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Comment: clarify instructions

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For physics-side nudging, available reanalysis data is pre-processed prior to model use. This preparation step interpolates the desired reanalysis data onto a given model grid, adjusts values to account for topographical differences between the reanalysis model and the current topography of CESM, and saves the results in individual files with one time slice per file. The scripts that carry out this processing must be configured for each combination of input reanalysis dataset and output model grid. The scripts are currently available for the FV and SE dycore grids.

The details below are for regridding GEOS and MERRA2 files, particularly on the NCAR HPC. Users wishing to use alternate reanalysis datasets should consult the README.

The processing scripts are slightly different for the two available dycores, so they are contained in separate directories in the IPT repository https://github.com/NCAR/IPT/tree/master/Meterological_Reanalysis_Data. in each directory, there is a README that provides general guidance for setting the script variables for a desired reanalysis product.

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casper%  cp -r Gen_Data_NEWGRID Gen_Data_ne0np4.SAM01.ne30x4

casper% cd Gen_Data_ne0np4.SAM01.ne30x4

casper% mv Gen_MERRA2_NEWGRID.csh Gen_MERRA2_ne0np4.SAM01.ne30x4.csh

...

  1. Edit your new script, and set the PBS commands:

#!/bin/csh
#PBS -N Gen_MERRA2_ne0np4.SAM01.ne30x4
#PBS -A Pxxxxxxx
#PBS -l select=2:ncpus=4:mpiprocs=4:mem=20GB
#PBS -l walltime=12:00:00
#PBS -q casper
#PBS -o Log.Gen_MERRA2_SAM01.err
#PBS -e Log.Gen_MERRA2_SAM01.out

module load ncl

After making the changes below you can submit this job on casper:

casper% qsub Gen_MERRA2_ne0np4.SAM01.ne30x4.csh

    2. In the Configuration section, set the reference date corresponding to the first day of data you desire, then number of days of data to process from that date, and the path where you wish to have the data stored:

 #=============================================================

 # CONFIGURATION SECTION:

 #=============================================================

 # Set a REFERENCE (Starting) Date and the number of days to process

 #--------------------------------------------------------------------------------------------------------

 set RUNNUM=01

 set REF_DATE='20121201'

 set NUM_DAYS=400


 # Set INPUT/OUTPUT/TMP directories

 #--------------------------------------------------------

 set NAMELIST='./Config/Config_makeIC-'$RUNNUM'.nl'

 set MYLOGDIR='./LOG/LOG_002.'$RUNNUM'/'

 set MYTMPDIR='./TMP/TMP_002.'$RUNNUM'/'

 set MYOUTDIR='/path/to/my/repo/ne0np4.SAM01.ne30x4/nudging/MERRA2_ne0np4.SAM01.ne30x4_L32/'

 set INPUTDIR='/glade/collections/rda/data/ds313.3/orig_res/'


 # Set ESMF options

 #---------------------------

 set ESMF_interp='conserve'

 set ESMF_pole='none'

 set ESMF_clean='False'

 set ESMF_clean='True'

3. For the processing options, set the CASE name. This is the root filename for your nudging data files. Note that some reanalysis datasets store winds in the form of vorticity and divergence values rather then U,V. It is important that the VORT_DIV_TO_UV flag is set to True for these datasets, this is a common source of processing errors. Finally, set the fname_grid_info value to point to a file containing the desired ouput grid, and set fname_phis_output to point to a file containing the model topography.

 # Set Processing options

 #-------------------------------------

 set CASE   = 'MERRA2_ne0np4.SAM01.ne30x4_L32'

 set DYCORE     = 'se'

 set PRECISION = 'float'

 set VORT_DIV_TO_UV = 'False'

 set SST_MASK           = 'False'

 set ICE_MASK           = 'False'

 set OUTPUT_PHIS      = 'True'

 set REGRID_ALL        = 'False'

 set ADJUST_STATE_FROM_TOPO = 'True'

 set MASS_FIX           = 'True'


 # Set files containing OUTPUT Grid structure and topography

 #--------------------------------------------------------------------------------------------

 set fname_grid_info = '/path/to/my/repo/ne0np4.SAM01.ne30x4/inic/cami-mam4_0000-01-01_ne0np4.SAM01.ne30x4_L32_c200309.nc'

 set fname_phis_output = '/path/to/my/repo/ne0np4.SAM01.ne30x4/topo/topo_ne30np4.SAM01.ne30x4_blin_200309.nc'

 set ftype_phis_output = 'SE_TOPOGRAPHY'

4. Update the path to WRAPIT:  /glade/u/apps/opt/ncl/6.6.2/bin/WRAPIT MAKEIC.stub MAKEIC.f90

The last modification that is needed for this example is to edit 5. Edit the file makeIC_se_002.ncl. At about line 430, the dstGridName variable has to be set to use the SCRIP file for your new grid:

   dstGridName="/path/to/my/repo/ne0np4.SAM01.ne30x4/grids/SAM01_ne30x4_SCRIP.nc"

After making the changes above you can submit this job on casper:

casper% qsub Gen_MERRA2_ne0np4.SAM01.ne30x4.csh

With these changes, the script can be submitted to generate the desired 400 days of data. The user must alway check the Log and output file to verify that the dataset was processed correctly. Selecting some files and browsing variables for valid values using ncdump can save a lot of time and effort if there were problems during the processing. 

...

A script for regridding to FV on casper (functioning as of 7/19/2024) is: /glade/u/home/emmons/my_IPT/Meterological_Reanalysis_Data/Finite_volume_dycore/Gen_Data_f09_83L/Gen_MERRA2_fv09_83L_001.csh