The purpose of this page is to document the procedure for adding support for new atmosphere grids. The process should be the same for new uniform resolutions as well as for new regionally-refined meshes, although some settings will need to be changed for new regionally-refined mesh configurations. This page is a work in progress, and will be updated as this process is refined and (eventually) made more automated. This documentation is an update of a document written by Mark Taylor and Colin Zarzycki, available as a Google Doc here.
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File | Tool | Type | Note |
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ncks, ncremap | NCO | ||
mapping files and mesh template files | TempestRemap | C++ | GenerateCSMesh: make cubed sphere Exodus (.g) files (spectral element "np" grid) |
RRM Exodus (.g) mesh files | SquadGen | C++ | |
topo files | homme_tool | Fortran | Included with E3SM. Should build and run on any system which can run the HOMME_P24.f19_g16_rx1.A test Generate (obsolete) SCRIP files for the spectral element "np" dual grid Used for topo smoothing for both FV "pg" and SE "np" grids. Can also do parallel interpolation from SE np4 grid to any SCRIP grid |
topo files | cube_to_target | Fortran | NCAR utility for generating unsmoothed topography from high-res USGF data, and generating surface roughness fields from smoothed topography |
mapping files | ESMF_Regridweightgen | Make FV->FV mapping files from SCRIP grid template files Only tool which supports the montone 2nd order "bilin" map | |
| CIME and ELM tools | ||
land surface dataset | mksurfdata.pl, mksurfdata_map, | Perl and Fortran | |
ELM initial condition | interpinic | Fortran | 4 options:
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Archives of already-created atmosphere grid and mapping files can be accessed at https://web.lcrc.anl.gov/public/e3sm/mapping/grids/ and https://web.lcrc.anl.gov/public/e3sm/mapping/maps/ . This page focuses on creating new versions of these files.
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Generating the topography and related surface roughness data sets is a detailed process that has been moved to it’s own page, with detailed instructions depending on the model version (V1, V2, V3)
Atmospheric Topography Generation
6. Generate and spin-up a new atmosphere initial condition
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Code Block |
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#!/bin/bash # Get machine-specific modules env_mach_specific=env_mach_specific.sh source ${env_mach_specific} e3sm_root=/home/bhillma/codes/e3sm/branches/master interp_root=${e3sm_root}/components/cameam/tools/interpic_new template_file=${interp_root}/template.nc input_atm_ic_file=/projects/ccsm/inputdata/atm/cam/inic/fv/cami-mam3_0000-01-01_0.9x1.25_L30_c100618.nc nlevels=72 atm_latlon_file=/gscratch/bhillma/e3sm/grids/conusx8v1/conusx8v1np4b_latlon_170526.nc # specify a file to pull information about vertical levels from if [ ${nlevels} -eq 72 ]; then vertical_file=/projects/ccsm/inputdata/atm/cam/inic/homme/cami_mam3_Linoz_0000-01-ne120np4_L72_c160318.nc elif [ ${nlevels} -eq 30 ]; then vertical_file=/projects/ccsm/inputdata/atm/cam/inic/homme/cami-mam3_0000-01-ne120np4_L30_c110928.nc else echo "No input specified for nlevels=${nlevels}." exit 1 fi datestring=`date +'%y%m%d'` grid_name="conusx8v1" output_root="/gscratch/bhillma/e3sm/grids/${grid_name}" output_atm_ic_file=${output_root}/cami-mam3_0000-01-${grid_name}_L${nlevels}_c${datestring}.nc # copy horizontal coordinates to template file /projects/ccsm/nco/bin/ncks -O -v lat,lon ${atm_latlon_file} ${template_file} # copy vertical coordinates from existing initial condition to template file /projects/ccsm/nco/bin/ncks -A -v hyai,hybi,hyam,hybm ${vertical_file} ${template_file} # build tool cd ${interp_root} make clean gmake # run the interpolation code ./interpic -t ${template_file} ${input_atm_ic_file} ${output_atm_ic_file} # if input initial condition was from an FV grid, rename US->U, VS->V # this is hard-coded above, so yes we need to rename US and VS /projects/ccsm/nco/bin/ncrename -O -v US,U -v VS,V ${output_atm_ic_file} # update configuration file if [ $? -eq 0 ]; then echo "Successfully created ${output_atm_ic_file}." else echo "Something went wrong." exit 1 fi |
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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/elm/tools/mkmapdata/)
mksurfdata.pl (found in components/clm/tools/clm4_5/mksurfdata_map/)
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Create mapping files for each land surface type if needed. An (older and deprecated) example of doing this can be found here. Updated instructions follow:
Obtain or generate a target grid file in SCRIP format. For these example, we will use a ne1024pg2 grid file, which we will need to create (note that most np4 grid files can be found within the inputdata repository, for example, the ne1024np4 grid file is at https://web.lcrc.anl.gov/public/e3sm/mapping/grids/ne1024np4_scrip_c20191023.nc). To generate the pg2 SCRIP file:
Code Block ${tempest_root}/bin/GenerateCSMesh --alt --res 1024 --file ne1024.g ${tempest_root}/bin/GenerateVolumetricMesh --in ne1024.g --out ne1024pg2.g --np 2 --uniform ${tempest_root}/bin/ConvertMeshToSCRIP --in ne1024pg2.g --out ne1024pg2_scrip.nc
Get list of input grid files for each land surface input data file. This is done by running the components/elm/tools/mkmapdata/mkmapdata.sh script in debug mode to output a list of needed files (along with the commands that will be used to generate each map file; also make sure GRIDFILE is set to the SCRIP file from the above step):
Code Block language bash cd ${e3sm_root}/components/elm/tools/mkmapdata ./mkmapdata.sh --gridfile ${GRIDFILE} --inputdata-path ${INPUTDATA_ROOT} --res ne1024pg2 --gridtype global --output-filetype 64bit_offset --debug -v --list
Download needed input grid files. The above command will output a list of needed files to
clm.input_data_list
. We need to download all of these before calling the script without the debug flag to actually perform the mapping. This is possible usingcheck_input_data
in CIME, but needs to be done from a dummy case directory. So, one can create a dummy case,cd
to that case, and then call./check_input_data --data-list-dir <path where mkmapdata was run from> --download
. However, this failed to connect to the CESM SVN server for me. So instead, I used the following one-off script:Code Block #!/bin/bash e3sm_inputdata_repository="https://web.lcrc.anl.gov/public/e3sm" cesm_inputdata_repository="https://svn-ccsm-inputdata.cgd.ucar.edu/trunk" inputdata_list=clm.input_data_list cat $inputdata_list | while read line; do localpath=`echo ${line} | sed 's:.* = \(.*\):\1:'` url1=${e3sm_inputdata_repository}/`echo ${line} | sed 's:.*\(inputdata/lnd/.*\):\1:'` url2=${cesm_inputdata_repository}/`echo ${line} | sed 's:.*\(inputdata/lnd/.*\):\1:'` if [ ! -f ${localpath} ]; then echo "${url1} -> ${localpath}" mkdir -p `dirname ${localpath}` cd `dirname ${localpath}` # Try to download using first URL, if that fails then use the second wget ${url1} || wget ${url2} else echo "${localpath} exists, skipping." fi done
Create mapping files. Should just be able to run the above
mkmapdata.sh
command without the–debug --list
flags. We need to append the--outputfile-type 64bit_offset
flag for our large files (no reason not to do this by default anyways). NOTE - This step requires NCL, which is no longer part of the E3SM unified environement. If the machine you are using does not have an NCL module, creating a custom environement that includes NCL is an easy work around. Fixing this issue to avoid the NCL dependency will require rewriting the rmdups.ncl and mkunitymap.ncl script in another language (python+xarray would make sense). We will also need to write a version of the gc_qarea() function, unless the geocat project writes a port that we can use (see geocat issue #31).Code Block ./mkmapdata.sh --gridfile ${GRIDFILE} --inputdata-path ${INPUTDATA_ROOT} --res ne1024pg2 --gridtype global --output-filetype 64bit_offset -v
Compile surface dataset source code (NOTE:
${e3sm_root}/components/clm/tools/clm4_5/mksurfdata_map/src/Makefile.common
needs to be edited to build on most machines; this is fixed in https://github.com/E3SM-Project/E3SM/pull/2757):Code Block # Setup environment (should work on any E3SM-supported machine) eval $(${e3sm_root}/cime/CIME/Tools/get_case_env) ${e3sm_root}/cime/CIME/scripts/configure --macros-format Makefile --mpilib mpi-serial source .env_mach_specific.sh # Build mksurfdata_map cd ${e3sm_root}/components/elm/tools/mksurfdata_map/src INC_NETCDF="`nf-config --includedir`" \ LIB_NETCDF="`nc-config --libdir`" USER_FC="`nc-config --fc`" \ USER_LDFLAGS="`nf-config --flibs`" make
Note for Perlmutter (Jan 2023) - The build line above did not work on PM until it was modified as follows:
Code Block INC_NETCDF="`nf-config --includedir`" LIB_NETCDF="`nc-config --libdir`" USER_FC="`nc-config --fc`" USER_FFLAGS="" USER_FCTYP="ftn" USER_FFLAGS='-fallow-invalid-boz -fallow-argument-mismatch -ffree-line-length-none' make
Run the mksurfdata.pl script in "debug" mode to generate the namelist (use year 2010 on ne120np4 grids as an example).
Code Block # For supported resolutions #(use year 2010 on ne120np4 grids as an example) cd $e3sm_dir/components/elm/tools/mksurfdata_map ./mksurfdata.pl -res ne120np4 -y 2010 -d -dinlc /global/cfs/cdirs/e3sm/inputdata -usr_mapdir /global/cfs/cdirs/e3sm/inputdata/lnd/clm2/mappingdata/maps/ne120np4 # For unsupported, user-specified resolutions # (use year 2010 on ne50np4 grid as an example) # (Assuming the mapping files created in step 1 has a time stamp of '190409' in the filenames and the location of mapping files are '/whatever/directory/you/put/mapping/files') ./mksurfdata.pl -res usrspec -usr_gname ne50np4 -usr_gdate 190409 -y 2010 -d -dinlc /global/cfs/cdirs/e3sm/inputdata -usr_mapdir /whatever/directory/you/put/mapping/files
(However, ./mksurfdata.pl -h shows -y is by default 2010. When running without "-y" option, standard output says sim_year 2000. I suspect the mksurfdata.pl help information is wrong. To be confirmed.)
Modify namelist file
(Should the correct namelist settings be automatically picked up if the default land build name list settings are modified accordingly?)Time-evolving Land use land cover change (LULCC) data should not be used for fixed-time compsets, but the LULCC information for that particular year should be used (right?)
Manually change to mksrf_fvegtyp = '/global/cfs/cdirs/e3sm/inputdata/lnd/clm2/rawdata/AA_mksrf_landuse_rc_1850-2015_06062017_LUH2/AA_mksrf_landuse_rc_2010_06062017.nc' for the F2010 ne120 compset.Create the land surface data by interactive or batch job
Code Block rm -f surfdata_ne120np4_simyr2010.bash cat <<EOF >> surfdata_ne120np4_simyr2010.bash #!/bin/bash #SBATCH --job-name=mksurfdata2010 #SBATCH --account=acme #SBATCH --nodes=1 #SBATCH --output=mksurfdata.o%j #SBATCH --exclusive #SBATCH --time=00:30:00 #SBATCH --qos=debug # Load modules module load nco module load ncl module load cray-netcdf module load cray-hdf5 # mksurfdata_map is dynamically linked export LIB_NETCDF=$NETCDF_DIR/lib export INC_NETCDF=$NETCDF_DIR/include export USER_FC=ifort export USER_CC=icc export USER_LDFLAGS="-L$NETCDF_DIR/lib -lnetcdf -lnetcdff -lnetcdf_intel" export USER_LDFLAGS=$USER_LDFLAGS" -L$HDF5_DIR/lib -lhdf5 -lhdf5_fortran -lhdf5_cpp -lhdf5_fortran_intel -lhdf5_hl_intel -lhdf5hl_fortran_intel" cd /global/homes/t/tang30/ACME_code/MkLandSurf/components/clm/tools/clm4_5/mksurfdata_map CDATE=c`date +%y%m%d` # current date ./mksurfdata_map < namelist EOF sbatch surfdata_ne120np4_simyr2010.bash
The land surface data in NetCDF format will be created at current directory. (How to verify the file is correct?)
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From the README for mkatmsrffile
tool at components/cameam/tools/mkatmsrffile
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Atmospheric drydeposition at the surface depends on certain surface
properties including soil and land use properties. In most cases
these calculations can be handled in the land model and passed to he
atmosphere through the coupler. This is the default namelist setting
drydep_method='xactive_lnd'. However with modal areosols this method
is not adequate and we must recalculate these fields in the atmosphere
(see subroutine interp_map in mo_drydep.F90). For unstructured grids
it was determined to create this offline interpolation tool rather
than generalize the subroutine interp_map.
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Change directory to tool root:
cd components/cameam/tools/mkatmsrffile
Create a .env_mach_specific.sh by running
../../../../cime/tools/configure --macros-format=Makefile
Get machine-specific environment settings via
source .env_mach_specific.sh
Make sure
NETCDF_ROOT
andFC
environment variables are set right for your system, and build the executable:On Cori:
env NETCDF_ROOT=$NETCDF_DIR FC=ifort make
Edit "nml_atmsrf" to update the input file paths
Run the newly built executable
Code Block ./mkatmsrffile
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TempestRemap for generating uniform grids
(in Paul’s external git repo - may have its own tests?)SQuadGen for generating RRM grids
(in Paul’s external repo - may have its own tests?)Generate topography via Atmospheric Topography Generation )
needs utilities: components/cameam/tools/topo_tool/cube_to_target and comopnents/homme/test/tool
run ncremap (an NCO command) to generate mapping files
cime/tools/mapping/gen_domain_files
mksurfdata.pl to generate the namelist needed to make fsurdat file
use mksurfdata_map for fsurdat
use the interpic_new tool to regrid atmos state to new grid for initial condition
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smoothtopo.job
script used to run HOMME to apply dycore-specific smoothing to interpolated topography. It would be nice for this to be able to run via command line arguments rather than having to edit the script (which should make this easier to include in an automated workflow), and we should remove dependence on NCL since this is not guaranteed to be available.Replaced with “homme_tool”, 2020/5. see (see Atmospheric Topography Generation )
makegrid.job
script used to run HOMME+NCL to produce the non-optimized dualgrid and latlon descriptions of the SE grid. Again, it would be nice for this to be able to run via command line arguments rather than having to edit the script (which should make this easier to include in an automated workflow), and we should remove dependence on NCL since this is not guaranteed to be available.TR and PG2 grids make this obsolete - we now longer need the “dualgrid”.
Land surface data scripts (TODO: add specifics about what needs to change here)
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