Version 58 (modified by dgoll, 4 years ago) (diff)



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:

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

1.1 create new experiment folder

cd ../../config/ORCHIDEE_OL/

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/, .), \
(/home/surface3/common/CNP_files/revXX/, .), \
(/home/surface3/common/CNP_files/, .), \

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

for deposition file (path,etc) see here:

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

(/home/surface3/common/CNP_files/revXX/,, \
(/home/surface3/common/CNP_files/revXX/,, \
(/XXX/,, \

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:


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 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:

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

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

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

1.3 adjust the libIGCM

disable XIOS in COMP/orchidee_ol.card

# Use XIOS as output library instead of IOIPSL

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

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
# default = 86400.0
WRITE_STEP = 1800.0

# Writefrequency in days in
# default = 10.

Set the 11-layer hydrology & scheme to 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

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
# to activate N cycle set =y
# make sure we dont fake

# 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 

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

for setting the nutrient boundary conditions see here:

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

# Activate river routing

for more information on the manipulation of run.def:

1.4a activate analytic solution

in COMP/stomate.card:

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

1.4b adjust the job as usual

modify config.card as usual (see here for more information howto set these parameters in general: 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                                                   
  #-- Start and End of Job                                                            
  #-- "YYYY-MM-DD"                                                                    
  # Forcing data between 1901 and 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:


1.5 create 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 -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):

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)

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

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

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.