HOWTO install/compile/run ORCHIDEE-CN-P for offline use with libIGCM.
This howto is based on the information which can be found in spread in the wiki as well as other sources. It aims at listing all steps needed from installing to running different experiments on a set of machines. Please check the wiki for more information regarding the respective commands listed here.
1. install libIGCM
1.1 where to install
You should install the model NOT in the home directory; it is even too small to handle diagnostics like "out_execution" or "out_orchidee". You can use , for example, your work directory: curie:
/ccc/work/cont003/dsm/<insert userID>
or project storage; here example for the IMBALANCE-P project on obelix:
/home/surface3/<insert userID>
1.2 install libIGCM & trunk ORCHIDEE
svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl cd modipsl/util ./model ORCHIDEE_trunk
2. Exchange the trunk ORCHIDEE with ORCHIDEE-CN-P
cd ../modeles rm -fr ORCHIDEE svn co svn://forge.ipsl.jussieu.fr/orchidee/branches/ORCHIDEE-CN-P ORCHIDEE cd ../util ; ./ins_make
3. Compile ORCHIDEE
adjust IOIPSL to be able to write more variables; increase value of max_var by 50 in ../modeles/IOIPSL/src/restcom.f90
& max_var=550, max_file=50, max_dim=NF90_MAX_VAR_DIMS
then go and compile ORCHIDEE
on obelix
cd ../modeles/ORCHIDEE
First do a "normal" make to compile XIOS & IPOSL components which are needed; don't worry if the compilation of ORCHIDEE crashes
make
then compile (do compile always with "-parallel mpi" as this executable can be run in sequential mode, too. But not vice versa)
./makeorchidee_fcm -driver -arch ifort_LSCE -noxios -parallel mpi
on curie
WARNING: before you do anything on curie; make sure you have copied the p86ipsl login environment to your home according to https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocBenvBtgcc:
cp ~p86ipsl/.bashrc_curie ~/. cp ~p86ipsl/.bash_profile ~/.
Then compile the standard way:
cd ../config/ORCHIDEE_OL gmake without_xios
Optional: I usually re-compile ORCHIDEE again with makeorchidee_fcm to set options (don't forget to disable xios):
cd ../../modeles/ORCHIDEE ./makeorchidee_fcm -driver -parallel mpi -arch X64_CURIE -driver -noxios
4. Run ORCHIDEE (obelix)
4.1 SPINUP_ANALYTIC
4.1.1 create new experiment folder
cd ../../config/ORCHIDEE_OL/ cp -fr SPINUP_ANALYTIC/ MY_SPINUP_ANALYTIC/ cd MY_SPINUP_ANALYTIC/
4.1.2 tell libIGCM about the new input files (write me an email if you need them)
modify the variable "ListNonDel?" in COMP/stomate.card:
ListNonDel= (${R_IN}/SRF/reftemp.nc, .), \
(<insert path>/USDA_SoilSuborder.nc, .), \
(<insert path>/lithology.nc, .), \
(<insert path>/deposition.nc, .)
WARNING: the deposition file is a static field at the moment; it does not include N deposition either. At the moment N deposition is set to P deposition in the ORCHIDEE code. Anyway N deposition is not accounted for in the calculations for the N & P cycle for now.
tell that we use the new “soil_param.nc”; in COMP/sechiba.card:
(<insert path>/soils_param.nc, .), \
4.1.3 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
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 the new flags for the nutrient cycles in PARAM/run.def:
# to activate P cycle set =y STOMATE_OK_PCYCLE=y # to activate N cycle set =y STOMATE_OK_NCYCLE=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
in addition you should add all the PFT and soil parameter values as set in /home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def
disable river routing if you run on non-global scale in run.def
# Activate river routing RIVER_ROUTING = n
4.1.4 adjust the job as usual
modify config.card as usual (see wiki)
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
4.1.5 create job
../../../libIGCM/ins_job
4.1.6 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/<insert userid>/RUN_DIR
4.1.7 submit the job
on obelix:
qsub Job_ID
on curie
ccc_msub Job_ID
4.2 ENSEMBLE: fluxnet sites http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation
4.2.1 create new experiment folder
cd ../../config/ORCHIDEE_OL/ cp -fr ENSEMBLE/ MY_ENSEMBLE/ cd MY_ENSEMBLE/
4.2.2 tell libIGCM about the new input files (write me an email if you need them)
The configuration which are used are stored in ../SPINUP/SUBJOB/OOL_SEC_STO/COMP/ so, do as in 4.1.2: change the path of soil_param.nc and add the new files
sechiba.card:
(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/soils_param.nc, .), \
stomate.card:
ListNonDel= (${R_IN}/SRF/reftemp.nc, .) \
(<insert path>/USDA_SoilSuborder.nc, .), \
(<insert path>/lithology.nc, .), \
(<insert path>/deposition.nc, .)
WARNING: the deposition file is a static field at the moment; it does not include N deposition either. At the moment N deposition is set to P deposition in the ORCHIDEE code. Anyway N deposition is not accounted for in the calculations for the N & P cycle for now.
4.2.3 adjust the libIGCM
add the new flags for the nutrient cycles in fluxnet.card:
# to activate P cycle set =y STOMATE_OK_PCYCLE=y # to activate N cycle set =y STOMATE_OK_NCYCLE=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
you need to add defaults for these switches into PARAM/orchidee.default
# STOMATE_OK_NCYLE ([FLAG]) : Activate the nitrogen cycle {OK_STOMATE}
STOMATE_OK_NCYCLE = n
# STOMATE_OK_PCYLE ([FLAG]) : Activate the phosphorus cycle {OK_STOMATE}
STOMATE_OK_PCYCLE = n
# STOMATE_MASS_CONSERVATION ([FLAG]) : activate mass conservation checks which force stop if violated {OK_STOMATE}
STOMATE_MASS_CONSERVATION = n
# STOMATE_DSG_DEBUG ([FLAG]) : activate checks for stoichiometry and negative pools {OK_STOMATE}
STOMATE_DSG_DEBUG = n
# LD_FAKE_HEIGHT ([FLAG]) : fakes height of vegetation (ORCHIDEE-CAN related) {OK_STOMATE}
LD_FAKE_HEIGHT = n
specify the spinup simulations in the config.card:
[SPINUP]
# Initialisation for spin-up :
# orchidee with sechiba alone (!!! if ok_stomate == n !!!)
duree_nostomate=0
# orchidee with stomate; number of years before n_iter cycles of duree_sechiba years of analytical spinup cycles
duree_inistomate=250
# teststomate (only if duree_inistomate > 0)
duree_offlineini=0
# Loop over ORCHIDEE runs (used for spin-up)
# The whole job is restarted n_iter times
# n_iter: the number of cycles with duree_sechiba years
n_iter=3
# orchidee with sechiba (and stomate if ok_stomate=y below)
duree_sechiba=50
# teststomate
duree_stomate=0
# forcesoil
duree_carbonsol=1
# Final run (full ORCHIDEE)
# This last parameter must be non-zero.
duree_final=100
xios is per default disabled in "PARAM/orchidee.default" routing is per default disabled in "fluxnet.card"
4.2.4 adjust the job as usual
modify config.card as usual (http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation)
modify run.def as usual (http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation)
if you want to archive set the variable ARCHIVE, here the example for IMBALANCE-P storage; add to config.card:
ARCHIVE=/home/surface3/<insert path>
4.2.5 create job
../../../libIGCM/ins_job
4.2.6 adjust job (optional)
4.2.7 start simulations
my_prompt>> ksh my_prompt>> nohup ./Job_ENSEMBLE fluxnet > out_Job 2>&1 &
4.2.8 check simulations
ccc_mstat -u userid
ccc_mdel jobid
