cd Build_WRF
mkdir LIBRARIES
cd LIBRARIESDownload and unzip the required libraries.
- nedcdf-c-4.9.2
wget -c https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz
tar xzvf netcdf-c-4.9.2.tar.gz- hdf5(you can also install the newest version)
wget -c https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.gz
tar xzvf hdf5-1.12.2.tar.gz- zlib(1.2.11)
wget -c https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/zlib-1.2.11.tar.gz
tar xzvf zlib-1.2.11.tar.gz- NETCDF-Fortran(4.6.1)
wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.1/netcdf-fortran-4.6.1.tar.gz
tar xzvf netcdf-fortran-4.6.1.tar.gz- PnetCDF(1.12.3)
wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
tar xzvf pnetcdf-1.12.3.tar.gz- LibPNG
wget -c https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/libpng-1.2.50.tar.gz
tar xzvf libpng-1.2.50.tar.gz- MPICH
module load mpichSet the environment variables
export DIR=/PATH/TO/Build_WRF/LIBRARIES
export CC=gcc
export CXX=g++
export FC=gfortran
export F77=gfortran
module load libxml2- Install the zlib
cd zlib-1.2.11/
./configure --prefix=$DIR
make
make install- Install the hdf5
cd hdf5-1.12.2/
./configure --prefix=$DIR --with-zlib=$DIR --enable-hl --enable-fortran
make check
make install
export HDF5=$DIR
export LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH- Build NETCDF-C
cd netcdf-c-4.9.2
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- Build NetCDF fortran library links with NETCDF-C, after successful installation, netcdf.inc will be ${NETCDF}/include file. For sometimes, it will show C compiler stop working, Please check the environment variable in LIBS="-lnetcdf -lhdf5_hl -lhdf5 -lz", make sure netcdf and hdf5 path in the environment variables.
export LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH
export CPPFLAGS="-I${DIR}/include -I/usr/include"
export LDFLAGS="-L${DIR}/lib -L/usr/lib"
export LIBS="-lnetcdf -lhdf5_hl -lhdf5 -lz"
./configure --prefix=$DIR --disable-shared
make check
make installLibrary Compatibility Tests( the result should show SUCCESS)
mkdir LibTests
cd libTests
wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_NETCDF_MPI_tests.tar
tar -xf Fortran_C_NETCDF_MPI_tests.tar
cp ${NETCDF}/include/netcdf.inc .
gfortran -c 01_fortran+c+netcdf_f.f
gcc -c 01_fortran+c+netcdf_c.c
gfortran 01_fortran+c+netcdf_f.o 01_fortran+c+netcdf_c.o \
-L${NETCDF}/lib -lnetcdff -lnetcdf
./a.out- Install the WRF The adios2 need to be installed with c-blocs, mpi, and hdf5.
cd ..
wget https://github.com/wrf-model/WRF/releases/download/v4.5.1/v4.5.1.tar.gz
tar xvzf v4.5.1.tar.gz
cd WRFV4.5.1
module load adios2/2.9.1-6fh7kh
export ADIOS2="/mnt/repo/software/spack/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/adios2-2.9.1-6fh7kh2v3tombadg56kmop72sjhf23dg"
export HDF5=$DIR
export NETCDF=$DIR
./configurePlease select from among the following Linux x86_64 options: Choose 34(dmpar), Compile for nesting? choose 1. If configure is done, you can see a configure.wrf file in the folder.
./compile em_real
#./compile em_real >& log.compile
export WRF_DIR=PATH/to/WRFV4.5.1You can see the following information shows the installation is successful.
---> Executables successfully built <---
-rwxrwxr-x 1 hxu40 hxu40 51667784 Sep 15 12:21 main/ndown.exe
-rwxrwxr-x 1 hxu40 hxu40 51794800 Sep 15 12:21 main/real.exe
-rwxrwxr-x 1 hxu40 hxu40 50930720 Sep 15 12:21 main/tc.exe
-rwxrwxr-x 1 hxu40 hxu40 59885752 Sep 15 12:21 main/wrf.exe
========================================================================== To check check whether it was successful
ls -ls main/*.exeIf you compiled a real case, you should see:
wrf.exe (model executable)
real.exe (real data initialization)
ndown.exe (one-way nesting)
tc.exe (for tc bogusing--serial only)TODO
Download and install required library
cd $DIR
wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/libpng-1.2.50.tar.gz
tar xzvf libpng-1.2.50.tar.gz
cd libpng-1.2.50
./configure --prefix=$DIR/grib2
make
make install
cd ..
wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/jasper-1.900.1.tar.gz
tar xzvf jasper-1.900.1.tar.gz
cd jasper-1.900.1
./configure --prefix=$DIR/grib2
make
make install
cd ..
cd $DIR
cd zlib_1.22.1
./configure --prefix=$DIR/grib2
make
make install
export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/includeDownload WPS and install
#go to WRF folder
mkdir WPS
wget https://github.com/wrf-model/WPS/archive/v4.5.tar.gz
tar -xvzf v4.5.tar.gz
cd WPS-4.5
export JASPERLIB=$DIR/grib2/lib
export JASPERINC=$DIR/grib2/include
./configure --build-grib2-libs #Option 3 for gfortran and distributed memory
./compileIF you see this message after ./configure, please ignore
Testing for NetCDF, C and Fortran compiler
This installation NetCDF is 64-bit
C compiler is 64-bit
Fortran compiler is 64-bit
Your versions of Fortran and NETCDF are not consistent.
```bash
If the compile successfully,
there should be 3 executables in the WPS top-level directory, that are linked to their corresponding src/ directories:
```bash
geogrid.exe -> geogrid/src/geogrid.exe
ungrib.exe -> ungrib/src/ungrib.exe
metgrid.exe -> metgrid/src/metgrid.exe- Download the benchmark dataset, here is the website for dataset: https://www2.mmm.ucar.edu/wrf/users/benchmark/v44/benchdata_v44.html Choose one of them for testing. Unzip the file. copy the wrfbdy_d01, wrfinput_d01 and namelist.input file to WRF/test/em_real file.
change the namelist.input file
The ADIOS2 I/O option for history and/or restart file is enabled by setting one of the following:
io_form_history = 14
io_form_restart = 14
frames_per_outfile = 1000000,
history_outname = '/Path/to/output/wrfout_d<domain>_<date>',
Do not change the wrfout_d<domain>_<date>
Run wrf with adios2 add adios2.xml file in the same folder(wrf/test/em_real) Here is the example of adios2.xml file:
<?xml version="1.0"?>
<adios-config>
<!-- <io name="wrfout_d01_2018-06-17_00:00:00"> -->
<io name="wrfout_d01_2019-11-26_12:00:00">
<!-- <engine type="BP4"> -->
<!-- </engine> -->
<engine type="BP4">
<parameter key="RendezvousReaderCount" value="0"/>
<parameter key="QueueLimit" value="1"/>
<parameter key="QueueFullPolicy" value="Discard"/>
<parameter key="OpenTimeoutSecs" value="30.0"/>
</engine>
<!-- <engine type="BP4"> -->
<!-- <parameter key="AggregatorRatio" value="18"/> -->
<!-- <parameter key="NumAggregators" value="36"/> -->
<!-- <parameter key="BurstBufferPath" value="/mnt/local/mike"/> -->
<!-- <parameter key="BurstBufferDrain" value="Off"/> -->
<!-- <parameter key="BurstBufferVerbose" value="1"/> -->
<!-- </engine> -->
</io>
</adios-config>
module load aadios2/2.9.1-6fh7kh
export DIR=~/Build_WRF/LIBRARIES
export CC=gcc
export CXX=g++
export FC=gfortran
export F77=gfortran
export HDF5=$DIR
export LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH
export NETCDF=$DIR
export PATH=$DIR/bin:$PATH
export LD_LIBRARY_PATH=/mnt/repo/software/spack/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/adios2-2.9.1-6fh7kh2v3tombadg56kmop72sjhf23dg/lib:$LD_LIBRARY_PATH
./wrf.exe or(mpirun -np <number of process> ./wrf.exeThe BP5 output will have mmd.0 file and the BP4 does not have mmd.0 file THe output file has the same name for different machine: "wrfout_d01_2019-11-26_12:00:00"
Here is the python script. Then add the same adios2.xml file into the same folder with python
import argparse
import adios2 # pylint: disable=import-error
import numpy as np # pylint: disable=import-error
import matplotlib.pyplot as plt # pylint: disable=import-error
import matplotlib.gridspec as gridspec # pylint: disable=import-error
from mpi4py import MPI # pylint: disable=import-error
import cartopy.crs as ccrs # pylint: disable=import-error
import cartopy.feature as cfeature # pylint: disable=import-error
from mpl_toolkits.axes_grid1 import make_axes_locatable # pylint: disable=import-error
#
#
def setup_args():
parser = argparse.ArgumentParser()
parser.add_argument("--instream", "-i", help="Name of the input stream", default="wrfout_d01_2019-11-26_23:00:00")
parser.add_argument("--outfile", "-o", help="Name of the output file", default="screen")
parser.add_argument("--varname", "-v", help="Name of variable read", default="T2")
args = parser.parse_args()
return args
def plot_var(var, fr_step):
lccproj = ccrs.LambertConformal(central_longitude=-74.5, central_latitude=38.8)
fig, ax = plt.subplots(figsize=(15, 18), subplot_kw=dict(projection=lccproj))
plt.subplots_adjust(right=0.88) # adjust the right margin of the plot
title = fr_step.read_string("Times")
plt.title("WRF-ADIOS2 Demo \n {}".format(title[0]), fontsize=17)
# format the spacing of the colorbar
divider = make_axes_locatable(ax)
cax = divider.new_horizontal(size='5%', pad=0.1, axes_class=plt.Axes)
fig.add_axes(cax)
displaysec = 0.5
cur_step = fr_step.current_step()
x = fr_step.read("XLONG")
y = fr_step.read("XLAT")
data = fr_step.read(var)
data = data * 9 / 5 - 459.67 #convert from K to F
# define the limits for the model to subset and plot
# model_lims = dict(minlon=-80, maxlon=-69, minlat=35, maxlat=43)
# # create boolean indices where lat/lon are within defined boundaries
# lon_ind = np.logical_and(x > model_lims['minlon'], x < model_lims['maxlon'])
# lat_ind = np.logical_and(y > model_lims['minlat'], y < model_lims['maxlat'])
# # find i and j indices of lon/lat in boundaries
# ind = np.where(np.logical_and(lon_ind, lat_ind))
# data = np.squeeze(data)[range(np.min(ind[0]), np.max(ind[0]) + 1),
# range(np.min(ind[1]), np.max(ind[1]) + 1)]
h = ax.pcolormesh(x, y, data, vmin=-20, vmax=110,
cmap='jet', transform=ccrs.PlateCarree())
cb = plt.colorbar(h, cax=cax)
cb.set_label(label="Temperature [F]", fontsize=14) # add the label on the colorbar
cb.ax.tick_params(labelsize=12) # format the size of the tick labels
# add contours
contour_list = [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100] # define contour levels
cs = ax.contour(x, y, data, contour_list, colors='black',
linewidths=.5, transform=ccrs.PlateCarree())
ax.clabel(cs, inline=True, fontsize=10.5, fmt='%d')
# add the latitude and longitude gridlines
gl = ax.gridlines(draw_labels=True, linewidth=1, color='gray', alpha=0.5,
linestyle='dotted', x_inline=False)
gl.top_labels = False
gl.right_labels = False
gl.xlabel_style = {'size': 13}
gl.ylabel_style = {'size': 13}
# add map features
land = cfeature.NaturalEarthFeature('physical', 'land', '10m')
ax.add_feature(land, zorder=5, edgecolor='black', facecolor='none')
state_lines = cfeature.NaturalEarthFeature(
category='cultural',
name='admin_1_states_provinces_lines',
scale='10m',
facecolor='none')
ax.add_feature(cfeature.BORDERS, zorder=6)
ax.add_feature(state_lines, zorder=7, edgecolor='black')
#plt.title(title)
# plt.ion()
#plt.show()
# plt.pause(displaysec)
# #clear_output()
# plt.clf()
imgfile = "image"+"{0:0>5}.png".format(cur_step)
plt.savefig(imgfile)
plt.clf()
if __name__ == "__main__":
args = setup_args()
fr = adios2.open(args.instream, "r", MPI.COMM_WORLD, "adios2.xml", "wrfout_d01_2019-11-26_23:00:00")
for fr_step in fr:
plot_var(args.varname, fr_step)
fr.close()
Run this python script with adios2.xml file in the same folder.