Run CTSM¶

NB! this example is connected to project nn2806k (for your own project, change the project code. To see available projects and resources, use cost -p):

export CESM_ACCOUNT=nn2806k

Run your very first CTSM case¶

LOAD externals of CTSM (FATES and so on; only necessary first time), in folder ~/ctsm. If you are updating FATES go here first: (https://github.com/NordicESMhub/ctsm-dev/blob/master/Updating_FATES.md)

./manage_externals/checkout_externals

navigate to ~/ctsm/cime/scripts/

Inputdata¶

(only first time or whenever it disappears in your workdir i.e. 45 days)

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

Make a case¶

./create_newcase --case ~/cases/I2000Clm50BgcCruGs  --compset I2000Clm50BgcCruGs   --res f19_g17 --machine abel --run-unsupported --project $CESM_ACCOUNT

navigate to ~/cases/I2000Clm50BgcCruGs

1) check the configuration¶

./xmlquery --l #(--l list --f file)

eg

./xmlquery STOP_OPTION

2) Change configuration¶

For instance, to change the duration of a simulation to 5 days:

./xmlchange STOP_OPTION=ndays #(nyears, nmonths)
./xmlchange STOP_N=5 #(then 5 days)

or edit the xml files is another way to change these parameters (not recommended).

3) setup case¶

./case.setup  #(--reset)

4) edit user_nl_clm¶

add this below

hist_mfilt=5 #(number of output files)
hist_nhtfrq=-24 #(means daily outputs)

hist_mfilt allows you to specify the number of output files and hist_nhtfrq the frequency; here -24 means daily outputs.

5) case build¶

./case.build

Remark: if your build fails or if you make changes and need to rebuild, make sure you clean the previous build:

./case.build --clean

6) run case¶

./case.submit

Run fates¶

NB! Fates is not automatically checked out with the latest version (as it is still under development), and this has to be done manually.

Follow https://github.com/NordicESMhub/ctsm-dev/blob/master/Updating_FATES (based on https://github.uio.no/huit/clm5.0_notes/issues/26 and https://github.com/ESCOMP/ctsm/wiki/Protocols-on-updating-FATES-within-CTSM)

./create_newcase --case ../../../ctsm_cases/fates_f19_g17 --compset 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --res f19_g17 --machine abel --run-unsupported --project $CESM_ACCOUNT

Run a single cell case¶

CLM supports running using single-point or regional datasets that are customized to a particular region.

In the section below we show you how to run ready to use single-point configurations (out of the box) and then show you how to create your own dataset for any location of your choice.

Out of the box¶

To run for the Brazil test site do the following:

export CESM_ACCOUNT=nn2806k

./create_newcase -case ~/cases/testSPDATASET -res 1x1_brazil -compset I2000Clm50SpGs  --machine abel --run-unsupported --project $CESM_ACCOUNT

Remark: make sure you set CESM_ACCOUNT to your project.

Change configuration¶

./xmlchange NTASKS=1 #(number of CPU's, can be increased if excitation error)

Run a regional case¶

Follow the below procedure to run CTSM over a specific region of interest for a specific resolution. For example, to run over Scandinavia region (latitude 41N to 48N, longitude 4E to 42E) at 0.5 degree resolution: First produce the domain and surface data files for the region using the python script subset_surfdata.py available under the CTSM tools directory (~/ctsm/tools/contrib/).

Domain and surface data¶

Change the variable values ln1 to 4.0,ln2 to 42.0, lt1 to 41.0 and lt2 to 48.0 in the subset_data.py. The python script file here: https://github.com/ESCOMP/CTSM/blob/master/tools/contrib/subset_data.py

This python script produces the domain file and surface data file.

Inputdata¶

Other inputdata files are needed:

Use the already available inputdata stored under shared directory on both FRAM and SAGA machines.

To use the atmospheric forcing data do the following:
export ATMDATA=/cluster/shared/noresm/inputdata/atm/datm7/

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