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Version 20 (modified by jgipsl, 13 years ago) (diff)
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Configuration LMDZOR_v4 =

LMDZOR_v4 is the current version using LMDZ and ORCHIDEE. It is a configuration in phase with the coupled model IPSL-CM5. It can be used with LMDZ4 production version LMDZ4_AR5 or with one of the latest versions of LMDZ5/trunk.

Before running this model set up, choice between 2 mode has to be done : Interannuel AMIP simulation or climatologic simulation. No default setup is done. Nearly all the time, modifications in the lmdz.card or orchidee.card have to be done. Contact me if you need to modifie the lmdz.driver or orchidee.driver.

/J Ghattas

This configuration is a modified copy of LMDZ4OR_v3. Modifications are :

the grille 280x280x39 is added. This grid contains a zoom over Africa
the CREATE experience does not have a PARAM directory. In CREATE/COMP/lmdz.card the parameter PARAM_DIR points to ../LMDZOR/PARAM.
only one run directory exist : LMDZOR. This directory can be used for different type of simulation for exemple AMIP interannual or climatolical run. Or nudged run with regular or zoomed grid. Only the .card changes for different run. The PARAM directory and the .driver are the same.

In the CREATE experience, 2 files exist in double versions : config_card and lmdz.card. Before run a manual copy or link must be done :

ln -s config.card_Interannuel config.card; cd COMP; ln -s lmdz.card_Interannuel lmdz.card

ln -s config.card_Climat config.card; cd COMP; ln -s lmdz.card_Climat lmdz.card

bug correction for CREATE run with leap calendar (gregorian), in config.card : CalendarType=leap => in run.def : calend=gregorian

scripts for interpolating files for nudging are stored in CREATE/SCRIPT. The script get_era.x is the master that will launch the other 2 (era2gcm.x and add_step.x).

In the LMDZOR experience, a climat or a AMIP(interannual) experience can be run. Before run a manual copy or link must be done :

cd LMDZOR/COMP; ln -s lmdz.card_Climat lmdz.card; ln -s orchidee.card_Climat orchidee.card

cd LMDZOR/COMP; ln -s lmdz.card_AMIP lmdz.card; ln -s orchidee.card_AMIP orchidee.card

Parametres in config.card such as JobName, CalendarType, DateBegin, DateEnd must be considered and eventally modified according to desired experience.

Problems running at VARGAS?

You should not compile with -O5 at VARGAS. Compile with -O3 or lower optimization. Default compiler xlf 13.1.0.3 is ok with -O3.
If the executable create_etat0_limit or ce0l exits with following error message you need to update your LMDZ version to revision 1476 at branch LMDZ4_AR5 or higher :

ERROR: 0032-184 MPI was not finalized in routine unknown, task 0

Check memory in your job. For higher resolutions you may need to add threads just to have more memory. You must then compile in mpi mode (default for create_etat0_limit.e.para) and not mixt mpi_openmpi. In your job, add @ parallel_threads = 8. This gives you 8 times more memory per process mpi availible and you can multiply data_limit and stack_limit by 8. When adding threads you should remove @ resources = ConsumableCpus(1). For exemple for resolution 280x280x39 put in your job :

# @ total_tasks = 32
# @ environment = "BATCH_NUM_PROC_TOT=32"
# @ parallel_threads = 8
# @ data_limit  = 18.0gb
# @ stack_limit = 6.0gb,6.0gb
### @ resources = ConsumableCpus(1)

You must desactivate the filtre fft if using branch LMDZ4_AR5 or earlier version of LMDZ. In run.def set use_filtre_fft = n.

In config.card you must change to
```
JobRunOptions=''
```
otherwise you'll have following error message :

ERROR: 0031-636 User requested or EOF termination of pm_command

Interpolation of nudge files

The files that will be used for the nudging must be interpolated to the model grid before running the gcm. This can be done either using a script get_era.x or using a patch in libIGCM, see below.

Interpolation using get_era.x

Follow step 1 to 3.

1) Create file grilles_gcm.nc
LMDZ contains a program that creates a file netcdf containg the grid u and v. This program is located in file LMDZ5/libf/dyn3d/grilles_gcm_netcdf.F. Compile this program with the same resolution as the gcm. For exemple if using the LMDZOR_v4/Makefile, add in Makefile :

(cd ../../modeles/LMDZ; ./makelmdz_fcm -cpp ORCHIDEE_NOOPENMP -d $(RESOL_LMDZ) -arch $(FCM_ARCH) grilles_gcm_netcdf ; cp bin/grilles_gcm_netcdf_$(RESOL_LMDZ)_phylmd_seq.e ../../bin/grilles_gcm_netcdf.e ; )

For a regular grid no parameter files are needed, just execute the program. If you have a zoom, execute the program together with your parameter files (run.def, gcm.def).

2) Modify and run get_era.x
The script get_era.x is stored in LMDZOR_v4/CREATE/SCRIPT and it is used together with era2gcm.x and add_step.x. These scripts have to be adapted according to the machine and file locations. To extract only interpolation scripts :

svn co http://forge.ipsl.jussieu.fr/igcmg/svn/CONFIG/LMDZOR/branches/LMDZOR_v4/CREATE/SCRIPT

Modifications :

in get_era.x set year and month to be interpolated. Set path to your grilles_gcm.nc file
in era2gcm.x set ANA_DIR to the path of ERAI files

During execution of get_era.x the directory OUT_ERAI will be created in the running directory.

3) Move interpolated files to archive directory

Interpolation using a patch in libIGCM

Interpolation is done in the CREATE job at the same time as execution of create_etat0_limit for creation of boudary files limit.nc. Using lmdz.card_Interannuel and config.card_Interannuel is necessary to interpolate over several years. libIGCM tag v1_10 is requierd.

To activate the patch modifications in CREATE/COMP/lmdz.card_Interannuel is needed. Add the files to interpolate in [BoundaryFiles]/List and in [OutputFiles]/List and add the paragraf [Nudge_Interp] in the end of lmdz.card. Here below is an exemple how to add u. In the same lmdz.card it is possible to add different files u,v,t,... using the same syntax :

[BoundaryFiles]
List=   (${R_INIT}/ATM/${config_UserChoices_TagName}/AMIP/amipbc_sst_360x180_${year}.nc, amipbc_sst_1x1.nc), \
	(${R_INIT}/ATM/${config_UserChoices_TagName}/AMIP/amipbc_sic_360x180_${year}.nc, amipbc_sic_1x1.nc), \
	(${R_INIT}/ATM/${config_UserChoices_TagName}/Ozone/HYBRIDE/v2.clim/tro3_${year}.new.nc, climoz.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}01.aphei.GLOBAL_075.nc, u_1_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}02.aphei.GLOBAL_075.nc, u_2_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}03.aphei.GLOBAL_075.nc, u_3_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}04.aphei.GLOBAL_075.nc, u_4_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}05.aphei.GLOBAL_075.nc, u_5_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}06.aphei.GLOBAL_075.nc, u_6_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}07.aphei.GLOBAL_075.nc, u_7_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}08.aphei.GLOBAL_075.nc, u_8_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}09.aphei.GLOBAL_075.nc, u_9_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}10.aphei.GLOBAL_075.nc, u_10_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}11.aphei.GLOBAL_075.nc, u_11_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year}/u.${year}12.aphei.GLOBAL_075.nc, u_12_${year}.nc), \
        (/u/rech/psl/rpsl376/ERAI/NETCDF/GLOBAL_075/4xdaily/AN_PL/${year_p1}/u.${year_p1}01.aphei.GLOBAL_075.nc, u_13_${year}.nc)

...

[OutputFiles]
List=	( limit.nc,       ${R_OUT_ATM_O}/Boundary/${config_UserChoices_JobName}_${year}_limit.nc,       NONE), \
	( climoz_LMDZ.nc, ${R_OUT_ATM_O}/Boundary/${config_UserChoices_JobName}_${year}_climoz_LMDZ.nc, NONE), \
	( start.nc,       ${R_OUT_ATM_O}/Restart/${config_UserChoices_JobName}_${year}_start.nc,        NONE), \
	( startphy.nc,    ${R_OUT_ATM_O}/Restart/${config_UserChoices_JobName}_${year}_startphy.nc,     NONE), \
        ( u_1_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}01_u.nc,       Post_Interp), \
        ( u_2_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}02_u.nc,       NONE), \
        ( u_3_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}03_u.nc,       NONE), \
        ( u_4_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}04_u.nc,       NONE), \
        ( u_5_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}05_u.nc,       NONE), \
        ( u_6_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}06_u.nc,       NONE), \
        ( u_7_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}07_u.nc,       NONE), \
        ( u_8_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}08_u.nc,       NONE), \
        ( u_9_${year}.nc,  ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}09_u.nc,       NONE), \
        ( u_10_${year}.nc, ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}10_u.nc,       NONE), \
        ( u_11_${year}.nc, ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}11_u.nc,       NONE), \
        ( u_12_${year}.nc, ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}12_u.nc,       NONE), \
        ( u_13_${year}.nc, ${R_OUT_ATM_O}/Nudgefiles/${config_UserChoices_JobName}_${year}13_u.nc,       NONE)



# This patch is applied to the first file but it will work on all files u01.nc - u13.nc
[Post_Interp]
Patches = (Patch_20101208_nudge_interp)
GatherWithInternal = ()
TimeSeriesVars2D = ()
ChunckJob2D = NONE
TimeSeriesVars3D = ()
ChunckJob3D = NONE
Seasonal=OFF

In config.card it is necessary to put :

RebuildFrequency=1Y

Differentes experiences

Différences actuelle entre LMDZOR et AMIP :

Fichier	LMDZOR	AMIP	Commentaires
COMP/lmdz.card	ELC-${RESOL_ATM_3D}	ELI-${RESOL_ATM_3D}	CREATE (nom du job create_etat0_limit)
	clim_start.nc	${year}_start.nc	fichier climat / inter annuelle
	clim_startphy.nc	${year}_startphy.nc	fichier climat / inter annuelle
	clim_limit.nc	${year}_limit.nc	fichier climat / inter annuelle
	aerosols_11YearsClim_1860.nc	aerosols_11YearsClim_1855.nc	aerosols.nat.nc
	aerosols_11YearsClim_1995.nc		aerosols1980.nc
		aerosols_11YearsClim_${year}.nc	aerosols${year}.nc, 1:12: (smoothfile : à partir de la 1ère toutes les 12 périodes (mois) [min]:[modulo:][max] )
	climoz_LMDZ_1995.nc	climoz_LMDZ_${year}.nc, climoz_LMDZ.nc, 1:12:	climoz_LMDZ.nc
		CO2_1765_2005.txt
		CH4_1765_2005.txt
		N2O_1765_2005.txt
		CFC11_1765_2005.txt
		CFC12_1765_2005.txt
		guide.def	a mettre aussi dans LMDZOR!\|\|

COMP/lmdz.driver		IPCC_CO2= ... ; LMDZ_sed physiq.def co2_ppm ${IPCC_CO2}	update physiq.def with values from file .txt :
			solaire, co2_ppm, CH4_ppb, N2O_ppb, CFC11_ppt, CFC12_ppt

COMP/orchidee.card	PFTmap_IPCC_2000.nc	${BC_SRF_PFTmap} = PFTmap_1850to2005_AR5_LUHa.rc2.nc	new function in driver will choose PFTmap
		or ORCHIDEE_PFTmap_2006to2100_AR5_RCP8.5_MESSAGE.nc

COMP/orchidee.driver		srf_period_start	new function for choice of PFTmap before and after 2004
		cas test : modif for certain years	VEGET_REINIT
		cas test : modif for certain years	VEGET_YEAR

PARAM/orchidee.def	0Y	1Y	VEGET_UPDATE
	n	y	LAND_COVER_CHANGE = n

PARAM/physiq.def_L39	0.008	0.0	pmagic
	1366.0896	1365.6537	solaire RQ: le valeur dans AMIP sera ecraser
	actuel	annuel	aer_type

Commentaires :

orchidee.driver pourrait être le même car srf_period_start prend effet en utilisant le variable ${BC_SRF_PFTmap}, qui se fait dans orchidee.card. On pourrait donc avoir : orchidee.card_Climat et orchidee.card_Interannuel
Les différentes valeurs dans les .def pourrait être mis dans lmdz.card et orchidee.card pour ensuite être modifié avec sed
guide.def pourrait etre mis dans les 2 expériences

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