WRF-CHEM

WRF-CHEM installation on Ubuntu 22.04

1. Prepare 准备工作

1.1 Log in and check name

# show ubuntu version.
cat /etc/os-release
# show user name.
whoami

1.2 Update

# update repository.
sudo apt update

1.3 Intall libs

sudo apt install csh m4 build-essential nasm cmake unzip libxmu-dev libcairo-dev libbz2-dev libxaw7-dev libx11-dev xorg-dev flex bison subversion liburi-perl evince tcsh cpp quota cvs libomp-dev python3-pip freeglut3-dev libjpeg-dev file vim

1.4 Install Compiler

# install compiler.
sudo apt install gcc g++ gfortran
# show compiler version.
gcc -v
g++ -v
gfortran -v
cpp --version

2. Libraries Installation 安装库文件

2.1 Install mpich

# Create directory
mkdir -p /home/ubuntu/Build_WRF/src
mkdir -p /home/ubuntu/Build_WRF/LIBRARIES
cd /home/ubuntu/Build_WRF/src

Download Source Code. (provided) 下载源码（已提供）

wget https://www.mpich.org/static/downloads/4.0.2/mpich-4.0.2.tar.gz

Uncompress Source Code and Compile. 解压源码并编译

tar -xzvf mpich-4.0.2.tar.gz
cd mpich-4.0.2
FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/mpich
make -j4
make install

Update PATH variables 更新PATH变量

vim /home/ubuntu/.profile

### mpich
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/mpich/bin:$PATH

source /home/ubuntu/.profile

2.2 Install zlib

cd /home/ubuntu/Build_WRF/src

wget http://www.zlib.net/fossils/zlib-1.2.12.tar.gz

Uncompress Source Code and Compile. 解压源码并编译

tar xzvf zlib-1.2.12.tar.gz
cd zlib-1.2.12
./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/zlib
make -j4
make install

2.3 Install hdf5

cd /home/ubuntu/Build_WRF/src

wget https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_12_2/source/hdf5-1.12.2.tar.gz

Uncompress Source Code and Compile. 解压源码并编译

tar xzvf hdf5-1.12.2.tar.gz
cd hdf5-1.12.2
./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/hdf5 --with-zlib=/home/ubuntu/Build_WRF/LIBRARIES/zlib --enable-fortran --enable-fortran2003 --enable-cxx --with-default-api-version=v18
make -j4
make install

Update PATH variables 更新PATH变量

vim /home/ubuntu/.profile

### hdf5
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/hdf5/bin:$PATH
export LD_LIBRARY_PATH=/home/ubuntu/Build_WRF/LIBRARIES/hdf5/lib:$LD_LIBRARY_PATH

source /home/ubuntu/.profile

2.4 Install curl

cd /home/ubuntu/Build_WRF/src

wget https://curl.se/download/curl-7.83.1.tar.gz

Uncompress Source Code and Compile. 解压源码并编译

tar xzvf curl-7.83.1.tar.gz
cd curl-7.83.1
./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/curl --with-zlib=/home/ubuntu/Build_WRF/LIBRARIES/zlib --without-ssl
make -j4
make install

2.5 Install netcdf

cd /home/ubuntu/Build_WRF/src

Download Source Code.

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.8.0.tar.gz
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.5.3.tar.gz

2.5.1 Install netcdf-c

Uncompress Source Code and Compile. 解压源码并编译

tar xzvf netcdf-c-4.8.0.tar.gz
cd netcdf-c-4.8.0
CFLAGS=-fPIC CPPFLAGS='-I/home/ubuntu/Build_WRF/LIBRARIES/hdf5/include -I/home/ubuntu/Build_WRF/LIBRARIES/curl/include' LDFLAGS='-L/home/ubuntu/Build_WRF/LIBRARIES/hdf5/lib -L/home/ubuntu/Build_WRF/LIBRARIES/curl/lib ' ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/netcdf --enable-netcdf-4 --enable-netcdf4 --enable-shared --enable-dap
make -j4
make install
cd ..

2.5.2 Install netcdf-fortran

Uncompress Source Code and Compile. 解压源码并编译

tar xzvf netcdf-fortran-4.5.3.tar.gz
cd netcdf-fortran-4.5.3
CPPFLAGS='-I/home/ubuntu/Build_WRF/LIBRARIES/netcdf/include' LDFLAGS='-L/home/ubuntu/Build_WRF/LIBRARIES/netcdf/lib' FCFLAGS='-m64' ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/netcdf
make -j4
make install

Update PATH variables 更新PATH变量

vim /home/ubuntu/.profile

### netcdf
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/netcdf/bin:$PATH
export NETCDF=/home/ubuntu/Build_WRF/LIBRARIES/netcdf
export LD_LIBRARY_PATH=/home/ubuntu/Build_WRF/LIBRARIES/netcdf/lib:$LD_LIBRARY_PATH

source /home/ubuntu/.profile

2.6 Install libpng

cd /home/ubuntu/Build_WRF/src

wget https://jaist.dl.sourceforge.net/project/libpng/libpng16/1.6.37/libpng-1.6.37.tar.gz

Uncompress Source Code and Compile. 解压源码并编译

tar xzvf libpng-1.6.37.tar.gz
cd libpng-1.6.37
CPPFLAGS='-I/home/ubuntu/Build_WRF/LIBRARIES/netcdf/include' FCFLAGS='-m64' ./configure --prefix=/home/ubuntu/Build_WRF/LIBRARIES/libpng
make -j4
make install

Update PATH variables 更新PATH变量

vim /home/ubuntu/.profile

#### jasper
export PATH=/home/ubuntu/Build_WRF/LIBRARIES/jasper/bin:$PATH
export LD_LIBRARY_PATH=/home/ubuntu/Build_WRF/LIBRARIES/jasper/lib:$LD_LIBRARY_PATH

source /home/ubuntu/.profile

2.7 Install ncl

cd /home/ubuntu/Build_WRF/src

Install miniconda.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh ./Miniconda3-latest-Linux-x86_64.sh

Install ncl.

source /home/ubuntu/.bashrc
conda create -n ncl_stable -c conda-forge ncl # 创建Conda环境
source activate ncl_stable

Test ncl. 测试ncl工具

ncl -V

Show version 6.6.2 is good. Update PATH variables 更新PATH变量

vim /home/ubuntu/.profile

#### ncl
source activate ncl_stable

source /home/ubuntu/.profile

3. Install WRF

3.1 WRF-chem and KPP

Variable setup. 设置变量

ulimit -s unlimited
export MALLOC_CHECK_=0
export EM_CORE=1
export NMM_CORE=0
export WRF_CHEM=1
export WRF_KPP=1
export YACC='/usr/bin/yacc -d'
export FLEX=/usr/bin/flex
export FLEX_LIB_DIR=/usr/lib/x86_64-linux-gnu
export KPP_HOME=/home/ubuntu/Build_WRF/WRFV4.4/chem/KPP/kpp/kpp-2.1
export WRF_SRC_ROOT_DIR=/home/ubuntu/Build_WRF/WRFV4.4
export PATH=$KPP_HOME/bin:$PATH
export SED=/usr/bin/sed
export WRFIO_NCD_LARGE_FILE_SUPPORT=1

cd /home/ubuntu/Build_WRF/

wget -c https://github.com/wrf-model/WRF/releases/download/v4.4/v4.4.tar.gz -O wrf-4.4.tar.gz

Uncompress Source Code and Compile. 解压源码并编译

tar -xvzf wrf-4.4.tar.gz
cd WRFV4.4/chem/KPP/kpp/kpp-2.1/src
/usr/bin/flex scan.l
cd /home/ubuntu/Build_WRF/WRFV4.4

vim configure

Change from	To
if [ "$USENETCDFPAR" == "1" ] ; then	if [ "$USENETCDFPAR" = "1" ] ; then

./configure

Enter selection [1-75] : 33
Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]: 1

Complie kpp.

./compile 2>&1 | tee compile_kpp.log

Complie em_real mode.

./compile em_real 2>&1 | tee compile_wrf.log # 等待30-50min（根据电脑性能）

这一步所需要的时间较长，需要耐心等待。
Wait 30-50 minutes for finish test by

ls -lah main/*.exe

如图中所示，出现这些.exe文件即表示WRF安装成功！
If you see real.exe and wrf.exe then correct. Else check Error in compile_wrf.log file.

3.2 WPS installation

cd /home/ubuntu/Build_WRF/
ln -sf WRFV4.4 WRF

Download Source Code

wget -c https://github.com/wrf-model/WPS/archive/refs/tags/v4.4.tar.gz -O wps-4.4.tar.gz

Uncompress Source Code.

tar -xvzf wps-4.4.tar.gz

Define variable.

cd WPS-4.4
export JASPERLIB=/home/ubuntu/Build_WRF/LIBRARIES/jasper/lib
export JASPERINC=/home/ubuntu/Build_WRF/LIBRARIES/jasper/include

Configure WPS.

./configure

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

vim configure.wps

COMPRESSION_LIBS = -L/home/ubuntu/Build_WRF/LIBRARIES/jasper/lib -ljasper -lpng -lz
COMPRESSION_INC = -I/home/ubuntu/Build_WRF/LIBRARIES/jasper/include

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

Complie WPS.

./compile 2>&1 | tee compile_wps.log

Wait for finish test by

ls -lah *.exe

如图，出现以上.exe文件表示WPS安装成功！

4. Create Directory for Data.

4.1 Geography Data

cd /home/ubuntu/Build_WRF/

Download Geography Data.

wget http://www2.mmm.ucar.edu/wrf/src/wps_files/albedo_modis.tar.bz2
wget http://www2.mmm.ucar.edu/wrf/src/wps_files/geog_complete.tar.gz
wget http://www2.mmm.ucar.edu/wrf/src/wps_files/maxsnowalb_modis.tar.bz2
wget http://www2.mmm.ucar.edu/wrf/src/wps_files/topo_2m.tar.bz2

Uncompress Geography Data.

tar -xvzf geog_complete.tar.gz
cd geog
tar -xvjf ../albedo_modis.tar.bz2
tar -xvjf ../maxsnowalb_modis.tar.bz2
tar -xvjf ../topo_2m.tar.bz2

4.2 Real-time Input Data.

Create Real-time Data Directory and Change to Directory.

mkdir -p /home/ubuntu/Build_WRF/data/fnl
cd /home/ubuntu/Build_WRF/data/fnl

Download Data from https://rda.ucar.edu/datasets/ds083.2/index.html#sfol-wl-/data/ds083.2?g=22010

Select Download Script and copy rda-download.csh to directory /home/ubuntu/Build_WRF/data/fnl Change Directory to WPS directory.

cp /home/ubuntu/rda-download.csh /home/ubuntu/Build_WRF/data/fnl
cd /home/ubuntu/Build_WRF/data/fnl
csh ./rda-download.csh
ls -al fnl*

5. Run WRF-chem

5.1 Run WPS

cd /home/ubuntu/Build_WRF/WPS-4.4

Change GEOGRID.TBL

cd geogrid
rm -rf GEOGRID.TBL
ln -svf GEOGRID.TBL.ARW_CHEM GEOGRID.TBL
cd ..

Create namelist.wps file.

rm -rf namelist.wps
vim namelist.wps

&share
wrf_core = 'ARW',
max_dom = 1,
start_date = '2010-07-14_00:00:00',
end_date = '2010-07-16_00:00:00',
interval_seconds = 10800,
io_form_geogrid = 2,
/
&geogrid
parent_id
= 1,
parent_grid_ratio = 1,
i_parent_start = 1,
j_parent_start = 1,
e_we
= 41,
e_sn
= 41,
geog_data_res = '10m',
dx
= 100000,
dy
= 100000,
map_proj = 'lambert',ref_lat = 35.0,
ref_lon = 25.0,
truelat1 = 30.0,
truelat2 = 40.0,
stand_lon = 25.0,
geog_data_path = '/home/ubuntu/Build_WRF/geog'
/
ref_x = 20.5
ref_y = 20.5
&ungrib
out_format = 'WPS',
prefix = 'FILE',
/
&metgrid
fg_name = 'FILE'
io_form_metgrid = 2,
/
opt_ignore_dom_center = .true.,
&mod_levs
press_pa = 201300 , 200100 , 100000 ,
95000 , 90000 ,
85000 , 80000 ,
75000 , 70000 ,
65000 , 60000 ,
55000 , 50000 ,
45000 , 40000 ,
35000 , 30000 ,
25000 , 20000 ,
15000 , 10000 ,
5000 , 1000
/

Create Geography Data.

./geogrid.exe

Wait for finish test by

ls -lah geo_em.d01.nc

If you see geo_em.d01.nc is correct.

link Real-time Data top WPS.

./link_grib.csh /home/ubuntu/Build_WRF/data/fnl/fnl_201007*

link Vtable

ln -sf ungrib/Variable_Tables/Vtable.GFS Vtable

create grib file.

./ungrib.exe

Wait for finish test by

ls -lah FILE*

create met file.

./metgrid.exe

ls -lah met_em.*

5.2 Run WRF

cd /home/ubuntu/Build_WRF/WRF/test/em_real/

link met file from WPS to WRF.

ln -sf /home/ubuntu/Build_WRF/WPS-4.4/met_em* .

remove namelist file.

rm -rf namelist.input

vim namelist.input

&time_control
run_days = 2,
run_hours = 0,
run_minutes = 0,
run_seconds = 0,
start_year = 2010,
start_month = 07,
start_day = 14,
start_hour = 00,
start_minute = 00,
start_second = 00,
end_year = 2010,
end_month = 07,
end_day = 16,
end_hour = 00,
end_minute = 00,
end_second = 00,
interval_seconds = 10800,
input_from_file = .true.,
history_interval = 60,
frames_per_outfile = 72,
restart = .false.,
restart_interval = 0,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
auxinput6_inname = 'wrfbiochemi_d01',
auxinput7_inname = 'wrffirechemi_d<domain>',
auxinput8_inname = 'wrfchemi_gocart_bg_d<domain>',
auxinput12_inname = 'wrf_chem_input',
auxinput5_interval_m = 86400,
auxinput7_interval_m = 86400,
auxinput8_interval_m = 86400,
io_form_auxinput2 = 2,
io_form_auxinput5 = 0,
io_form_auxinput6 = 0,
io_form_auxinput7 = 0,
io_form_auxinput8 = 0,
io_form_auxinput12 = 0,
debug_level = 0,
auxinput1_inname = "met_em.d<domain>.<date>",
auxinput13_inname = 'wrfchemv_d<domain>',
auxinput13_interval_m = 86400,
io_form_auxinput13 = 0,
/

&dfi_control
/

&domains
time_step = 600,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
s_we = 1,
e_we = 41,
s_sn = 1,
e_sn = 41,
e_vert = 31,
num_metgrid_levels = 27,
num_metgrid_soil_levels = 4,
dx = 100000,
dy = 100000,
grid_id = 1,
parent_id = 0,
i_parent_start = 1,
j_parent_start = 1,
parent_grid_ratio = 1,
parent_time_step_ratio = 1,
p_top_requested = 10000,
feedback = 1,
smooth_option = 0,
p_top_requested = 10000,
zap_close_levels = 50,
interp_type = 1,
t_extrap_type = 2,
force_sfc_in_vinterp = 0,
use_levels_below_ground = .true.,
use_surface = .true.,
lagrange_order = 1,
sfcp_to_sfcp = .true.,
/

&physics
num_land_cat = 21,
mp_physics = 4,
progn = 0,
ra_lw_physics = 1,
ra_sw_physics = 2,
radt = 30,
sf_sfclay_physics = 1,
sf_surface_physics = 2,
bl_pbl_physics = 1,
bldt = 0,
cu_physics = 5,
cu_diag = 1,
cudt = 0,
ishallow = 0,
isfflx = 1,
ifsnow = 1,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 0,
mp_zero_out = 2,
mp_zero_out_thresh = 1.e-12,
maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,
cu_rad_feedback = .true.,
/

&fdda
/

&dynamics
rk_ord = 3,
w_damping = 1,
diff_opt = 1,
km_opt = 4,
diff_6th_opt = 0,
diff_6th_factor = 0.12,
base_temp = 290.
damp_opt = 0,
zdamp = 5000.,
dampcoef = 0.01,
khdif = 0,
kvdif = 0,
non_hydrostatic = .true.,
moist_adv_opt = 2,
scalar_adv_opt = 2,
chem_adv_opt = 2,
tke_adv_opt = 2,
time_step_sound = 4,
h_mom_adv_order = 5,
v_mom_adv_order = 3,
h_sca_adv_order = 5,
v_sca_adv_order = 3,
/

&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .true.,
nested = .false.,
/

&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

&chem
kemit = 1,
chem_opt = 401,
bioemdt = 0,
photdt = 0,
chemdt = 10,
io_style_emissions = 0,
emiss_opt = 3,
emiss_opt_vol = 0,
emiss_ash_hgt = 20000.,
chem_in_opt = 0,
phot_opt = 0,
gas_drydep_opt = 0,
aer_drydep_opt = 1,
bio_emiss_opt = 0,
ne_area = 0,
dust_opt = 1,
dmsemis_opt = 0,
seas_opt = 0,
depo_fact = 0.25,
gas_bc_opt = 0,
gas_ic_opt = 0,
aer_bc_opt = 1,
aer_ic_opt = 1,
gaschem_onoff = 0,
aerchem_onoff = 1,
wetscav_onoff = 0,
cldchem_onoff = 0,
vertmix_onoff = 1,
chem_conv_tr = 0,
conv_tr_wetscav = 0,
conv_tr_aqchem = 0,
biomass_burn_opt = 0,
plumerisefire_frq = 30,
have_bcs_chem = .false.,
aer_ra_feedback = 0,
aer_op_opt = 0,
opt_pars_out = 0,
diagnostic_chem = 0,
/

create real case.

mpirun -np 1 ./real.exe

And see file wrfbdy_d01 wrfinput_d01.

ls -alh wrfbdy_d01 wrfinput_d01

Run WRF

mpirun -np 2 ./wrf.exe

ls -alh wrfout_*

5.3 Show Result

list data inside wrfout.

ncdump -h wrfout_d01*
ncdump -v DUST_5 wrfout_d01*

Create pdf from wrfout.

cd /home/ubuntu/Build_WRF/WRF/test/em_real

Create ncl script.

vim plot_dust_5.ncl

;*************************************************
; WRF: DUST_5
;************************************************
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRF_contributed.ncl"
begin
  f = addfile ("wrfout_d01_2010-07-14_00:00:00", "r")
  wks = gsn_open_wks("pdf" ,"WRF_DUST_5") ; ps,pdf,x11,ncgm,eps
  gsn_define_colormap(wks,"BlAqGrYeOrReVi200") ; select color map
  res = True ; plot mods desired
  res@gsnMaximize = True ; uncomment to maximize size
  res@gsnSpreadColors = True ; use full range of colormap
  res@cnFillOn = True ; color plot desired
  res@cnLinesOn = False ; turn off contour lines
  res@cnLineLabelsOn = False ; turn off contour labels
  WRF_map_c(f, res, 0) ; reads info from file
  res@tfDoNDCOverlay = True
  res@pmTickMarkDisplayMode = "Always"  ; turn on tickmarks
  times = wrf_user_getvar(f,"times",-1) ; get all times in the file
  ntimes = dimsizes(times) ; number of times in the file
  
  do nt=0,ntimes,6
    x = f->DUST_5(nt,0,:,:) ; (Time,level, south_north, west_east)
    res@tiMainString = "WRF-CHEM (DUST_5) " + times(nt)
    res@gsnLeftString = x@description
    plot = gsn_csm_contour_map(wks,x(:,:),res)
  end do
end

Create PDF

ncl plot_dust_5.ncl

Output is WRF_DUST_5.pdf

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README.md

README.md

WRF-CHEM

1. Prepare 准备工作

1.1 Log in and check name

1.2 Update

1.3 Intall libs

1.4 Install Compiler

2. Libraries Installation 安装库文件

2.1 Install mpich

2.2 Install zlib

2.3 Install hdf5

2.4 Install curl

2.5 Install netcdf

2.5.1 Install netcdf-c

2.5.2 Install netcdf-fortran

2.6 Install libpng

2.7 Install ncl

3. Install WRF

3.1 WRF-chem and KPP

3.2 WPS installation

4. Create Directory for Data.

4.1 Geography Data

4.2 Real-time Input Data.

5. Run WRF-chem

5.1 Run WPS

5.2 Run WRF

5.3 Show Result

Files

README.md

Latest commit

History

README.md

File metadata and controls

WRF-CHEM

1. Prepare 准备工作

1.1 Log in and check name

1.2 Update

1.3 Intall libs

1.4 Install Compiler

2. Libraries Installation 安装库文件

2.1 Install mpich

2.2 Install zlib

2.3 Install hdf5

2.4 Install curl

2.5 Install netcdf

2.5.1 Install netcdf-c

2.5.2 Install netcdf-fortran

2.6 Install libpng

2.7 Install ncl

3. Install WRF

3.1 WRF-chem and KPP

3.2 WPS installation

4. Create Directory for Data.

4.1 Geography Data

4.2 Real-time Input Data.

5. Run WRF-chem

5.1 Run WPS

5.2 Run WRF

5.3 Show Result