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TempestRemap needs to be built from source from the Github repository. This is straightforward on Cori and Edison. Note that a parallel version of netCDF should be used. This can be accomplished on cori/edison be executing module swap cray-netcdf cray-netcdf-hdf5parallel or by sourcing an env_mach_specific.sh from a working case on the target machine before building. Then, 

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Step (a) downscale USGS topography data to the atmosphere grid
Step (b) apply dycore-specific smoothing to reduce the amount of gravity wave noise if the topography is too rough. This is a tunable parameter, and a rigorous analysis probably needs to be performed to determine the optimal tuning parameter for future very-high-resolution atmosphere grids.  For pg2 grids there is the extra step of generating consistent topo data on both the GLL (dynamics) and pg2 (physics) grid.  
Step (c) based on the smoothed topography, compute the SGH and SGH30 surface roughness fields used by some parameterizations

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Step (b) requires running the homme_tool's smoothing algorithm.  The namelist should be edited to specify the resolution (NE value) or grid file (RRM) grid and the amount of smoothing
(TODO: allow running this script with command line arguments instead of manual editing so that the task can be automated).   

For physics and dynamics on the GLL grid (E3SM V1): see (move text below to separate page)

For "pg2" grids (E3SM v2):  see the instructions on  Special Considerations for FV Physics Grids

Step (a)

To begin Step (a) with a SCRIP file in hand,  interpolate the high resolution USGS data. The source topography file is the USGS high resolution topography on a 3 km cube sphere grid. This data exists on the CESM inputdata server here.  The data has also been downloaded to NERSC computing facilities and is located here:

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1. For cubed sphere grids:
   1. Set resolution via set ne = 4  (for ne4 example here).
   2. Set  smooth_phis_numcycle=16.    (adjustable paramemter, lower for less smoothing)
   3. Set smooth_phis_nudt.  This is a resolution dependent parameter, recommend value for cubed sphere grids is 28e7 * ( 30/NE)**2
2. For RRM grids, we use the tensor laplace operator so that the amount of smoothing is proportional to the resolution
   1. ne=0, mesh_file=/path/to/exodus-rrm-grid-file.g
   2. Set  smooth_phis_numcycle=12.    (adjustable paramemter, lower for less smoothing)
   3. smooth_phis_nudt = 4e-16.  
3. Set infilenames=/path/to/unsmoothed/PHISdata

After running the tool, the output will be named "geos", in the file phis-smoothed1.nc, along with other unnecessary fields.  To convert this file into an EAM topo file:

• ncks -O -v geos,lat,lon phis-smoothed1.nc phis-smoothed2.nc
• ncrename -v geos,PHIS phis-smoothed2.nc

Step (c)

The topography tool then needs to be re-ran to compute the subgrid surface roughness. This is done by passing an extra argument to the topography tool with the smoothed topography output from the standalone HOMME run above:

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• land grid descriptor file in SCRIP format 
• ESMF_RegridWeightGen
• geographic distribution for each land surface type along with grid descriptor files for each of those surface types
• mkmapdata.sh (found in components/clm/tools/shared/mkmapdata/)
• mksurfdata.pl (found in components/clm/tools/clm4_5/mksurfdata_map/)

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