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regional_case.rst

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Here, the regional case procedure is explained for running the model over Fennoscandia and Svalbard region at 0.25 degree spatial resolution on Abel.

Required input files (domain and surface data) are already produced and stored under the main inputdata directory. So, start with linking the main inputdata files to your working directory.

cd ~/ctsm/cime/scripts
./link_dirtree $CESM_DATA /work/users/$USER/inputdata
export MYCTSMDATA=/work/users/$USER/inputdata

Definitions

As mentioned earlier in this documentation, you need to define your project account (e.g. nn2806k) before running the model. To be sure that you are using the correct version of netcdf and practical purposes, we will export the paths and some environment variables :

export CESM_ACCOUNT=nn2806k
export PROJECT=nn2806k
export CTSMROOT=/cluster/home/$USER/ctsm

export INC_NETCDF=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1/
export LIB_NETCDF=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1/
export NETCDF_ROOT=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1

Make a case

To run the model with Satellite Phenology mode, do the following

cd $CTSMROOT/cime/scripts
./create_newcase -case ~/cases/SCA_SpRun -res CLM_USRDAT -compset I2000Clm50SpGs --machine abel --run-unsupported --project $CESM_ACCOUNT

Here, the compset I2000Clm50SpGs initialize the model from 2000 conditions with GSWP3 atmospheric forcing data. If you want to run CTSM with BGC mode and force with CRU NCEP v7 data set, use I2000Clm50BgcCruGs compset. To see available compset aliases and their long names, type the following :

$CTSMROOT/cime/scripts/query_config --compsets clm

Note that you can use only the compsets with SGLC (Stub glacier (land ice) component) for single point and regional cases. Otherwise, simulation fails.

Set up the case

Now, we are setting up our test simulation for three years between 2000-2002.

cd ~/cases/SCA_SpRun
export GRIDNAME=0.25_SCA
export SCA_DATA=$MYCTSMDATA/share/domains/
export ATMDOM=domain.0.25x0.25_SCA.nc

./xmlchange DIN_LOC_ROOT=$MYCTSMDATA
./xmlchange ATM_DOMAIN_PATH=$SCA_DATA,LND_DOMAIN_PATH=$SCA_DATA
./xmlchange ATM_DOMAIN_FILE=$ATMDOM,LND_DOMAIN_FILE=$ATMDOM
./xmlchange CLM_USRDAT_NAME=$GRIDNAME
./xmlchange STOP_OPTION=nyears
./xmlchange STOP_N=3
./xmlchange NTASKS=16
./xmlchange JOB_WALLCLOCK_TIME="03:59:00"
./xmlchange PROJECT=$CESM_ACCOUNT
./xmlchange RUN_STARTDATE="2000-01-01"
./xmlchange RESUBMIT="0"
./xmlchange DATM_CLMNCEP_YR_ALIGN="2000"
./xmlchange DATM_CLMNCEP_YR_START="2000"
./xmlchange DATM_CLMNCEP_YR_END="2002"
./xmlchange DOUT_S="FALSE"
./xmlchange GMAKE_J="8"
./case.setup
./preview_run

Customizing the CLM namelist

In order to define the location of surface data file for our Scandinavia region, we add the fsurdat setting to the land model's namelist.

cat << EOF > user_nl_clm
fsurdat="$MYCTSMDATA/lnd/clm2/surfdata_map/surfdata_0.25_SCA_hist_16pfts_Irrig_CMIP6_simyr2000_c190814.nc"
EOF

If you run your simulation with BGC mode, then you need to set another surface data map as follows:

cat << EOF > user_nl_clm
fsurdat="$MYCTSMDATA/lnd/clm2/surfdata_map/surfdata_0.25_SCA_hist_78pfts_CMIP6_simyr2000_c190819.nc"
EOF

If you want to print out only selected variables in hourly resolution in the model output files for each year:

cat << EOF > user_nl_clm
fsurdat="$MYCTSMDATA/lnd/clm2/surfdata_map/surfdata_0.25_SCA_hist_16pfts_Irrig_CMIP6_simyr2000_c190814.nc"
hist_empty_htapes = .true.
hist_fincl1 = 'TSA', 'TSKIN', 'EFLX_LH_TOT', 'FSH', 'WIND', 'TWS', 'SNOWLIQ', 'SNOWICE', 'SNOW_DEPTH', 'TSOI', 'H2OSOI'
hist_nhtfrq = -1
hist_mfilt = 365
EOF

Note that the variable names (e.g. 'TSA', 'TSKIN', 'EFLX_LH_TOT', etc.) are following the CESM name convention.

Build and submit the case

Final step is to build the case and submit the job to the queue.

./case.build
./case.submit