wiki:DevelopmentActivities/ORCHIDEE-CNP/howtoSPINAL

Version 59 (modified by dgoll, 4 years ago) (diff)

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SPINUP_ANALYTIC

This page gives you information how to modify the default way of adjusting the analytical spinup configuration. If you want a simulation w/o analytical spinup please see here how to activate/deactivate the analytical spinup: https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic

The description assumes you already know how to run the trunk version of ORCHIDEE.

The same procedure has to be done when using the OOL_SEC_STO configuration, except that you have (1) to set the switch for the analytical spinup in COMP/stomate.card to no, (2) comment out the variables CyclicBegin? CyclicEnd? in config.card, and (3) use the variable year instead of CyclicYear? in stomate.card f If you want changing atmospheric CO2 concentration see here https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/ChangeCO2

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= (/home/surface3/common/CNP_files/revXX/lithology.nc, .), \
(/home/surface3/common/CNP_files/revXX/USDA_SoilSuborder.nc, .), \
(/home/surface3/common/CNP_files/LMDzINCA_DEP_2000.nc, .), \
(/XXX/deposition_1850.nc,  deposition.nc)

REMARK: make sure there are no blanks behind the "\"!

for deposition file (path,etc) see here: https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/inputRoutine

add/exchange these files in list of "[InitialStateFiles?]" in COMP/sechiba.card:

(/home/surface3/common/CNP_files/revXX/soils_param.nc, soils_param.nc), \
(/home/surface3/common/CNP_files/revXX/soils_param_usda_new.nc, soils_param_usda.nc), \
(/XXX/deposition_1850.nc,  deposition.nc), \

REMARK: make sure that in PARAM/run.def you have set the following two variables according to the names you set in COMP/stomate.card:

SOILALB_FILE     = soils_param.nc
SOILCLASS_FILE   = soils_param_usda.nc

REMARK: Although the file with N deposition is used in sechiba we must 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.

REMARK: On obelix, one cannot have the same file in sechiba.card and stomate.card as it is not allowed to overwrite any file.

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 is done by adding deposition files in list of "[BoundaryFiles?]"(!) file to COMP/sechiba(!).card:

[BoundaryFiles]
List=   (/ccc/work/cont003/dsm/p529goll/AmaFACE_forcing/v01/deposition/deposition_${CyclicYear}.nc, deposition.nc)

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

ListNonDel= (${R_IN}/SRF/reftemp.nc, .),\
(/home/surface3/common/CNP_files/revXX/lithology.nc, .), \
(/home/surface3/common/CNP_files/LMDzINCA_DEP_2000.nc, .), \
(/XXX/deposition_${CyclicYear}.nc, .)

1.3 adjust the libIGCM

1.3.1 disable XIOS (not needed anymore)

-- In case you want to use XIOS (default) make sure you compile orchide with gmake without_xios. --

disable XIOS in COMP/orchidee_ol.card

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

make sure XIOS is set to "_AUTOBLOCKER_" (if you set it to "n", libIGCM will trigger a stop) in PARAM/run.def:

# Use XIOS for writing diagnostics file
XIOS_ORCHIDEE_OK = _AUTOBLOCKER_

disable XIOS in config.card:

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

1.3.2 other

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

Make sure the 11-layer hydrology & scheme is used by settting it explicitly to "y" ; this is the default hydrological scheme in ORCHIDEE-CN-P (r4166). If it is on "_AUTO_" it will cause a stop of the orchidee executable. For activating the 11-layer hydrology see here http://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP/activate11HYDRO.

add a set of parameters with their values from the ORCHIDEE-CAN components as well as for the nutrient components to the PARAM/run.def. Make sure you do not overwrite PARAM/run.def but add the additional parameters.

cp /home/surface3/common/CNP_files/revXX/run.def PARAM/run.def

these flags are needed for the nutrient cycles in PARAM/run.def, so make sure they are in there and you set them according to your plans:

# 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

# if you spinup the nitrogen and phosphorus; 
#the mineral N stocks can occasionally get over-depleted due to SOM accumulation;
# to avoid that; set this true 
SPINUP_CNP=y

# you can enable mass conservation and stoichiometry checks by =y
STOMATE_MASS_CONSERVATION=y
STOMATE_DSG_DEBUG=y

for setting the nutrient boundary conditions see here: https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/inputRoutine

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

# Activate river routing
RIVER_ROUTING = n

for more information on the manipulation of run.def: http://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/ManipulationDefFile

1.4a 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

1.4b adjust the job as usual

modify config.card as usual (see here for more information howto set these parameters in general: https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic) I achieved an equilibrium for Europe using sets of 300-350 yr simulations (first step imposing NP concentration, second step prognostic NP concentrations restarting from step 1):

  #-- leap(gregorian), noleap, 360d                                                   
  CalendarType=noleap                                                                 
  #-- Start and End of Job                                                            
  #-- "YYYY-MM-DD"                                                                    
  DateBegin=1960-01-01
  DateEnd=2260-12-31
  # Forcing data between 1901 and 1920                                                
  CyclicBegin=1901
  CyclicEnd=1920

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)

1.6.1. simulations sequential mode

Header to run a site scale simulation on obelix using a single execution unit (ppn):

######################
	## 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

make sure in config.card you told libIGCM to run ORCHIDEE with one execution unit (1MPI):

OL= (orchidee_ol, orchidee_ol, 1MPI)

1.6.2. simulations parallel mode

specify a multiple of 8 for MPI in config.card and increase nodes and ppn in the Header of Job_. see here howto use more processors (info for all machines): http://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCaseBatch

1.6.4. other options in Jobfile

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 the experiment output in IGCM_OUT, etc

2.0 problems which might occur

2.1. executable causes a stop

In general, you should check the out_orchidee_ol and out_execution files for error messages.

known problems

if you can find in "out_orchidee_ol" a message that a LOGICAL has an inappropriate value, you must set in PARAM/run.def the LOGICAL to "y" or "n", for example:

# Activate the multi-layer diffusion scheme adapted from CWRR
# by default the Choisnel hydrology is used.
HYDROL_CWRR = n