models/lnd/clm/tools/README Jun/04/2013 CLM tools for analysis of CLM history files -- or for creation or modification of CLM input files. I. General directory structure: clm4_0 mksurfdata_map --- Create surface datasets. interpinic ------- Interpolate initial datasets to a different resolution. (has optimized and OMP options) clm4_5 mksurfdata_map --- Create surface datasets. interpinic ------- Interpolate initial datasets to a different resolution. (has optimized and OMP options) shared mkmapgrids ------- Create SCRIP grid files needed by mkmapdata [input is CLM grid files] (deprecated) mkmapdata -------- Create SCRIP mapping data from SCRIP grid files (uses ESMF) gen_domain ------- Create data model domain datasets from SCRIP mapping datasets. (also in the top level mapping directory [../../../../tools/mapping]) mkprocdata_map --- Convert output unstructured grids into a 2D format that can be plotted easily ncl_scripts ------ NCL post or pre processing scripts. Note that there are different versions of mksurfdata_map and interpinic for CLM4.0 vs. CLM4.5. Other tools are shared between the two model versions. However, note that mkmapdata makes mapping files for CLM4.5 by default; to make mapping files for CLM4.0, run the tool with the option: -p clm4_0 II. Notes on building/running for each of the above tools: Each tool that has FORTRAN source code has the following files: README -------------- Specific help for using the specific tool and help on specific files in that directory. src/Filepath -------- List of directories needed to build the tool (some files in ../src directories are required). src/Makefile -------- Customization of the make for the particular tool in question src/Makefile.common - General GNU Makefile for creating FORTRAN tools (these are identical between tools). src/Srcfiles -------- List of source files that are needed. src/Mkdepends ------- Dependency generator program mkmapdata and ncl_scripts only contain scripts so don't have the above build files. Most tools have copies of files from other directories -- see the README.filecopies file for more information on this. Tools may also have files with the directory name followed by: namelist, or runoptions. .namelist ------ Namelist to create a global file. .runoptions ---- Command line options to use the given tool. These files are also used by the test scripts to test the tools (see the README.testing) file. NOTE: Be sure to change the path of the datasets references by these namelists to point to where you have exported your CESM inputdata datasets. To build: cd setenv INC_NETCDF setenv LIB_NETCDF gmake The process will create a file called "Depends" which has the dependencies for the build of each file on other files. By default some codes may be compiled non-optimized so that you can use the debugger, and with bounds-checking, and float trapping on. To speed up do the following... gmake OPT=TRUE (by default already on for interpinic and mksurfdata_map) Also some of the tools allow for OpenMP shared memory parallelism (such as interpinic) with gmake SMP=TRUE To run a program with a namelist: ./program < namelist To get help on running a program with command line options (e.g., interpinic): ./program To run a program built with SMP=TRUE: setenv OMP_NUM_THREADS= run normally as above III. Process sequence to create input datasets needed to run CLM NOTE: The following assumes you want to create files for CLM4.5. If you want to use CLM4.0, you will need to do the following: - In the following commands, change references to the clm4_5 directory to clm4_0 - Add the option '-p clm4_0' to the mkmapdata.sh command. 1.) Create SCRIP grid files (if needed) a.) For standard resolutions these files will already be created. (done) b.) To create regular lat-lon regional/single-point grids run mknoocnmap.pl This will create both SCRIP grid files and a mapping file that will be valid if the region includes NO ocean whatsoever (so you can skip step 2). You can also use this script to create SCRIP grid files for a region (or even a global grid) that DOES include ocean if you use step 2 to create mapping files for it (simply discard the non-ocean map created by this script). Example, for single-point over Boulder Colorado. cd shared/mkmapdata ./mknoocnmap.pl -p 40,255 -n 1x1_boulderCO c.) General case You'll need to convert or create SCRIP grid files on your own (using scripts or other tools) for the general case where you have an unstructured grid, or a grid that is not regular in latitude and longitude. example format ================== netcdf fv1.9x2.5_090205 { dimensions: grid_size = 13824 ; grid_corners = 4 ; grid_rank = 2 ; variables: double grid_center_lat(grid_size) ; grid_center_lat:units = "degrees" ; double grid_center_lon(grid_size) ; grid_center_lon:units = "degrees" ; double grid_corner_lat(grid_size, grid_corners) ; grid_corner_lat:units = "degrees" ; double grid_corner_lon(grid_size, grid_corners) ; grid_corner_lon:units = "degrees" ; int grid_dims(grid_rank) ; int grid_imask(grid_size) ; grid_imask:units = "unitless" ; 2.) Create ocean to atmosphere mapping file (if needed) a.) Standard resolutions (done) If this is a standard resolution with a standard ocean resolution -- this step is already done, the files already exist. b.) Region without Ocean (done in step 1.b) IF YOU RAN mknoocnmap.pl FOR A REGION WITHOUT OCEAN THIS STEP IS ALREADY DONE. c.) New atmosphere or ocean resolution If the region DOES include ocean, use gen_domain to create a mapping file for it. Example: cd ../../../../tools/mapping/gen_domain_files/src ./gen_domain -m $MAPFILE -o $OCNGRIDNAME -l $ATMGRIDNAME 3.) Add SCRIP grid file(s) created in (1) into XML database in CLM (optional) See the "Adding New Resolutions or New Files to the build-namelist Database" Chapter in the CLM User's Guide http://www.cesm.ucar.edu/models/cesm1.0/clm/models/lnd/clm/doc/UsersGuide/book1.html If you don't do this step, you'll need to specify the file to mkmapdata in step (3) using the "-f" option. 4.) Create mapping files for use by mksurfdata_map with mkmapdata (See mkmapdata/README for more help on doing this) - this step uses the results of (1) that were entered into the XML database by step (3). If you don't enter datasets in, you need to specify the SCRIP grid file using the "-f" option to mkmapdata.sh. - note that mkmapdata generates maps for CLM4.5 by default; to generate mapping files for CLM4.0, add the option '-p clm4_0' Example: to generate all necessary mapping files for the ne30np4 grid cd shared/mkmapdata ./mkmapdata.sh -r ne30np4 NOTE: ON yellowstone YOU'll NEED TO SUBMIT THIS TO BATCH USE the regridbatch.sh SCRIPT TO DO THAT! 5.) Add mapping file(s) created in step (4) into XML database in CLM (optional) See notes on doing this in step (3) above. Edit ../bld/namelist_files/namelist_defaults_clm.xml to incorporate new mapping files. If you don't do this step, you'll need to specify the grid resolution name and file creation dates to mksurfdata_map in step (5) below. 6.) Convert map of ocean to atm for use by DATM and CLM with gen_domain (See tools/mapping/README for more help on doing this) - gen_domain uses the map from step (2) (or previously created CESM maps) Example: cd ../../../../tools/mapping/gen_domain_files/src gmake cd .. setenv CDATE 090206 setenv OCNGRIDNAME gx1v6 setenv ATMGRIDNAME fv1.9x2.5 setenv MAPFILE $CSMDATA/cpl/cpl6/map_${OCNGRIDNAME}_to_${ATMGRIDNAME}_aave_da_${CDATE}.nc ./gen_domain -m $MAPFILE -o $OCNGRIDNAME -l $ATMGRIDNAME Normally for I compsets running CLM only you will discard the ocean domain file, and only use the atmosphere domain file for datm and as the fatmlndfrc file for CLM. Output domain files will be named according to the input OCN/LND gridnames. 7.) Create surface datasets with mksurfdata_map (See mksurfdata_map/README for more help on doing this) - Run clm4_5/mksurfdata_map/mksurfdata.pl - This step uses the results of step (4) entered into the XML database in step (5). - If datasets were NOT entered into the XML database, set the resolution to "usrspec" and use the "-usr_gname", and "-usr_gdate" options. Example: for 0.9x1.25 resolution cd clm4_5/mksurfdata_map/src gmake cd .. ./mksurfdata.pl -r 0.9x1.25 NOTE that surface dataset will be used by default for fatmgrid - and it will contain the lat,lon,edges and area values for the atm grid - ASSUMING that the atm and land grid are the same 8.) Interpolate initial conditions using interpinic (optional) (See interpinic/README for more help on doing this) IMPORTANT NOTE on interpinic!!!:: BE SURE TO USE NetCDF4.3 WHEN BUILDING! If your template file was written using pnetcdf -- interpinic will corrupt the resulting file and make it unusable! 9.) Add new files to XML data or using user_nl_clm (optional) See notes on doing this in step (3) above. IV. Example of creating single-point datasets without entering into XML database. Here we apply the process described in III. for a single-point dataset where we don't enter the datasets into the XML database (thus skipping steps 3, 5 and 9), but use the needed command line options to specify where the files are. This also skips step (2) since step 1 creates the needed mapping file. We also skip step (8) and do NOT create a finidat file. 0.) Set name of grid to use and the creation date to be used later... setenv GRIDNAME 1x1_boulderCO setenv CDATE `date +%y%m%d` 1.) SCRIP grid and atm to ocn mapping file cd shared/mkmapdata ./mknoocnmap.pl -p 40,255 -n $GRIDNAME # Set pointer to MAPFILE that will be used in step (6) setenv MAPFILE `pwd`/map_${GRIDNAME}_noocean_to_${GRIDNAME}_nomask_aave_da_${CDATE}.nc cd ../.. 2.) skip 3.) skip 4.) Mapping files needed for mksurfdata_map # NOTE: ON yellowstone YOU'll NEED TO SUBMIT THIS TO BATCH. # here we use the execca script to submit the command line cd shared/mkmapdata setenv GRIDFILE ../mkmapgrids/SCRIPgrid_${GRIDNAME}_nomask_${CDATE}.nc execca ./mkmapdata.sh -r $GRIDNAME -f $GRIDFILE -t regional cd .. 5.) skip 6.) Generate domain file for datm and CLM cd ../../../../tools/mapping/gen_domain_files/src gmake cd .. setenv OCNDOM domain.ocn_noocean.nc setenv ATMDOM domain.lnd.{$GRIDNAME}_noocean.nc ./gen_domain -m $MAPFILE -o $OCNDOM -l $ATMDOM cd ../../../../lnd/clm/tools 7.) Create surface dataset for CLM cd clm4_5/mksurfdata_map/src gmake cd .. ./mksurfdata.pl -r usrspec -usr_gname $GRIDNAME -usr_gdate $CDATE 8.) skip 9.) skip V. Notes on which input datasets are needed for CLM global or regional/single-point grids - need fsurdata and fatmlndfrc fsurdata ---- from mksurfdata_map in step (III.7) fatmlndfrc -- use the domain.lnd file from gen_domain in step (III.6) (NOTE: THIS FILE IS POINTED TO USING ATM_DOMAIN_PATH/ATM_DOMAIN_FILE/LND_DOMAIN_PATH/LND_DOMAIN_FILE env_run.xml variables -- do NOT simply add this to your user_nl_clm as it will fail)