WRF

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= Additional information =
  
= Additional information =
 
For more additional information and further details visit [[WRFextras]]
  
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]]

Revisión de 16:50 27 oct 2017

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.


Compilation

Model (version 3.9.1) has already been compiled in hydra

  • 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/
  • ERA-Interim
    • Thus, part of ERA-Interim forcings are: 
/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

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 domain at 25 km for SESA only

  • geogrid: generation of the domain
    • Creation of a folder for the geogrid section 
$ mkdir geogrid
$ cd geogrid
    • Take the necessary files: 
 $ 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/WRFsensSESA20k
  • 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 
$ 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....) 
$ 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 ./
    • 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 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
    • 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
(...)

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

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