Changes between Initial Version and Version 1 of DevelopmentActivities/ORCHIDEE-CNP/howtoUse

Timestamp:

2016-03-15T14:01:26+01:00 (8 years ago)

Author:

dgoll

Comment:

--

DevelopmentActivities/ORCHIDEE-CNP/howtoUse

@@ +1 @@
+
+= HOWTO install/compile/run ORCHIDEE-CN-P for offline use with libIGCM. ==
+This howto is based on the information which can be found in the ORCHIDEE wiki regarding the trunk version of ORCHIDEE.
+Please check the wiki for information regarding the respective commands listed here. 
+----
+----
+== 1. install libIGCM & ORCHIDEE-CN-P ==
+=== 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/<userID>
+}}}
+or project storage; here example for the IMBALANCE-P project on obelix:
+{{{
+/home/surface3/dgoll
+}}}
+=== 1.2 install libIGCM & trunk ORCHIDEE ===
+{{{
+svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl
+cd modipsl/util
+./model ORCHIDEE_trunk
+}}} 
+
+=== 1.3 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
+}}}
+
+----
+----
+
+== 2. Compile ORCHIDEE ==
+=== 2.1 modify IOIPSL ===
+adjust IOIPSL to be able to write more variables into the output by increase the value of max_var by 50 in ../modeles/IOIPSL/src/restcom.f90
+{{{
+ &  max_var=550, max_file=50, max_dim=NF90_MAX_VAR_DIMS
+}}}
+=== 2.2 compile orchidee ===
+==== A: 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
+}}}
+==== B: 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
+}}}
+
+----
+----
+
+== 3. Run ORCHIDEE ==
+There are different setups possible with libIGCM. Please check the documentation of libIGCM for more information, here I just tell you what you need to do.
+
+=== 3.1 SPINUP_ANALYTIC ===
+==== 3.1.1 create new experiment folder ====
+{{{
+cd ../../config/ORCHIDEE_OL/
+cp -fr SPINUP_ANALYTIC/ MY_SPINUP_ANALYTIC/
+cd MY_SPINUP_ANALYTIC/
+}}}
+==== 3.1.2 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, .), \       
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/USDA_SoilSuborder.nc, .), \
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/lithology.nc, .), \
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/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:
+{{{
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/soils_param.nc, .), \
+}}}
+==== 3.1.3 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
+}}}
+
+
+==== 3.1.4 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 
+}}} 
+
+==== 3.1.5 create job ====
+{{{
+../../../libIGCM/ins_job
+}}}
+
+==== 3.1.6 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
+}}}
+==== 3.1.7 submit the job  ====
+on obelix:
+{{{
+qsub Job_ID
+}}}
+on curie
+{{{
+ccc_msub Job_ID
+}}}
+
+
+
+=== 3.2 ENSEMBLE: fluxnet sites [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation] ===
+==== 3.2.1 create new experiment folder ====
+{{{
+cd ../../config/ORCHIDEE_OL/
+cp -fr ENSEMBLE/ MY_ENSEMBLE/
+cd MY_ENSEMBLE/
+}}}
+
+==== 3.2.2 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, .) \        
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/USDA_SoilSuborder.nc, .), \
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/lithology.nc, .), \
+(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/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.
+
+copy a run.def with all parameters needed to PARAM, for example this one:
+{{{
+cp ~/ORCHIDEE/DEFS_n_CARDS/run.def_NV PARAM/run.def
+}}}
+
+==== 3.2.3 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"
+
+==== 3.2.4 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])
+plus
+if you want to archive, for example in the IMBALANCE-P storage; add to config.card:
+{{{
+ARCHIVE=/home/surface3/dgoll 
+}}} 
+
+modify fluxnet.card as usual (no information):
+- if you want to keep the output files of the spinup you need to set the following variables
+{{{
+# DEBUG mode for SPINUP 
+#
+# This mode keep all SPINUP directory in ARCHIVE
+# If disable, all ARCHIVE is automaticly cleaned.
+DEBUG_SPIN=y
+# If you don't want to keep old spinup steps, but last one
+CONSERVE=y
+}}}
+
+==== 3.2.5 create job ====
+{{{
+../../../libIGCM/ins_job
+}}}
+
+==== 3.2.6 adjust job  (optional) ====
+
+==== 3.2.7 start simulations ====
+{{{
+my_prompt>> ksh
+my_prompt>> nohup ./Job_ENSEMBLE fluxnet > out_Job 2>&1 &
+}}}
+==== 3.2.8 check simulations ====
+to see the decomposition of the spatial domain among the processors check in the run dir "Load_balance_orchidee.dat"
+
+
+on curie
+{{{
+ccc_mstat -u userid
+}}}
+{{{
+ccc_mdel jobid
+}}}
+
+==== 3.2.8 post processing ====
+ensure the Jobname and the path to the reference simulation is set in fluxnet.card; in case there is no reference set it to NONE
+{{{
+# History file of former ORCHIDEE runs (Reference) to compare with the current simulations
+reference_base_path=/home/scratch01/dgoll/IGCM_OUT/OL2/DEVT/ensemble
+reference_config=DSG04EnsCN
+}}}