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

Timestamp:

2016-04-04T14:40:58+02:00 (8 years ago)

Author:

dgoll

Comment:

--

DevelopmentActivities/ORCHIDEE-CNP/howtoFLUXNET

@@ +1 @@
+= ENSEMBLE: fluxnet sites [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation] =
+[[Image(fluxnet_sequence.png)]]
+Figure shows the sequence of simulations: the labels(TOP), the time length(MIDDLE) and the spinup_analytic(BOTTOM). Adopted from NV scheme.
+
+
+== 1.1 create new experiment folder ==
+{{{
+cd ../../config/ORCHIDEE_OL/
+cp -fr ENSEMBLE/ ENSEMBLE_CNP/
+cd ENSEMBLE_CNP/
+}}}
+
+== 1.2 tell libIGCM about the new input files ==
+For now, I store all files needed on the IMBALANCE-P disk on obelix (you find the path below). Please ensure you are using the newest revision (rev00 is not fully tested).
+
+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/surface3/common/CNP_files/rev00/soils_param.nc, .), \
+}}}
+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/surface3/common/CNP_files/rev00/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.
+
+exchange the spinup.driver file in ../SPINUP/COMP/ with the new modified driver from NV.
+{{{
+cp /home/surface3/common/CNP_files/rev00/spinup.driver ../SPINUP/COMP/
+}}}
+
+
+copy a run.def with all parameters needed for the ORCHIDEE-CAN parts of the model to PARAM, for example this one:
+{{{
+cp /home/surface3/common/CNP_files/rev00/run.def_NV2 PARAM/run.def
+}}}
+
+== 1.3 adjust the libIGCM  ==
+modify the configuration of the SPINUP. These variables were originally used for the outdated spinup method using FORCESOIL.
+Thus the variable names are misleading.
+
+modify them in ensemble.card and fluxnet.card:
+{{{
+[SPINUP]
+# Initialisation for spin-up :
+# orchidee with sechiba alone (!!! if ok_stomate == n !!!)
+duree_nostomate=0
+#  normal SEC_STO simulation to fill biomass pools (equilibrate litter fluxes) of duree_inistomate years
+duree_inistomate=1000
+# teststomate (only if duree_inistomate > 0); DSG: don't touch this one
+duree_offlineini=0
+
+# Loop over ORCHIDEE runs (used for spin-up)
+# The analytical spinup is restarted n_iter times ...
+n_iter=3
+# ... for duree_sechiba years
+duree_sechiba=50
+# teststomate; DSG: don't touch this one
+duree_stomate=0
+# forcesoil; DSG: don't touch this one
+duree_carbonsol=1
+
+# Final run after the analytical spinup
+# This last parameter must be non-zero.
+duree_final=100
+
+
+}}}
+
+make sure that the variable SPINUP_ANALYTIC is set to "n":
+{{{
+SPINUP_ANALYTIC=n
+}}}
+add the variables to turn on/off the nutrients cycles  to PARAM/run.def:
+{{{
+# switch for N cycle
+STOMATE_OK_NCYCLE=y
+# switch for P cycle
+STOMATE_OK_PCYCLE=y
+# switch to either impose N content of vegetation (to surpass N limitation):
+STOMATE_IMPOSE_CN=n
+# switch to either impose N content of vegetation (to surpass P limitation):
+STOMATE_IMPOSE_NP=n
+# do not fake the initial height (DOFOCO parameter)
+LD_FAKE_HEIGHT=n
+
+Nammonium_FILE =NONE
+Nnitrate_FILE =NONE
+Nfert_FILE=NONE
+Nbnf_FILE=NONE
+NINPUT_UPDATE=-1
+}}}
+if you want to debug the model, set printlev to 4 for full debug information in PARAM/run.def:
+{{{
+PRINTLEV=4
+}}}
+
+you can add defaults for the nutrient 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
+
+}}}
+
+REMARKS:
+Do not enable XIOS, it is per default disabled in "PARAM/orchidee.default".
+Do not enable river routing in site scale simulation, is per default disabled in "fluxnet.card"
+
+== 1.4 adjust the job as usual to your specific needs ==
+1. modify config.card following [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation]
+give information on Job Name, Tag Name, Dates and Restart. Make sure the path ARCHIVE is correct for the machine you are using. You must set the ARCHIVE on curie or your simulation will crash.
+for example in the IMBALANCE-P storage; add to config.card:
+{{{
+ARCHIVE=/home/surface3/dgoll 
+}}} 
+2. modify run.def following [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation]
+
+3. modify fluxnet.card following [http://forge.ipsl.jussieu.fr/orchidee/wiki/Scripts/FluxnetValidation]
+
+In case you want to check if the spinup works well, increase output level of the spinup simulations & prevent libIGCM from removing these files.
+The files can be found in the respective site folders in the experiment folder.
+
+modify in fluxnet.card and ensemble.card:
+{{{
+# level of the history files for each iteration of the SPINUP
+level_hist=10
+# level of the history files for the final iteration of the SPINUP
+level_hist_final=10
+
+# 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
+}}}
+You find the files in the folder "JobName"STOI in the IGCM_OUT path for the STOI simulation. Exchange "STOI" with "ORC-1", "FIN" etc for the simulations you want to check.
+
+== 1.5 create job ==
+{{{
+../../../libIGCM/ins_job
+}}}
+
+== 1.6 adjust job  ==
+'''on obelix'''
+change the queue to longp to increase the allocated time (the default queue mediump is too short and you will exceed wall clock time).
+{{{
+#PBS -q longp
+}}}
+
+If you want to debug on obelix: set the variable RUN_DIR_PATH to disk with enough space (the default path is not accessible for the user)
+{{{
+# for example on scratch01
+RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR
+}}}
+ACHTUNG: On curie, do not set RUN_DIR_PATH in the Job_*. If you do, the configuration will crash. You find the default path to the RUN_DIR_PATH in the section "3.2.8 check simulations".
+
+
+== 1.7 start simulations ==
+{{{
+ksh
+nohup ./Job_ENSEMBLE fluxnet > out_Job 2>&1 &
+}}}
+
+== 1.8 check simulations ==
+to see the decomposition of the spatial domain among the processors check in the run dir "Load_balance_orchidee.dat"
+'''on curie'''
+The RUN_DIR is in 
+{{{
+/ccc/scratch/cont003/dsm/<userid>/RUN_DIR
+}}}
+
+to check the status of the job; type
+{{{
+ccc_mstat -u <userid>
+}}}
+to delete a job; type
+{{{
+ccc_mdel <jobid>
+}}}
+=== 1.8.1 what to do when a simulation crash ===
+You cannot use clean_month and clean_year. You should remove the sites that crashed from the IGCM_OUT path
+and rerun the same experiment with a fluxnet.card containing only the sites which crashed.
+
+
+== 1.9 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
+}}}
+start the skript
+{{{
+ksh
+nohup ./Job_Post_FLUXNET fluxnet > out_Post 2>&1 &
+}}}
+you will find the graphics in the experiment folder in the IGCM_OUT path. There is a pdf in the folder starting with "fluxnet_taylor_diff".