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. Customized ~~~~~~~~~~~

Step-1:

Step-2: For atmospheric forcing (own atm forcing and surface data) (include scripts)

# 0) mkdir ~/single_cell_experiment #Create a directory in your home directory calles "single_cell_experiment".
# 0) cd ~/single_cell_experiment
#Then put all the scripts below in "single_cell_experiment".
# 1) MAIN SCRIPT : call it as you wish (run_clm_single.sh)
# 2) regridbatch.sh
# 3) run_locality_append.sh
# 4) stream_file_1901_to_2014
# 5) prepare_atm_forcing_data_CRUNCEP_1901-1920.ncl # this file must be duplicated and modified to fit the dates and the forcing (gswp or cru)

########################################____MAIN_SCRIPT___############################################## #!/bin/sh

path1=”~/single_cell_experiment” #main directory path path2=”~/ctsm” #clm path path3=”/work/users/marlam/inputdata” #inputdata path path4=”~/cases” #directory where the case will be run

#For single cell only compsets with SGLC work!! compset0=I2000Clm50BgcCruGs #2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV

#If you want to use CRU as atm forcing : put these files in “single_cell_directory and adapt them. #This process must be separated in periods shorter than 50 years prepare_atm_data1=”prepare_atm_forcing_data_CRUNCEP_1901-1920.ncl” prepare_atm_data2=”prepare_atm_forcing_data_CRUNCEP_1921-1955.ncl” prepare_atm_data3=”prepare_atm_forcing_data_CRUNCEP_1956-1990.ncl” prepare_atm_data4=”prepare_atm_forcing_data_CRUNCEP_1991-2016.ncl”

#If you want to use GSWP3 as atm forcing : put these files in “single_cell_experiment” and adapt them. prepare_atm_dataA=”prepare_atm_forcing_data_GSWP_1901-1935.ncl” prepare_atm_dataB=”prepare_atm_forcing_data_GSWP_1936-1972.ncl” prepare_atm_dataC=”prepare_atm_forcing_data_GSWP_1973-2010.ncl”

regridbatch_file=”regridbatch.sh” # You will find this script below–> put it in “single_cell_experiment” stream_file=”stream_file_1901_to_2014” # if you use your own atm forcing you will need to modify this file, take it from below #and put it in the “single_cell_experiment” directory. imports=”run_locality_append.sh” # You will find this script below–> put it in “single_cell_experiment”

#this are the stations for GRIDNAME in “1x1_Abisko_pan” #”1x1_Kytalyk_pan” “1x1_Bayelva_pan” “1x1_Zackenberg_pan” do

echo echo $GRIDNAME case $GRIDNAME in

1x1_Abisko_pan)

plot_lat=68.35 plot_lon=19.05 CDATE=181219 #`date +%y%m%d` ;;

1x1_Bayelva_pan)

plot_lat=78.92 plot_lon=11.93 CDATE=190103 #today YYMMDD ;;

1x1_Kytalyk_pan)

plot_lat=70.83 plot_lon=147.5 CDATE=190110 #today YYMMDD ;;

1x1_Zackenberg_pan)

plot_lat=74.5 plot_lon=339.4 CDATE=190103 #today YYMMDD ;;

esac

module load python2/2.7.10 module load ncl module load nco module unload netcdf.gnu/4.4.1.1

###############################¸¸¸¸¸¸¸¸¸ SURFACEDATA¸¸¸¸¸¸¸¸¸¸¸#######################_________________________A if false #1 Make SCRIPgrid of single cell______________________________________________________________________________A.1 then

cd ${path2}/tools/mkmapdata

./mknoocnmap.pl -p $plot_lat,$plot_lon -n $GRIDNAME mv ../mkmapgrids/SCRIPgrid_${GRIDNAME}_nomask_c${CDATE}.nc ../mkmapgrids/SCRIPgrid_${GRIDNAME}_nomask.nc mkdir -p ${path2}/tools/mkmapdata/$GRIDNAME mv ${path2}/tools/mkmapdata/map_${GRIDNAME}_noocean_to_${GRIDNAME}_nomask_aave_da_${CDATE}.nc ${path2}/tools/mkmapdata/$GRIDNAME/map_${GRIDNAME}_noocean_to_${GRIDNAME}_nomask_aave_da_${CDATE}.nc

# 2)Create the mapping files needed by mksurfdata_map__________________________________________________________A.2 #here we create a temporary file were we include GRIDNAME and then another were we include CDATE –> CDATE must be CORRECT!!!!!!!!

echo “________________________________________Start creating mappig files” cd ${path1} tmp=$(<${regridbatch_file}) echo “${tmp//GRIDNAME/$GRIDNAME}” > regridbatch_$GRIDNAME.sh mv -f regridbatch_$GRIDNAME.sh ${path2}/tools/mkmapdata/regridbatch_$GRIDNAME.sh cd ${path2}/tools/mkmapdata chmod u+x regridbatch_$GRIDNAME.sh sbatch regridbatch_$GRIDNAME.sh sleep 300m

fi

if false #2 then

cd ${path2}/tools/mkmapdata mv -f map_*$GRIDNAME* $GRIDNAME/

# 3) Create the domain file_____________________________________________________________________________________A.3

echo “__________________________________________Start creating domain file” cd ${path1}

. ./$imports

cd ${path2}/cime/tools/mapping/gen_domain_files/src ../../../configure –macros-format Makefile –mpilib mpi-serial –machine abel –compiler intel –clean . ./.env_mach_specific.sh gmake cd .. OCNDOM=domain.ocn_noocean.nc ATMDOM=domain.lnd.{$GRIDNAME}_noocean.nccd MAPFILE=”${path2}/tools/mkmapdata/${GRIDNAME}/map_${GRIDNAME}_noocean_to_${GRIDNAME}_nomask_aave_da_${CDATE}.nc” ./gen_domain -m $MAPFILE -o $OCNDOM -l $ATMDOM mkdir -p $GRIDNAME mv domain* $GRIDNAME/ mv -f $GRIDNAME/domain.lnd.*{$GRIDNAME}*.nc $GRIDNAME/domain.lnd.{$GRIDNAME}_noocean.nc

fi

if false #3 then # 4) Finally create the surface dataset_________________________________________________________________________A.4

echo “__________________________________________Start creating surface data” cd ${path1} . ./run_locality_append.sh cd ${path2}/tools/mksurfdata_map/src gmake clean gmake cd .. ./mksurfdata.pl -r usrspec -usr_gname $GRIDNAME -usr_gdate $CDATE -dinlc ${path3} -allownofile -usr_mapdir ../mkmapdata/$GRIDNAME -years 2000 -no-crop #not working for years 1850 :/ #-no-crop necessary because model is expecting 16 pfts, or with crop but change xml variables mv ${path2}/tools/mksurfdata_map/surfdata_${GRIDNAME}_*.nc ${path3}/lnd/clm2/surfdata_map/surfdata_${GRIDNAME}_simyr2000.nc rm -rf surfdata*.log surfdata*.namelist rm -rf ${path2}/tools/mkmapdata/${GRIDNAME}

fi

OCNDOM=domain.ocn_noocean.nc ATMDOM=domain.lnd.{$GRIDNAME}_noocean.nc GENDOM_PATH=${path2}/cime/tools/mapping/gen_domain_files/$GRIDNAME

###########################,,,,,,,,,,,ATMOSPHERIC FORCING,,,,,,,,,,,,,###_______________________________________B if false #4 then

cd ${path1} module load ncl ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_data1} ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_data2} ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_data3} ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_data4} #output is there: /work/users/marlam/inputdata/atm/datm7/CLM1PT_data/

fi if false #4 then

cd ${path1} module load ncl ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_dataA} ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_dataB} ncl ‘plot_name=”’$GRIDNAME’”’ plot_lat=$plot_lat plot_lon=$plot_lon ${prepare_atm_dataC} #output is there: /work/users/marlam/inputdata/atm/datm7/CLM1PT_data2/

fi

#00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 #00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000

############################,,,,,,,,,,CASE__SETUP,,,,,,,,,,,,,,,,,,,,,,####______________________________________ if true #5 then

cd ${path2}/cime/scripts echo “_____________________________________________Start create case” export CESM_ACCOUNT=geofag ./create_newcase –case ~/cases/${GRIDNAME}_${compset0} –compset ${compset0} –res CLM_USRDAT –machine abel –run-unsupported –project geofag

fi

if true #6 then

echo “____________________________________________Start changes” cd ${path4}/${GRIDNAME}_${compset0} ./xmlchange ATM_DOMAIN_PATH=$GENDOM_PATH,LND_DOMAIN_PATH=$GENDOM_PATH ./xmlchange ATM_DOMAIN_FILE=$ATMDOM,LND_DOMAIN_FILE=$ATMDOM ./xmlchange CLM_USRDAT_NAME=$GRIDNAME ./xmlchange STOP_OPTION=nyears ./xmlchange STOP_N=114 ./xmlchange RUN_STARTDATE=”1901-01-01” ./xmlchange DATM_MODE=”CLM1PT” ./xmlchange RESUBMIT=”0” ./xmlchange DIN_LOC_ROOT_CLMFORC=”${path3}/atm/datm7/CLM1PT_data” ./xmlchange JOB_WALLCLOCK_TIME=”03:59:00” ./xmlchange PROJECT=”geofag” ./xmlchange DATM_CLMNCEP_YR_ALIGN=”1901” ./xmlchange DATM_CLMNCEP_YR_START=”1901” ./xmlchange DATM_CLMNCEP_YR_END=”2014” ./xmlchange DOUT_S=”FALSE” ./xmlchange GMAKE_J=”8” ./xmlchange CLM_ACCELERATED_SPINUP=”off” #fire_method=’nofire’ cat > user_nl_clm << EOF

&clm_inparm: create_crop_landunit = .true. fsurdat=’${path3}/lnd/clm2/surfdata_map/surfdata_${GRIDNAME}_simyr2000.nc’ hist_mfilt=365 hist_nhtfrq=-24

/ &ndepdyn_nml

ndepmapalgo = ‘nn’

/ &popd_streams

popdensmapalgo = ‘nn’

/ &light_streams

lightngmapalgo = ‘nn’

/ EOF

cat> user_nl_datm <<EOF

&shr_strdata_nml: vectors = ‘null’ mapmask = ‘nomask’,’nomask’,’nomask’ mapalgo = ‘nn’,’nn’,’nn’ tintalgo = ‘nearest’,’linear’,’lower’ taxmode = ‘cycle’,’extend’,’extend’ streams = ‘datm.streams.txt.CLM1PT.CLM_USRDAT 1901 1901 2014 ‘,

‘datm.streams.txt.presaero.clim_2000 1 1 1’, ‘datm.streams.txt.topo.observed 1 1 1’

/ EOF

echo “____________________________________________Changes done” cd ${path1} . ./$imports cd ${path4}/${GRIDNAME}_${compset0} ./case.setup # –reset echo “____________________________________________Case setup successfully”

# ./case.build –clean: ./case.build echo “____________________________________________Case build successfully”

fi

if false #7 then

cd ${path1} . ./$imports tmp=$(<${stream_file}) echo “${tmp//GRIDNAME/$GRIDNAME}” > user_datm.streams.txt.CLM1PT.CLM_USRDAT_${GRIDNAME} cd ${path4}/${GRIDNAME}_${compset0} ./preview_namelists mv -f ${path1}/user_datm.streams.txt.CLM1PT.CLM_USRDAT_${GRIDNAME} user_datm.streams.txt.CLM1PT.CLM_USRDAT chmod u+w user_datm.streams.txt.CLM1PT.CLM_USRDAT

# ./case.submit

fi cd ${path1} done

###############################################################_____END_OF_MAIN_SCRIPT_____#########################################################

###############################################################REGRIDBATCH.SH##################################################¶

#!/bin/bash # # Batch script to submit to create mapping files for all standard # resolutions. If you provide a single resolution via “$RES”, only # that resolution will be used. In that case: If it is a regional or # single point resolution, you should set ‘#PBS -n’ to 1, and be sure # that ‘-t regional’ is specified in cmdargs.

#———————————————————————- # Set parameters #———————————————————————- #SBATCH –account=geofag #SBATCH –job-name=mkmapdata #SBATCH –mem-per-cpu=256G –partition=hugemem #SBATCH –ntasks=1 #SBATCH –time=05:00:00

source /cluster/bin/jobsetup module load esmf/6.3.0rp1 #module load nco #module load ncl export ESMF_NETCDF_LIBS=”-lnetcdff -lnetcdf -lnetcdf_c++” #export ESMF_DIR=/usit/abel/u1/huit/ESMF/esmf export ESMF_COMPILER=intel export ESMF_COMM=openmpi #export ESMF_NETCDF=”test” export ESMF_NETCDF_LIBPATH=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1/lib export ESMF_NETCDF_INCLUDE=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1/include ulimit -s unlimited

export ESMFBIN_PATH=/cluster/software/VERSIONS/esmf/6_3_0rp1/bin/binO/Linux.intel.64.openmpi.default export CSMDATA=/work/users/marlam/inputdata export MPIEXEC=mpirun

phys=”clm4_5” RES=GRIDNAME

GRIDFILE=../mkmapgrids/SCRIPgrid_GRIDNAME_nomask.nc regrid_num_proc=8 #———————————————————————- # Begin main script #———————————————————————-

if [ -z “$RES” ]; then

echo “Run for all valid resolutions” resols=`../../bld/queryDefaultNamelist.pl -res list -silent` if [ ! -z “$GRIDFILE” ]; then

echo “When GRIDFILE set RES also needs to be set for a single resolution” exit 1

fi

else

resols=”$RES”

fi if [ -z “$GRIDFILE” ]; then

grid=”“

else

if [[ ${#resols[@]} > 1 ]]; then: echo “When GRIDFILE is specificed only one resolution can also be given (# resolutions ${#resols[@]})” echo “Resolutions input is: $resols” exit 1

fi grid=”-f $GRIDFILE”

fi

if [ -z “$MKMAPDATA_OPTIONS” ]; then: echo “Run with standard options” options=” “
else: options=”$MKMAPDATA_OPTIONS”

fi echo “Create mapping files for this list of resolutions: $resols”

#———————————————————————-

for res in $resols; do

echo “Create mapping files for: $res”

#———————————————————————-

cmdargs=”-r $res $grid $options”

# For single-point and regional resolutions, tell mkmapdata that # output type is regional if [[ echo “$res” | grep -c “1x1_” -gt 0 || echo “$res” | grep -c “5x5_” -gt 0 ]]; then

res_type=”regional”

else: res_type=”global”

fi # Assume if you are providing a gridfile that the grid is regional if [ $grid != “” ];then

res_type=”regional”

fi

cmdargs=”$cmdargs -t $res_type”

echo “$res_type” if [ “$res_type” = “regional” ]; then

echo “regional” # For regional and (especially) single-point grids, we can get # errors when trying to use multiple processors - so just use 1. # We also do NOT set batch mode in this case, because some # machines (e.g., yellowstone) do not listen to REGRID_PROC, so to # get a single processor, we need to run mkmapdata.sh in # interactive mode. regrid_num_proc=1

else

echo “global” regrid_num_proc=8 if [ ! -z “$LSFUSER” ]; then

echo “batch” cmdargs=”$cmdargs -b”

fi if [ ! -z “$PBS_O_WORKDIR” ]; then

cd $PBS_O_WORKDIR cmdargs=”$cmdargs -b”

fi

echo “args: $cmdargs” echo “time env REGRID_PROC=$regrid_num_proc ./mkmapdata.sh $cmdargsn” time env REGRID_PROC=$regrid_num_proc ./mkmapdata.sh $cmdargs

done #######################################################____RUN_LOCALITY_APPEND.SH___########################################### ###############################################################################################################################

#!/bin/sh: export INC_NETCDF=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1/include export LIB_NETCDF=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1/lib export NETCDF_ROOT=/cluster/software/VERSIONS/netcdf.intel-4.3.3.1

######################################################___STREAM_FILE___##########################################################¶

<dataSource>: GENERIC

</dataSource> <domainInfo>

<variableNames>

time time

xc lon yc lat area area mask mask

</variableNames> <filePath>

/usit/abel/u1/marlam/ctsm/cime/tools/mapping/gen_domain_files/GRIDNAME

</filePath> <fileNames>

domain.lnd.{GRIDNAME}_noocean.nc

</fileNames>

</domainInfo> <fieldInfo>

<variableNames>

TBOT tbot SHUM shum WIND wind PRECTmms precn FSDS swdn PSRF pbot

</variableNames> <filePath>

/work/users/marlam/inputdata/atm/datm7/CLM1PT_pan/GRIDNAME

</filePath> <fileNames>

1901-01.nc

1901-02.nc 1901-03.nc 1901-04.nc ……………. ……….. 2014-12.nc

</fileNames> <offset>

0

</offset>

</fieldInfo>

#######################################__PREPARE_ATMOSPHERIC_FORCING_1901_1920_#################################¶

load “$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl” load “$NCARG_ROOT/lib/ncarg/nclscripts/csm/popRemap.ncl” load “$NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl” load “$NCARG_ROOT/lib/ncarg/nclscripts/contrib/cd_string.ncl”

begin

clim_output = “/work/users/marlam/inputdata/atm/datm7/CLM1PT_data/”+plot_name+”/” clim_input = “/work/users/marlam/inputdata/atm/datm7/atm_forcing.datm7.cruncep_qianFill.0.5d.v7.c160715/”

system(“mkdir -p “+ clim_output)

cruCreat=True varCOMB=False varMOD=False timCOMB=False varTIMEsub=False

mon = ispan(0,11,1) mon@units = “month” month =cd_string(mon,”%N”) print(month)

if (cruCreat) then: do year=1901,1920,1

do m=0,11,1

frsds=addfile(clim_input+”Solar6Hrly/clmforc.cruncep.V7.c2016.0.5d.Solr.”+year+”-“+month(m)+”.nc”,”r”) fprec=addfile(clim_input+”Precip6Hrly/clmforc.cruncep.V7.c2016.0.5d.Prec.”+year+”-“+month(m)+”.nc”,”r”) ftphw=addfile(clim_input+”TPHWL6Hrly/clmforc.cruncep.V7.c2016.0.5d.TPQWL.”+year+”-“+month(m)+”.nc”,”r”)

rsds=frsds->FSDS(:,:,:) prec=fprec->PRECTmms(:,:,:) psrf=ftphw->PSRF(:,:,:) tbot=ftphw->TBOT(:,:,:) wind=ftphw->WIND(:,:,:) qbot=ftphw->QBOT(:,:,:)

lon=frsds->LONGXY(0,:) lat=frsds->LATIXY(:,0) time=frsds->time(:) edgew =frsds->EDGEW edgee =frsds->EDGEE edges =frsds->EDGES edgen =frsds->EDGEN longxy =frsds->LONGXY latxy =frsds->LATIXY

loni=ind_nearest_coord(plot_lon, lon, 0) latj=ind_nearest_coord(plot_lat, lat, 0) print(loni) print(latj)

;###

system(“rm -f “+clim_output+year+”-“+month(m)+”.nc”) ; remove if exists fclim = addfile(clim_output+year+”-“+month(m)+”.nc”,”c”) ;”clm1pt_1x1_”+plot_name+”_” ntim = dimsizes(time) ; get dimension sizes nlat = 1 nlon = 1 nscalar = 1

setfileoption(fclim,”DefineMode”,True)

fAtt = True ; assign file attributes fAtt@case_title = “CRUNCEP: norway ” fAtt@conventions = “CF-1.0” fAtt@title = “CLM single point datm input data” fAtt@history = “Original data from CRUNCEP data” fAtt@creation_date = systemfunc (“date”) fileattdef( fclim, fAtt ) ; copy file attributes

dimNames = (/”scalar”,”lon”,”lat”,”time”/) dimSizes = (/ nscalar, nlon, nlat, -1 /) dimUnlim = (/ False, False, False, True/) filedimdef(fclim,dimNames,dimSizes,dimUnlim)

filevardef(fclim, “EDGEW” ,typeof(edgew),getvardims(edgew)) filevardef(fclim, “EDGEE” ,typeof(edgee),getvardims(edgee)) filevardef(fclim, “EDGES” ,typeof(edges),getvardims(edges)) filevardef(fclim, “EDGEN” ,typeof(edgen),getvardims(edgen)) filevardef(fclim, “LONGXY” ,typeof(longxy) ,getvardims(longxy)) filevardef(fclim, “LATIXY” ,typeof(latxy) ,getvardims(latxy)) filevardef(fclim, “FSDS”,typeof(rsds),getvardims(rsds)) filevardef(fclim, “PRECTmms”,typeof(prec),getvardims(prec)) filevardef(fclim, “TBOT”,typeof(tbot),getvardims(tbot)) filevardef(fclim, “WIND”,typeof(wind),getvardims(wind)) filevardef(fclim, “PSRF”,typeof(psrf),getvardims(psrf)) filevardef(fclim, “SHUM”,typeof(qbot),getvardims(qbot)) filevardef(fclim, “time”,typeof(time),getvardims(time))

filevarattdef(fclim,”EDGEW”,edgew) filevarattdef(fclim,”EDGEE”,edgee) filevarattdef(fclim,”EDGES”,edges) filevarattdef(fclim,”EDGEN”,edgen) filevarattdef(fclim,”LONGXY”,longxy) filevarattdef(fclim,”LATIXY”,latxy) filevarattdef(fclim,”FSDS”,rsds) filevarattdef(fclim,”PRECTmms”,prec) filevarattdef(fclim,”TBOT”,tbot) filevarattdef(fclim,”WIND”,wind) filevarattdef(fclim,”PSRF”,psrf) filevarattdef(fclim,”SHUM”,qbot) filevarattdef(fclim,”time”,time)

setfileoption(fclim,”DefineMode”,False)

print(time) fclim->time = (/time/) ; “(/”, “/)” syntax tells NCL to only output the data values to the predefined locations on the file. print(fclim->time) xfloor=plot_lon-0.01 xceil =plot_lon+0.01 yfloor=plot_lat-0.01 yceil =plot_lat+0.01 print(yceil) print(xceil) fclim->EDGEW = (/xfloor/) fclim->EDGEE = (/xceil/) fclim->EDGES = (/yfloor/) fclim->EDGEN = (/yceil/)

printVarSummary(plot_lon) fclim->LONGXY = (/plot_lon/) fclim->LATIXY = (/plot_lat/) fclim->FSDS = (/rsds(:,latj,loni)/) fclim->PRECTmms = (/prec(:,latj,loni)/) ; !!!! time variable can be modified in the attributes of the variable is also copied. make sure to use (/ /) to only copy data. fclim->TBOT = (/tbot(:,latj,loni)/) fclim->WIND = (/wind(:,latj,loni)/) fclim->PSRF = (/psrf(:,latj,loni)/) fclim->SHUM = (/qbot(:,latj,loni)/)

print(fclim->time)

delete(rsds) delete(time) delete(prec) delete(tbot) delete(qbot) delete(wind) delete(psrf)

end do

end do

end if

if (varCOMB) then

do year=1996,2015,1: system(“cp “+clim_output+”clm1pt_1x1_”+plot_name+”_FSDS_”+year+”01010130-“+year+”12312230.nc “+clim_output+”clm1pt_1x1_”+plot_name+”_”+year+”.nc”) system(“ncks -h -A “+clim_output+”clm1pt_1x1_”+plot_name+”_PRECTmms_”+year+”01010130-“+year+”12312230.nc “+clim_output+”clm1pt_1x1_”+plot_name+”_”+year+”.nc”) system(“ncks -h -A “+clim_output+”clm1pt_1x1_”+plot_name+”_TBOT_”+year+”01010130-“+year+”12312230.nc “+clim_output+”clm1pt_1x1_”+plot_name+”_”+year+”.nc”) system(“ncks -h -A “+clim_output+”clm1pt_1x1_”+plot_name+”_WIND_”+year+”01010130-“+year+”12312230.nc “+clim_output+”clm1pt_1x1_”+plot_name+”_”+year+”.nc”) system(“ncks -h -A “+clim_output+”clm1pt_1x1_”+plot_name+”_PSHUM_”+year+”01010130-“+year+”12312230.nc “+clim_output+”clm1pt_1x1_”+plot_name+”_”+year+”.nc”)

end do

end if

if (varMOD) then

do year=1981,2010,1

system(“ncrename -v LATXY,LATIXY “+clim_output+”clm1pt_1x1_”+plot_info(0,1)+”_”+year+”.nc”)

end do

end if

if (varTIMEsub) then

do year=1981,2010,1

system(“ncrcat -O -d time,0,2919,2 “+clim_output+”clm1pt_1x1_”+plot_info(0,1)+”_”+year+”.nc “+clim_output+”clm1pt_1x1_”+plot_info(0,1)+”_”+year+”.nc”)

end do

end if

;if (varSHUMMOD) then ; do year=1981,2010,1 ; ncrcat -O clm1pt_322_1982-*.nc clm1pt_322_1983.nc ; ncks -v PSRF clm1pt_322_1981-01.nc test.nc ; system(“ncrename -v LATXY,LATIXY “+clim_output+”clm1pt_”+plot_info(0,1)+”_”+year+”.nc”) ; end do ;end if

if (timCOMB) then

do m=0,20,1: system(“ncrcat -O “+clim_output+”clm1pt_1x1_”+plot_name+”_*.nc “+clim_output+”clm1pt_1x1_”+plot_name+”_1981-2010.nc”)

end do

end if

end

Change configuration¶

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

Run a regional case¶

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

Run CTSM¶

Run your very first CTSM case¶

Inputdata¶

Make a case¶

1) check the configuration¶

2) Change configuration¶

3) setup case¶

4) edit user_nl_clm¶

5) case build¶

6) run case¶

Run fates¶

Run a single cell case¶

Out of the box¶

###############################################################__REGRIDBATCH.SH__##################################################¶

######################################################___STREAM_FILE___##########################################################¶

#######################################__PREPARE_ATMOSPHERIC_FORCING_1901_1920_#################################¶

Change configuration¶

Run a regional case¶

Definitions¶

Make a case¶

Set up the case¶

Customizing the CLM namelist¶

Build and submit the case¶

###############################################################REGRIDBATCH.SH##################################################¶