| Version 24 (modified by dgoll, 8 years ago) (diff) |
|---|
SPINUP_ANALYTIC
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= (${R_IN}/SRF/reftemp.nc, .),\
(/home/surface3/common/CNP_files/rev00/USDA_SoilSuborder.nc, .), \
(/home/surface3/common/CNP_files/rev00/lithology.nc, .), \
(/home/users/dgoll/ORC_data/N_deposition/LMDzINCA_DEP_2000.nc, .), \
(/home/surface3/common/CNP_files/rev00/deposition.nc, .)
REMARK: make sure there are no blanks behind the "\"!
REMARK: Although the file with N deposition is used in sechiba we add the file to the stomate.card. This is needed to ensure it is copied when we restart from a simulation with impose_cn. In that case, the N deposition variable will not be present in the sechiba_restart_out.nc but the libIGCM assumes all sechiba variables are present.
WARNING: The double entry of deposition will cause a stop on obelix, as the "cp" option are set to not overwrite files (issue not solved yet; please ask Fabienne or Josefine how the cp option in libIGCM can be changed, so that you can overwrite files)
obelix: tell that we use the new “soil_param.nc”; in COMP/sechiba.card:
(/home/surface3/common/CNP_files/rev00/soils_param.nc, .), \
You want account for inter-annual variability of deposition ?
You can loop over a couple for years of deposition to account for inter annual variability during a spinup using CyclicYear?. This done by adding deposition file to COMP/sechiba(!).card:
List= (${R_IN}/SRF/routing.nc, .), \
(/ccc/cont003/home/dsm/p529goll/ORC-CNP_input/soils_param.nc, soils_param.nc), \
(${R_IN}/SRF/cartepente2d_15min.nc, .), \
(${R_IN}/SRF/floodplains.nc, .), \
(${R_IN}/SRF/PFTmap_1850to2005_AR5_LUHa.rc2/PFTmap_IPCC_${year}.nc, PFTmap.nc), \
(/ccc/work/cont003/dsm/p529vui/ORCHIDEE_trunk_CN/LMDzINCA_DEP_2000.nc, .),\
(/ccc/work/cont003/dsm/p529goll/NP_deposition/final/deposition_${CyclicYear}.nc, deposition.nc)
as well as(!) in COMP/stomate.card:
ListNonDel= (${R_IN}/SRF/reftemp.nc, .),\
(/home/surface3/common/CNP_files/rev00/USDA_SoilSuborder.nc, .), \
(/home/surface3/common/CNP_files/rev00/lithology.nc, .), \
(/home/users/dgoll/ORC_data/N_deposition/LMDzINCA_DEP_2000.nc, .), \
(/home/surface3/common/CNP_files/rev00/deposition_${CyclicYear}.nc, .)
1.3 adjust the libIGCM
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)
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
set the 11-layer hydrololgy scheme to explicitly to "n" ("_AUTO_" will cause a stop of the orchidee executable):
# Activate the multi-layer diffusion scheme adapted from CWRR
# by default the Choisnel hydrology is used.
HYDROL_CWRR = n
{{{E
At the moment, (although strongly recommended as the 2-layer scheme performs poorly in the this model version), the 11-layer hydrology scheme is not working in the version of ORCHIDEE-CNP (r3530) due to (technical) bug(s) in the handling of logical switches related to CWRR (I am working on that).
add all the PFT and soil parameter values as set in
/home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def_NV2; for example by copying:
{{{
cp /home/users/dgoll/ORCHIDEE/DEFS_n_CARDS/run.def_NV2 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
# you can enable mass conservation and stoichiometry checks by =y
STOMATE_MASS_CONSERVATION=y
STOMATE_DSG_DEBUG=y
Nammonium_FILE=LMDzINCA_DEP_2000.nc
Nnitrate_FILE=LMDzINCA_DEP_2000.nc
Nnitrate_VAR = NOY
Nammonium_VAR = NHX
Nfert_FILE=NONE
Nbnf_FILE=NONE
NINPUT_UPDATE=-1
}}}
disable river routing if you run on non-global scale in run.def
{{{
# Activate river routing
RIVER_ROUTING = n
}}}
== 1.4 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
}}}
== 1.4 adjust the job as usual ==
modify config.card as usual (see wiki), for example 1k yr simulation with climatic forcing of 1960-1978:
{{{
#-- leap(gregorian), noleap, 360d
CalendarType=noleap
#-- Start and End of Job
#-- "YYYY-MM-DD"
DateBegin=1960-01-01
DateEnd=2960-12-31
# Forcing data between 1901 and 1920
CyclicBegin=1960
CyclicEnd=1978
}}}
'''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) ==
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
}}}
== 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
