WRF

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= Compilation =
  
= Compilation =
  +
<code>hydra</code>
  +
 
Model (version 3.9.1) has already been compiled in <code>hydra</code>
  
Model (version 3.9.1) has already been compiled in <code>hydra</code>
   

Revisión de 10:11 22 mayo 2023

Contenido

Model description

Weather Research and Forecast model (WRF, Skamarock, 2008) is a limited area atmospheric model developed by a consortium of american institutions with contributions from the whole community. It is a non-hydrostatic primitive equations model used in a large variety of research areas.

Techincal aspects of the model (v 4.0) are provided in this pdf

Compilation

hydra

Model (version 3.9.1) has already been compiled in hydra

For compilation using the gcc copmilers see here WRFgcc

  • From an instalation folder [INSTALLDIR] (/share/WRF, in hydra), creation of a folder structure 
[INSTALLDIR]/[WRFversion]/[compiler]/[compilation_kind]/
  • As example WRFv3.9.1 compiled with intel-compilers with distributed memory only 
$ mkdir /share/WRF/WRFV3.9.1/ifort/dmpar/
$ cd /share/WRF/WRFV3.9.1/ifort/dmpar/
  • Decompressing code source files 
$ tar xvfz ../../../WRFV3.9.1.1.TAR.gz 
$ mv WRF WRFV3 
$ tar xvfz ../../../WPS.9.1.TAR.gz
  • Compilation of model (wrf.exe, real.exe)
    • Going to the model source folder 
cd WRFV3
    • Declaration of location of netcdf libraries and large file support (> 2GB) 
$ export NETCDF='/usr/local'
$ export WRFIO_NCD_LARGE_FILE_SUPPORT=1
    • Running configuration of the compilation and picking up INTEL (ifort/icc) and distributed memory (dmpar) (option 15 and `basic' 1) 
$ ./configure
    • Making a copy of the configuration file to make two modifications 
$ cp configure.wrf configure.ifort.dmpar.wrf
    • Modifying the file configure.ifort.dmpar.wrf 
#DM_FC          =      mpif90 -f90=$(SFC) 
#DM_CC          =      mpicc -cc=$(SCC) -DMPI2_SUPPORT
DM_FC          =      mpif90 
DM_CC          =      mpicc -DMPI2_SUPPORT
    • Using the modified file 
$ cp configure.ifort.dmpar.wrf configure.wrf 
$ ./compile em_real >& compile.log
    • If everything went fine one should have 
$ ls main/*.exe
main/ndown.exe  main/real.exe  main/tc.exe  main/wrf.exe
    • And empty: 
$ cat -n compile.log | grep Error
$ cat -n compile.log | grep undefined
  • Compilation of the WRF-preprocessing (WPS: geogrid.exe, ungrib.exe, metgrid.exe)
    • Going there 
cd ../WPS
    • Running configure and picking up 20 (Linux x86_64, Intel compiler (dmpar_NO_GRIB2)) 
./configure
    • Compiling 
./compile >& compile.log
    • If everything went right, one should have 
$ ls */*.exe
geogrid/geogrid.exe  util/avg_tsfc.exe      util/int2nc.exe 
metgrid/metgrid.exe  util/calc_ecmwf_p.exe  util/mod_levs.exe
ungrib/g1print.exe   util/g1print.exe       util/rd_intermediate.exe
ungrib/g2print.exe   util/g2print.exe 
ungrib/ungrib.exe    util/height_ukmo.exe

Forcings

Atmospheric forcings

Provide the atmospheric conditions to the model at a given date.

  • There is a shared space called /share
  • At hydra all forcings are at: 
/share/DATA/
/share/DATA/re-analysis/ERA-Interim/
    • Global monthly files at 0.75° horizontal resolution and all time-steps: 00, 06, 12, 18 are labelled as:
      • ERAI_pl[YYYY][MM]_[var1]-[var2].grib: pressure levels variables (all levels). GRIB codes as:
        • 129: geopotential
        • 157: relative humidty
        • 130: Temperature
        • 131: u-wind
        • 132: v-wind
      • ERAI_sfc[YYYY][MM].grib: all surface levels variables (step 0)
    • To download data:
      • Generate files from ECMWF web-page ERA-Interim
      • Go to the folder in hydra 
cd /share/DATA/re-analysis/ERA-Interim/
      • get the file (as link from ECMWF web-page (right bottom on `Download grib'), as e.g.: 
$ wget https://stream.ecmwf.int/data/atls05/data/data02/scratch/_mars-atls05-a82bacafb5c306db76464bc7e824bb75-zn7P44.grib
      • Rename file according to its content 
$ mv _mars-atls05-a82bacafb5c306db76464bc7e824bb75-zn7P44.grib ERAI_sfc201302.grib
  • ERA5
    • Thus, part of ERA5 forcings are: 
/share/DATA/re-analysis/ERA5/
  • 'NCEP-NNRP1'
    • Thus, full NCEP-NNRP1 forcings are (NOTE: no land data!!!): 
/share/DATA/re-analysis/NCEP_NNRP/


Morphological forcings

Provide the geomorphological information for the domain of simulation: topography, land-use, vegetation-types, etc...

  • In WRF there is a huge amount of data ans sources at different resolutions. At hydra everything is already there at: 
/share/GEOG/
  • They are ready to be use

Model use

WRF has two main parts:

  • WPS: Generation of the domain, initial and boundary condition: Runs 4 programs:
    • geogrid: domain generation
    • ungrib: unpack atmospheric forcing \verb+grib+ files
    • metgrid: horizontal interpolation of the unpacked atmospheric forcing files at the domain of simulation
    • real: generation of the initial and boundary conditions using \verb+metgrid+ output
  • WRF: model it self: wrf.exe

At hydra all the code is already compiled at (with folders WPS and WRFV3: 

/share/WRF/[WRFversion]/[compiler]/[compilation_kind]/

As example WRFv3.9.1 compiled with intel-compilers with distributed memory only 

/share/WRF/WRFV3.9.1/ifort/dmpar/

WPS

Let's assume that we work in a folder called WORKDIR (at users' ${HOME} at hydra). As example, let's create a two nested domain at 30 km for the entire South America and a second one at 4.285 km for Córdoba mountain ranges (see the WRF/namelist.wps)

(thumbnail)
WRF two domain configuration 30 and 4.285 km
  • geogrid: generation of the domain
    • Creation of a folder for the geogrid section 
$ mkdir geogrid
$ cd geogrid
    • Take the necessary files (do not forget opt_geogrid_tbl_path = './', into &geogrid section) in namelist !!): 
 $ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/geogrid/geogrid.exe ./
$ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/geogrid/GEOGRID.TBL.ARW  ./GEOGRID.TBL
$ cp /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/geogrid/namelist.wps  ./
    • Domain configuration is done via namelist.wps (more information at: WPS user guide) 
vim namelist.wps
    • Once it is defined, run it: 
./geogrid.exe >& run_geogrid.log
    • It will create the domain files, one for each domain 
geo_em.d[nn].nc
    • Some variables:
      • LANDMASK: sea-land mask
      • XLAT_M: latitude on mass point
      • XLONG_M: longitude on mass point
      • HGT_M: orographical height
    • At hydra the domain for SESA at 20 km for WRFsensSFC is located at 
home/lluis.fita/estudios/dominios/CDXWRF
  • ungrib: unpack grib files
    • Creation of the folder (from $WORKDIR) 
$ mkdir ungrib 
$ cd ungrib
    • Linking necessary files from compiled source 
$ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/ungrib/ungrib.exe ./
$ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/link_grib.csh ./
    • Creation of a folder for the necessary GRIB files and linking the necessary files (4 files per month) 
$ mkdir GribDir
$ cd GribDir
$ ln -s /share/DATA/re-analysis/ERA-Interim/*201212*.grib ./ 
$ cd ..
    • Re-link files for WRF with its own script 
./link_grib.csh GribDir/*
    • Should appear: 
$ ls GRIBFILE.AA*
GRIBFILE.AAA\  GRIBFILE.AAB  GRIBFILE.AAC  GRIBFILE.AAD
    • We need to provide equivalences of the GRIB codes to the real variables. WRF comes with already defined GRIB equivalencies from different sources in folder Variable_Tables. In our case we use ECMWF ERA-Interim at pressure levels, thus we link 
ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/ungrib/Variable_Tables/Vtable.ERA-interim.pl ./Vtable
    • We need to take the domain file and get the right dates 
$ cp ../geogrid/nameslist.wps ./
    • Files can be unpacked 
./ungrib.exe >& run_ungrib.log
    • If everything went fine, should appear: 
FILE:[YYYY]-[MM]-[DD]_[HH]
  • And... 
$ tail run_ungrib.log 
(...) 
********** 
Done deleting temporary files. 
********** 

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 
!  Successful completion of ungrib.   ! 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  • metgrid horizontal interpolation of atmospheric forcing data at the domain of simulation
    • Creation of the folder (from $WORKDIR) 
$ mkdir metgrid 
$ cd metgrid
    • Getting necessary files (do not forget opt_metgrid_tbl_path = './', into &metgrid section in namelist !! to avoid: ERROR: Could not open file METGRID.TBL) 
$ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/metgrid/metgrid.exe ./ 
$ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WPS/metgrid/METGRID.TBL.ARW ./METGRID.TBL
    • Getting the ungrib output 
ln -s ../ungrib/FILE* ./
    • Link the domains of simulation 
$ ln -s ../geogrid/geo_em.d* ./
    • Link the namelist from ungrib (to make sure we are using the same!) 
$ ln -s ../ungrib/namelist.wps ./
    • Get the PBS (job queue script) to run the metrid.exe 
$ cp /share/WRF/run_metgrid.pbs ./
    • And run it 
qsub run_metgrid.pbs
    • If everything went fine one should have 
met_em.d[nn].[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS].nc
    • And... 
$ tail run_metgrid.log
(...)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 
!  Successful completion of metgrid.  ! 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  • real vertical interpolation of atmospheric forcing at the domain of simulation
    • Creation of the folder (from $WORKDIR) 
$ mkdir run 
$ cd run
    • Link all the necessary files from WRF (it already links all the necessary to run the model) 
$ ln -s /share/WRF/WRFV3.9.1/ifort/dmpar/WRFV3/run/* ./
    • Remove and copy the configuration file (namelist.input) 
$ rm namelist.input 
$ cp /share/WRF/WRFV3.9.1/ifort/dmpar/WRFV3/run/namelist.input ./
    • Edit the file and prepare the configuration for the run (re-adapt domain, physics, dates, output....). See an example for the two nested domain here WRF/namelist.input 
$ vim namelist.input
    • Linking the metgrid generated files 
ln -s ../metgrid/met_em.d*.nc ./
    • Getting the PBS job script for real.exe 
$ cp /share/WRF/run_real.pbs ./
    • Getting a bash script to run executables in hydra (there is an issue with ulimit which does not allow to run with more than one node) 
$ cp /share/WRF/launch_pbs.bash ./
    • And run it 
qsub run_real.pbs
    • If everything went fine one should have (the basic ones): 
wrfbdy_d[nn]  wrfinput_d[nn]  ...
      • wrfbdy_d01: Boundary conditions file (only for the first domain)
      • wrfinput_d[nn]: Initial conditions file for each domain
      • wrffdda_d[nn]: Nudging file [optional]
      • wrflowinp_d[nn]: File with updating (every time-step of the atmospheric forcing) surface characteristics [optional]
    • And... 
$ tail realout/[InitialDATE]-[EndDATE]/rsl.error.0000
(...)
real_em: SUCCESS COMPLETE REAL_EM INIT

WRF

  • wrf Simulation (look on description of namelist for namelist configuration/specifications).
    • Getting the necessary PBS job (same folder for real) 
$ cp /share/WRF/run_wrf.pbs ./
    • And run it 
qsub run_wrf.pbs
    • If everything went fine one should have (the basic ones): 
wrfout_d[nn]_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]  wrfrst_d[nn]_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]  ...
      • wrfout/wrfout_d[nn]_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]: simulation output (at η=(p-ptop)/(psfc-ptop) levels)
      • wrfout/wrfrst_d[nn]_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]: restart file (to continue simulation)
      • wrfout/wrfxtrm_d[nn]_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]: file with extremes from internal integration [optional]
      • wrfout/wrfpress_d[nn]_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]: file at vertical pressure levels [optional]
      • namelist.output_[YYYY]-[MM]-[DD]_[HH]:[MI]:[SS]: All the parameters used for the simulation
      • stations: folder with the time-series files (tslist)
    • While running one can check the status on regarding on the rsl.error.0000 file, e.g.: 
$ tail rsl.error.0000
(...)
Timing for main: time 2012-12-01_00:13:30 on domain  1:  3.86105 elapsed seconds

WRF: known errors

CFL

  • But if something went wrong:
    • CFL: At wrfout/[InitialDATE]-[EndDATE]/ there are the files rsl.[error/out].[nnnn] (two per cpu). Use to appear SIGSEV segmentation fault, and to look different sources, usually cfl. e.g. (usually look for the largest rsl file (after the 0000); [$ ls -rS rsl.error.*]) 
$ wrfout/20121201000000-20121210000000/rsl.error.0009
(...) 
d01 2012-12-01_01:30:00  33 points exceeded cfl=2 in domain d01 at time 2012-12-01_01:30:00 hours 
d01 2012-12-01_01:30:00  MAX AT i,j,k:    100    94    21 vert_cfl,w,d(eta)=    5.897325    17.00738    3.2057911E-02
(...)

NO working restart

Since a given version there is a need to include a new namelist parameter (in &time_control section) [WRF restart] in order to make available the option to continue a simulation from a given restart 

override_restart_timers                = .true.

If we want to get values at the output files at the time of the restart, you need to add at the (&time_control section) the parameter 

write_hist_at_0h_rst                   = .true.

Additional information

For more additional information and further details visit WRFextras

WRF4L: Lluís' WRF work-flow management

For information about Lluí's WRF work-flow management visit here WRF4L

CDXWRF: WRF for CORDEX

A new module developed in CIMA to attain CORDEX variable demands visit here CDXWRF

WRFles

LES simulations with WRF model here WRFles

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