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Comment: Typo megan

Table of Contents

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cd /n/holylfs/LABS/`id -gn`/$USER/new-wrf-root/412-WRF/
cp -ai run 00run  # 5s on holylogin03
cd 00run/
# make sure you have sourced source_wrf
ln -s ../../410-WPS/met_em.d01.2000-01-2* ./
vim namelist.input  # no edits
./real.exe  # 3s on holylogin03
tail rsl.error.0000  # expect to see "SUCCESS COMPLETE REAL_EM INIT"
vim job_wrf.sbatch  # no required edits
sbatch job_wrf.sbatch  # 2m36s with 4 huce_intel cpus
tail rsl.error.0000*  # expect to see "SUCCESS COMPLETE WRF"

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# expect to see "SUCCESS COMPLETE REAL_EM INIT"
vim job_wrf.sbatch  # no required edits
sbatch job_wrf.sbatch  # 2m36s with 4 huce_intel cpus
tail rsl.error.0000*  # expect to see "SUCCESS COMPLETE WRF"

REAL cases

Choose versions of WRF & WPS:

Latest releases on official GitHub: Image AddedImage Added

WRF v4.1.2 (precompiled without chem) is downloaded in /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/wrf/412-WRF
WPS v4.1 (precompiled) is downloaded in /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/wrf/410-WPS

WRF v3.6.1 (precompiled with chem) is downloaded in /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1/WRFV3
WPS v3.6.1 (precompiled) is downloaded in /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1/WPS

WRF v3.0beta with RAVE (pls recompile) is in ~kuang/Model/WRFV3
WPS v3.2.1 (pls recompile) is in ~dingma/Model2/WPSv3

Read the user's guide:
WRF (ARW) User's Guides: v3, v4
WRF-Chem: https://ruc.noaa.gov/wrf/wrf-chem/Users_guide.pdf #This is for a different WRF-Chem version (3.9), but it's still a relevant guide.
https://ruc.noaa.gov/wrf/wrf-chem/Emission_guide.pdf #This is a separate supplementary WRF-Chem guide to chemical input data processing.
https://ruc.noaa.gov/wrf/wrf-chem/wrf_tutorial_nepal/talks/Setup.pdf  #Some helpful WRF-Chem slides from NOAA

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  • Instructions in this part assume you want to compile and run your own version of WRF. However, note that a compiled usable version of WRF/WRF-Chem v3.6.1 including all external utilities and supplementary geography datasets that you can copy to your preferred run directory is already located at: 

    /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1

    This folder (hereafter $CLIMATE_MODELS) contains the WRF-ARW model, the WRF Pre-processing system (WPS; used for real test cases), the chemistry module add-on, the complete WRF geography dataset (for use with WPS and WRF-Chem), and other utilities needed for WRF-Chem. Note: WPS, WRF-Chem not relevant for idealized cases.

    Note 2: With the exception of the geography data set which is really big, copy the WRF_CHEM_3-6-1 folder to a location you are going to run it from. Soft link to the geography data set in the $CLIMATE_MODELS folder.
    .

  • If you want to use another version, you will first need to register as a user to download WRF source codes
    WRF: http://www2.mmm.ucar.edu/wrf/users/download/get_source.html

  • Once you've registered, you will be able to navigate to the downloads section. Select the WRF components relevant to you. For example:
    http://www2.mmm.ucar.edu/wrf/src/WPSV3.6.1.TAR.gz #WPS 3.6.1
    http://www2.mmm.ucar.edu/wrf/src/WRFV3.6.1.TAR.gz #WRF 3.6.1
    http://www2.mmm.ucar.edu/wrf/src/WRFV3-Chem-3.6.1.TAR.gz #Chem module add-on for WRF 3.6.1

  • If you're going to be using WRF meteorology output to drive the STILT LPDM (http://stilt-model.org/index.php/Main/HomePage) you will need to make some changes to the Registry file before compiling. Some basic instructions for this are located in $CLIMATE_MODELS folder as a README_WRF-STILT_modifications.txt file. 

  • Once you've downloaded the necessary tar.gz files, confirm your bashrc file looks something like:
    # (1) Load required modules (here we use Intel and Intel MPI) 
       module load intel/17.0.4-fasrc01
       module load impi/2017.2.174-fasrc01
       module load netcdf/4.1.3-fasrc02
       module load libpng/1.6.25-fasrc01
       module load jasper/1.900.1-fasrc02
       module load intel/17.0.4-fasrc01 impi/2017.2.174-fasrc01 ncview/2.1.7-fasrc01 
       module load ncl_ncarg/6.4.0-fasrc01
    # (2) Define required environment variables
       export NETCDF=${NETCDF_FORTRAN_HOME:-${NETCDF_HOME}}
       export JASPERLIB=${JASPER_LIB}
       export JASPERINC=${JASPER_INCLUDE}
       export WRFIO_NCD_LARGE_FILE_SUPPORT=1
       export HDF5=${HDF5_HOME}
       unset MPI_LIB  #unset for WPS, where WPS is used for real WRF simulations
    ### ...... For WRF-Chem: ...... ###
       export WRF_EM_CORE=1
       export WRF_NMM_CORE=0
       export WRF_CHEM=1


  • Now, configure and compile. WRF must be compiled before WPS.

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Regardless of whether you are running WRF or WRF-Chem, it is important that you do the following first and in this order (detailed instructions follow, including in the examples in Part III and IV):

(1) Run WPS (geogrid.exe, ungrib.exe, metgrid.exe) to create real data-based initialization files with of form met_em.d0X.YYYY-MM-DD_hh:mm:ss.nc

(2) Run real.exe to generate input and boundary files of form wrfinput_d0*, wrfbdy_d01 (and optionally wrffdda_d0*) to initialize WRF model 

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      3. You should see met_em.d01(or d02 or d03....).YYYY-MM-DD_hh:mm:ss.nc files created. These are your WPS final output files that real.exe ingests.


Step 2. Running WRF

  • Navigate to your WRF/WRFV3/run folder

  • Step 2b. PROGRAM REAL: real data initialization program to set up the model domain and initialize WRF

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  • You will need access to the relevant MEGAN initial files, from https://www.acom.ucar.edu/wrf-chem/download.shtml
  • Make sure you are still using an interactive shell ('srun -n 1 --mem=10000 --pty --x11=first -p test -t 200 bash' should be sufficient). Navigate to the MEGAN directory in the $CLIMATE_MODELS directory (or wherever you have saved your local copy of everything)
  • Create a new text file called megan_bio_emiss.inp. This is your MEGAN namelist file. Note that as the README instructs, the leaf area index (lai) months requires the simulation month and the previous month such that for January (as our example here is) we have to simulate all months.   Following Following the instructions in the README, you should populate to look like follows ... with the paths obviously reflecting where your WRF + external utility directories are located.
&control
domains = 3,
start_lai_monthmnth = 1,
end_lai_monthmnth = 12,
wrf_dir = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/UTILINP',
megan_dir = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/MEGAN'
/
  • You should be ready to run the MEGAN bio emission utility

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