SPINUP_ANALYTIC

1.1 create new experiment folder

cd ../../config/ORCHIDEE_OL/
cp -fr SPINUP_ANALYTIC/ MY_SPINUP_ANALYTIC/
cd MY_SPINUP_ANALYTIC/

1.2 tell libIGCM about the new input files (they are stored on the IMBALANCE-P disk on obelix)

modify the variable "ListNonDel?" in COMP/stomate.card:

ListNonDel= (${R_IN}/SRF/reftemp.nc, .),\
(/home/surface3/common/CNP_files/rev00/USDA_SoilSuborder.nc, .), \
(/home/surface3/common/CNP_files/rev00/lithology.nc, .), \
(/home/users/dgoll/ORC_data/N_deposition/LMDzINCA_DEP_2000.nc, .), \
(/home/surface3/common/CNP_files/rev00/deposition.nc, .)

REMARK: make sure there are no blanks behind the "\"! REMARK: Although the file with N deposition is used in sechiba we add the file to the stomate.card. This is needed to ensure it is copied when we restart from a simulation with impose_cn. In that case, the N deposition variable will not be present in the sechiba_restart_out.nc but the libIGCM assumes all sechiba variables are present.

obelix: tell that we use the new “soil_param.nc”; in COMP/sechiba.card:

(/home/surface3/common/CNP_files/rev00/soils_param.nc, .), \

You want account for inter-annual variability of deposition ?

You can loop over a couple for years of deposition to account for inter annual variability during a spinup using CyclicYear?. This done by adding deposition file to COMP/sechiba(!).card:

List=       (${R_IN}/SRF/routing.nc, .),     \
            (/ccc/cont003/home/dsm/p529goll/ORC-CNP_input/soils_param.nc, soils_param.nc), \
            (${R_IN}/SRF/cartepente2d_15min.nc, .), \
            (${R_IN}/SRF/floodplains.nc, .), \
            (${R_IN}/SRF/PFTmap_1850to2005_AR5_LUHa.rc2/PFTmap_IPCC_${year}.nc, PFTmap.nc), \
            (/ccc/work/cont003/dsm/p529vui/ORCHIDEE_trunk_CN/LMDzINCA_DEP_2000.nc, .),\
            (/ccc/work/cont003/dsm/p529goll/NP_deposition/final/deposition_${CyclicYear}.nc, deposition.nc)

as well as(!) in COMP/stomate.card:

ListNonDel= (${R_IN}/SRF/reftemp.nc, .),\
(/home/surface3/common/CNP_files/rev00/USDA_SoilSuborder.nc, .), \
(/home/surface3/common/CNP_files/rev00/lithology.nc, .), \
(/home/users/dgoll/ORC_data/N_deposition/LMDzINCA_DEP_2000.nc, .), \
(/home/surface3/common/CNP_files/rev00/deposition_${CyclicYear}.nc, .)

1.3 adjust the libIGCM

disable XIOS in COMP/orchidee_ol.card

# Use XIOS as output library instead of IOIPSL
XIOS=n

disable XIOS in PARAM/run.def

# Use XIOS for writing diagnostics file
# defulat = n
XIOS_ORCHIDEE_OK = n

disable XIOS in config.card:

#IOS= (xios, XIOS)

[...]

#IOS= (xios_server.exe, xios.x, 1MPI)

set the IO frequency to avoid crashes in PARAM/run.def

# Writefrequency in seconds in sechiba_history.nc
# default = 86400.0
WRITE_STEP = 1800.0

# Writefrequency in days in stomate_history.nc
# default = 10.
STOMATE_HIST_DT = 1

add all the PFT and soil parameter values as set in /home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def_NV2

cp /home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def_NV2 PARAM/run.def

these flags are needed for the nutrient cycles in PARAM/run.def:

# to activate P cycle set =y
STOMATE_OK_PCYCLE=y
STOMATE_IMPOSE_NP=y
# to activate N cycle set =y
STOMATE_OK_NCYCLE=y
STOMATE_IMPOSE_CN=y
# make sure we dont fake
LD_FAKE_HEIGHT=n
# you can enable mass conservation and stoichiometry checks by =y
STOMATE_MASS_CONSERVATION=y
STOMATE_DSG_DEBUG=y

Nammonium_FILE=LMDzINCA_DEP_2000.nc
Nnitrate_FILE=LMDzINCA_DEP_2000.nc
Nnitrate_VAR = NOY
Nammonium_VAR = NHX
Nfert_FILE=NONE
Nbnf_FILE=NONE
NINPUT_UPDATE=-1

disable river routing if you run on non-global scale in run.def

# Activate river routing
RIVER_ROUTING = n

1.4 activate analytic solution

in COMP/stomate.card:

[UserChoices]
# SPINUP_ANALYTIC=y/n : Activate the spinup analytic option to solve the carbon in soil balance
SPINUP_ANALYTIC=y

1.4 adjust the job as usual

modify config.card as usual (see wiki), for example 1k yr simulation with climatic forcing of 1960-1978:

  #-- leap(gregorian), noleap, 360d                                                   
  CalendarType=noleap                                                                 
  #-- Start and End of Job                                                            
  #-- "YYYY-MM-DD"                                                                    
  DateBegin=1960-01-01
  DateEnd=2960-12-31
  # Forcing data between 1901 and 1920                                                
  CyclicBegin=1960
  CyclicEnd=1978

REMARK (curie only): If you want to run ORCHIDEE on spatial subdomain (here the example for a single grid box) you need to adjust the number before MPI line:

#OOL= (orchidee_ol, orchidee_ol, 32MPI)
OOL= (orchidee_ol, orchidee_ol, 1MPI)

modify run.def as usual (see wiki) plus if you want to archive, for example in the IMBALANCE-P storage; add to config.card:

ARCHIVE=/home/surface3/dgoll 

1.5 create job

../../../libIGCM/ins_job

1.6 adjust job_file (optional)

Header to run a site scale simulation on obelix

######################
	## OBELIX      LSCE ##
	######################
	#PBS -N test
	#PBS -m a
	#PBS -j oe
	#PBS -q short
	#PBS -o Script_Output_test.000001
	#PBS -S /bin/ksh
	#PBS -v BATCH_NUM_PROC_TOT=1
	#PBS -l nodes=1:ppn=1

to automatically have existing files deleted, set JobType?=DEV

 	#D- Experience type : DEB(ug), DEV(elopment), RUN (default)
	JobType=DEV 

to avoid queuing take full advantage of your job time; the value depends on #PBS -q short and computation time of orchidee

#D- Number of execution in one job
	PeriodNb=60

to have a temp directory you can access on obelix; exchange dgoll with your ID

#D- Define running directory
#D- Default=${TMPDIR} ie temporary batch directory
#D-
#RUN_DIR_PATH=/workdir/or/scratchdir/of/this/machine
RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR

1.7 submit the job

on obelix:

qsub Job_ID

on curie

ccc_msub Job_ID

1.8 restart / rerun a job after crash

It is important that you stick to the libIGCM regulations. You /libIGCM/clean_Month to reset run.card or delete run.card if you want to start from scratch. To avoid headaches, it is recommended to always delete all file which you want to redo , for example in IGCM_OUT, etc