ORCHIDEE

2025-03-21T20:02:48Z

Daira.rosales: /* Test: let's look at Marcos Juárez, Córdoba, Argentina */

= ORCHIDEE =

This manual provides the information about the land-surface model [https://orchidee.ipsl.fr/ ORCHIDEE] (technical page for [http://forge.ipsl.jussieu.fr/orchidee advanced users]) from ''Institute Pierre Simone Laplace'' ([https://www.ipsl.fr/en IPSL]). Its installation on the HPC of the CIMA called <code>hydra</code>.

= Model description =

* ORCHIDEE: sechiba & stomate
* Two major modes of simulations: Off-line (no feedback) / on-line (LMDZ, WRF)

All forcing data to run ORCHIDEE is located here in CIMA's HPC:
<pre>
${ORforcing}=/share/DATA/ORCHIDEE/IGCM/
</pre>

== Off-line atmospheric forcings ==
Desdcribed here: [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/Forcings ORforcings]

Atmoshperic variables required by ORCHIDEE: <code>LWdown, PSurf, Qair, Rainf, SWdown, Snowf, Tair, Wind_E, Wind_N</code>

Available data-bases in hydra:
* WFDE5 CRU GPCC (v1, 0.5°): mixing ERA5 CRU and GPCC: <code>WFDE5_CRU_GPCC_[YYYY].nc</code> at <code>hydra</code>:
<pre>${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/</pre>

== Morphological forcings as data-base ==
Installed in CIMA's HPC hydra at
<pre>
/share/DATA/ORCHIDEE/IGCM/SRF
</pre>

To be interpolated to the domain of simulation (region and resolution) at the first time step (done by ORCHIDEE)
Mandatory:

=== PFT map ===

15 PFT, percentage of each by grid-point (<code>maxvegetfrac</code>, see table for equivalencies of PFT)

{| class="wikitable"
! num
! description
|-
| 1 || bare ground
|-
| 2 || tropical broad-leaved evergreen
|-
| 3 || tropical broad-leaved raingreen
|-
| 4 || temperate needleleaf evergreen
|-
| 5 || temperate broad-leaved evergreen
|-
| 6 || temperate broad-leaved summergreen
|-
| 7 || boreal needleleaf evergreen
|-
| 8 || boreal broad-leaved summergreen
|-
| 9 || boreal needleleaf summergreen
|-
| 10 || C3 grass
|-
| 11 || C4 grass
|-
| 12 || C3 agriculture
|-
| 13 || C4 agriculture
|-
| 14 || C3 tropical natural grassland
|-
| 15 || C4 boreal natural grassland
|}

<code>PFTmap_IPCC_[YYYY].nc</code> (0.5°, basic), a file per/year ESA-LUH2, v2 at:
<pre>${ORforcing}/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_2000.nc</pre>
<code>carteveg5km.nc</code> (Olson's global classification of 94 PFT, 5km transformation)

No temporal evolution at:
<pre>${ORforcing}/PFTMAPS/</pre>

[[File:Olson_vegetmap.png|frame|50px|Global Olson vegetation at 5 km of resolution Homolosine projection]]

=== Soil characterisitcs ===

* <code>soilcolor</code> used to define background-albedo: albedowet, albedodry (using values from 1 to 8). To be find in <code>soils_param.nc, soils_param_zobler.nc</code>
* <code>soiltexture</code> to define soil type, to be grouped as 3 types: corse, medium, fine (from 7 values). 3 different sources:
* <code>soils_param.nc</code> (1.°, basic)
* <code>soils_param_zobler.nc</code>: 7 types (1°)
* <code>soils_param_usda.nc</code>: 12 types (0.08331404°)

=== WOODHARVEST ===


=== SOIL_BULK ===


=== Additional ===
* LAI: on runs without <code>stomate</code> (otherwise, LAI is dynamic), one needs to provide climatologies of the LAI: 13 LAI values which evolves along time (monthly climatology) <code>lai2D_[00/01/03].nc</code>
* Albedo: on runs without <code>stomate</code> (otherwise, albedo is dynamic) new maps only for the bare soil albedo at higher resolution to avoid the use of <code>soilcolor</code> from <code>soils_param.nc</code>. Fixed values for wet/dry background albedo. Or a new file
** <code>alb_bg_jrctip.nc</code>: albedos climatologies retrieved from MODIS satellite JRC-TIP package
** <code>alb_bg_modisopt_2D.nc</code>: Another non.climatological albedo from MODIS
<pre>${ORforcing}/albedo</pre>
* Routing: <code>routing.nc</code>: worldwide data-base of river basins at 0.5°: 1-8 direction, <89 point at the sea, ... (<code>trip</code>), riverID (<code>basins</code>), water retention (<code>topoind</code>), etc..., <code>cartepente2d_15min.nc</code> topography slope (0.25°)
* Floodplains: <code>floodplain.nc</code> To account for maximum flooded area: <code>lake, dam, swamp, saline, pond, irrig</code>
* Chemistry: <code>orchidee_fertilizer_1995.nc</code> with fertilization (for N<sub>2</sub>) for rice and the others
* Reference Temperature: To be used as a reference temperature for the soil (<code>reftemp.nc</code>)

All ORCHIDEE configuration is controlled by <code>run.def</code>.: Domain, period, physics activation, sechiba/stomate, routing, floodplains, ... [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters ORparameters]

I/O controlled by <code>*.xml</code> files from [http://forge.ipsl.jussieu.fr/ioserver/ XIOS] libraries
* <code>iodef.xml</code>: main XIOS configuration
* <code>context_orchidee.xml</code>: I/O global configuration for ORCHIDEE
* <code>field_def_orchidee.xml</code>: definition of I/O variables (names, units, dimensions, long-name, ...)
* <code>file_def_orchidee.xml</code>: definition of variables at each file (output frequency, level of output, ...)

= Installation =
This installation guide is based on the installation in different machines from CIMA/DCAO computational resources:
* CIMA's HPC [[ORcompHYDRA hydra]]
* DCAO's computational classroom [[ORcompDCAO DCAO]]

which it must have pre-installed: netCDF libraries (netcdf-dev, netcdff), MPI libraries (mpi, mpich), Fortan and C compilers (gcc, gcc++ gfortran), pre-processing tools (cpp), subversion repository code tool (svn), Makefile (make, gmake), shells (ksh, csh)

''' NOTE '''
<pre>
Each new version of the code, has its own XIOS files! Make sure that you're using the right ones!! (otherwise, you would have an error...)
</pre>

= Running the model =
ORCHIDEE can run in a large variety of forms. Here is desribed a simple way to run a year of simulation using the off-line configuration and the trunk branch.

== Benchmark ==

Following this [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCase1 instructions] we downloaded the necessary forcings in <code> /share/DATA/ORCHIDEE/benchmark </code>

For this experiment, our <code>WORKDIR</code>:
<pre>
/home/lluis.fita/estudios/ORbenchmark
</pre>

Linking all data:
<pre type="shell">
ln -s /share/DATA/ORCHIDEE/benchmark/link_ORbenchmark_files.bash ./
./link_ORbenchmark_files.bash
</pre>

Configuring XIOS:
<pre type="shell">
cp /share/ORCHIDEE/modipsl/modeles/ORCHIDEE/src_xml/* ./

diff file_def_orchidee.xml /share/ORCHIDEE/modipsl/modeles/ORCHIDEE/src_xml/file_def_orchidee.xml
44c44
< <file id="sechiba1" name="sechiba_history" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="sechiba1" name="sechiba_history" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
391c391
< <file id="sechiba2" name="sechiba_out_2" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="sechiba2" name="sechiba_out_2" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
633c633
< <file id="sechiba3" name="sechiba_history_4dim" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="sechiba3" name="sechiba_history_4dim" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
837c837
< <file id="stomate1" name="stomate_history" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="stomate1" name="stomate_history" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
1246c1246
< <file id="stomate2" name="stomate_ipcc_history" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="stomate2" name="stomate_ipcc_history" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
1329c1329
< <file id="stomate3" name="stomate_history_4dim" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="stomate3" name="stomate_history_4dim" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
1407c1407
< <file id="stomate4" name="stomate_fixed_dia" output_level="10" output_freq="1d" enabled=".TRUE.">
---
> <file id="stomate4" name="stomate_fixed_dia" output_level="_AUTO_" output_freq="_AUTO_" enabled="_AUTO_">
</pre>

Getting the configuration and modifying its values:
<pre type="shell">
cp /share/ORCHIDEE/modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/run.def ./
diff run.def /share/ORCHIDEE/modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/run.def
12c12
< TIME_LENGTH = 1D
---
> TIME_LENGTH = _AUTO_
17c17
< TIME_SKIP = 0
---
> TIME_SKIP = _AUTO_
21c21
< DRIVER_reset_time = n
---
> DRIVER_reset_time = _AUTO_
24c24
< RESTART_FILEIN = NONE
---
> RESTART_FILEIN = _AUTOBLOCKER_
28c28
< ATM_CO2 = 350.
---
> ATM_CO2 = _AUTO_: DEFAULT = 350.
33,36c33,36
< LIMIT_WEST=-5
< LIMIT_NORTH=5
< LIMIT_SOUTH=40
< LIMIT_EAST=55
---
> #LIMIT_WEST=8
> #LIMIT_NORTH=48
> #LIMIT_SOUTH=46
> #LIMIT_EAST=10
</pre>

Getting orchidee's configuration:

<PRE STYLE="shell">
cp /share/ORCHIDEE/modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/orchidee.def ./
diff orchidee.def /share/ORCHIDEE/modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/orchidee.def
41c41
< SECHIBA_restart_in = NONE
---
> SECHIBA_restart_in = _AUTOBLOCKER_
45c45
< STOMATE_RESTART_FILEIN = NONE
---
> STOMATE_RESTART_FILEIN = _AUTOBLOCKER_
52c52
< XIOS_ORCHIDEE_OK = y
---
> XIOS_ORCHIDEE_OK = _AUTOBLOCKER_
56c56
< SECHIBA_HISTFILE2 = n
---
> SECHIBA_HISTFILE2 = _AUTO_
61c61
< WRITE_STEP = 0
---
> WRITE_STEP = _AUTO_
65c65
< WRITE_STEP2 = 0
---
> WRITE_STEP2 = _AUTO_
69c69
< STOMATE_HIST_DT = 0
---
> STOMATE_HIST_DT = _AUTO_
74c74
< STOMATE_IPCC_HIST_DT = 0
---
> STOMATE_IPCC_HIST_DT = _AUTO_
135c135
< RIVER_DESC = n
---
> RIVER_DESC = _AUTO_
146c146
< VEGET_UPDATE = 0Y
---
> VEGET_UPDATE = _AUTO_
196c196
< STOMATE_OK_STOMATE = y
---
> STOMATE_OK_STOMATE = _AUTOBLOCKER_
206c206
< NINPUT_UPDATE = 0Y
---
> NINPUT_UPDATE = _AUTO_
209c209
< STOMATE_IMPOSE_CN = n
---
> STOMATE_IMPOSE_CN = _AUTO_
</PRE>

And ORCHIDEE's PFTs
<PRE STYLE="shell">
cp /share/ORCHIDEE/modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/orchidee_pft.def_15pft.1ac ./orchidee_pft.def
</PRE>

Getting the basic PBS job to run ORCHIDEE:
<pre type="shell">
cp /share/ORCHIDEE/launch_orchidee.pbs ./
</pre>

Launching
<pre type="shell">
qsub launch_orchidee.pbs
</pre>

== Test: let's look at Marcos Juárez, Córdoba, Argentina ==

Assuming a working directory <code>${WORKDIR}</code> (e.g.: <code>/home/lluis.fita/estudios/SensLuLc_MarcosJuarez/trunk</code>)

Writing of a simple <code>run.def</code> with stomate and routing activated for the 1980 year (the meaning and default values of all parameters are available [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters here]

<pre>
*****************************************************************************
START_DATE = 2001-01-01 00:00:00
END_DATE = 2001-12-31 24:00:00
TIME_LENGTH = 1Y
DT_SECHIBA = 900
#SPREAD_PREC_SEC = 3600 # The default is half the forcing time step
FORCING_FILE = forcing_yearm1.nc forcing_year.nc forcing_yearp1.nc

GRID_FILE = NONE
# South America
#LIMIT_WEST = -90.0
#LIMIT_EAST = -30.0
#LIMIT_SOUTH = -60.0
#LIMIT_NORTH = 15.0
# Marcos Juarez
LIMIT_WEST = -64.0
LIMIT_EAST = -60.0
LIMIT_SOUTH = -34.0
LIMIT_NORTH = -30.0
#*****************************************************************************

# Activate Stomate component (default y)
STOMATE_OK_STOMATE= y
STOMATE_OK_NCYCLE=FALSE

#
# Parameters related to the restart file and the start date
#**************************************************************************
# Time in the forcing file at which the model start if start date is not set by the forcing file (default 0)
TIME_SKIP = 0

# Time length for one intergration
# (default full lenght of forcing file)
#TIME_LENGTH = _AUTO_

# If DRIVER_reset_time=y, read the year from forcing file instead of taking it from restart file (default n)
#DRIVER_reset_time = _AUTO_

# Name of restart file for the driver (default NONE)
RESTART_FILEIN = NONE

# Name of restart file for sechiba part of the model (default NONE)
#SECHIBA_restart_in = _AUTOBLOCKER_

# Name of restart file for stomate part of the model (default NONE)
#STOMATE_RESTART_FILEIN = _AUTOBLOCKER_

# Parameters related to the diagnostic output files
#**************************************************************************
# Use XIOS for writing diagnostics file (default y)
XIOS_ORCHIDEE_OK = n

# Flag to activate sechiba_out_2.nc history file when using IOIPSL for SECHIBA (defulat n)
SECHIBA_HISTFILE2 = n

# Writefrequency in seconds in sechiba_history.nc when using IOIPSL (default 86400)
# If WRITE_STEP=0 then all IOIPSL output are deactivated
WRITE_STEP = 0

# Writefrequency in seconds sechiba_out_2.nc when using IOIPSL (default 1800)
WRITE_STEP2 = 0

# Writefrequency in days in stomate_history.nc when using IOIPSL (default 10)
STOMATE_HIST_DT = 0

# Writefrequency in days or -1 for monthly output in stomate_ipcc_history.nc when using IOIPSL (default 0)
STOMATE_IPCC_HIST_DT = 0

PRINTLEV=1000

# Hydrology parameters
#**************************************************************************
# Activate the multi-layer diffusion scheme adapted from CWRR (default y)
HYDROL_CWRR = y

# Activate river routing (default y)
RIVER_ROUTING = n
ROUTING_METHOD = highres
ROUTING_FILE = routing.nc
DT_ROUTING = 900
# Activate creation of river_desc.nc file
# RIVER_DESC will be activated only the first execution in the simulation
RIVER_DESC = y

# SOILTYPE_CLASSIF : Type of classification used for the map of soil types (default zobler)
SOILTYPE_CLASSIF = zobler

# Parameters related to vegetation map
#**************************************************************************
# Update vegetation frequency (default 0Y)
VEGET_UPDATE = 0Y

# Read lai map (default n)
LAI_MAP = n

# Prescribed vegetation (default n)
IMPOSE_VEG = n

# Parameters related to surface and thermal physical properties
#************************************************************************
# ROUGH_DYN : Account for a dynamic roughness height (activation of Su et al. parametrization) (default y)
ROUGH_DYN=y

# OK_FREEZE : Activate the complet soil freezing scheme (default y)
OK_FREEZE=y

# OK_EXPLICITSNOW : Activate explict snow scheme (default y)
OK_EXPLICITSNOW=y

# Carbon related parameters
#**************************************************************************
# Analytic spinup (default n)
SPINUP_ANALYTIC = n
SPINUP_PERIOD = -1

# Value for atmospheric CO2 (default=350)
ATM_CO2 = 350

# Activate harvest of wood (default y)
DO_WOOD_HARVEST=y

# Deactivate fire (default FIRE_DISABLE=y)
FIRE_DISABLE=y

# Optimized parameters to be used with PFTmap with 15 pfts such as
# files in IGCM/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v1
#**************************************************************************
# Use 15 PFTs. Note that PFTmap.nc must contains 15PFTs.
# PFT=10, 14 and 15 share the same parametrization except for VCMAX25, LAI_MAX, FRAC_GROWTHRESP,
# MAINT_RESP_SLOPE_C and ALWAYS_INIT specified below.
# (default NVM=13)
NVM=15
PFT_TO_MTC=1,2,3,4,5,6,7,8,9,10,11,12,13,10,10
PFT_NAME__10='temperate C3 grass '
PFT_NAME__14='tropical C3 grass '
PFT_NAME__15='boreal C3 grass '

VCMAX25__10 = 50.0
VCMAX25__14 = 50.0
VCMAX25__15 = 40.0

LAI_MAX__10 = 2.5
LAI_MAX__14 = 2.5
LAI_MAX__15 = 2.0

FRAC_GROWTHRESP__10 = 0.28
FRAC_GROWTHRESP__14 = 0.35
FRAC_GROWTHRESP__15 = 0.35

MAINT_RESP_SLOPE_C__10 = 0.16
MAINT_RESP_SLOPE_C__14 = 0.12
MAINT_RESP_SLOPE_C__15 = 0.25

ALWAYS_INIT__10 = y
ALWAYS_INIT__14 = n
ALWAYS_INIT__15 = y
</pre>

Linking atomspheric forcing files (0.5° WFDE5 CRU GPCC v1 files)
<pre>
ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2000.nc ./forcing_yearm1.nc
ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2001.nc ./forcing_year.nc
ln -s ${ORforcing}/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_2002.nc ./forcing_yearp1.nc
</pre>

Linking the routing data-base
<pre>ln -s ${ORforcing}/routing.nc ./</pre>

Linking the topographical slope
<pre>ln -s ${ORforcing}/cartepente2d_15min.nc ./</pre>

Initial temperature of the soil
<pre>ln -s /share/DATA/ORCHIDEE/IGCM/SRF/reftemp.nc ./</pre>

Linking the morphological files
<pre>ln -s ${ORforcing}/SOIL/soils_param_zobler.nc ./soils_param.nc
ln -s ${ORforcing}/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_1980.nc ./PFTmap.nc
ln -s /share/DATA/ORCHIDEE/IGCM/SRF/SOIL/soil_bulk_and_ph.nc ./
</pre>

Linking the files related with the Nitrogen's cycle (with <code>R_IN=/share/ORCHIDEE/IGCM/, simYR=2001</code>)
<pre type="shell">
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/synthetic/historical/Nfer_pasture_${simYR}.nc ./nfer_pasture.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/synthetic/historical/Nfer_cropland_${simYR}.nc ./nfer_cropland.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/manure/historical/Nmanure_pasture_${simYR}.nc ./nmanure_pasture.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/manure/historical/Nmanure_cropland_${simYR}.nc ./nmanure_cropland_${simYR}.nc
ln -s ${R_IN}/SRF/NITROGEN/N_DEPOSITION/CCMI_ndep/historical/CCMI_ndep_nhx_${simYR}.nc ./ndep_nhx.nc
ln -s ${R_IN}/SRF/NITROGEN/N_DEPOSITION/CCMI_ndep/historical/CCMI_ndep_noy_${simYR}.nc ./ndep_noy.nc
ln -s ${R_IN}/SRF/NITROGEN/BNF/bnf_1850.nc ./bnf.nc
ln -s ${R_IN}/SRF/NITROGEN/N_DEPOSITION/CMIP6.2/historical/nhx__${simYR}.nc ./Nammonium.nc
ln -s ${R_IN}/SRF/NITROGEN/N_DEPOSITION/CMIP6.2/historical/noy__${simYR}.nc ./Nnitrate.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP2/synthetic/historical/nfer_crop_nh4_${simYR}.nc ./Nfert_ammo_cropland.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP2/synthetic/historical/nfer_pas_nh4_${simYR}.nc ./Nfert_ammo_pasture.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP2/synthetic/historical/nfer_crop_no3_${simYR}.nc ./Nfert_nitr_cropland.nc
ln -s ${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP2/synthetic/historical/nfer_pas_no3_${simYR}.nc ./Nfert_nitr_pasture.nc
</pre>

Getting the XIOS files (they might be version-dependant, therfore, it is recommended to get them directly from the same folder where the compiled version of ORCHIDEE is located, INSTALLDIR=/share/ORCHIDEE/)
<pre>cp $INSTALLDIR/modipsl/modeles/ORCHIDEE/src_xml/*xml ./</pre>

Edit the <code>file_def_orchidee.xml</code> to define output frequency and level of of output (remove all the <code>_AUTO_</code>)
<pre>vim file_def_orchidee.xml</pre>

The final configuration gets:
<pre>$ cat file_def_orchidee.xml | grep 'file id'
<file id="sechiba1" name="sechiba_history" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba2" name="sechiba_out_2" output_level="2" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba3" name="sechiba_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="sechiba1_alma" name="sechiba_history_alma" output_level="10" output_freq="1mo" enabled=".FALSE.">
<file id="sechiba2_alma" name="sechiba_out_2_alma" output_level="10" output_freq="1d" enabled=".FALSE.">
<file id="sechiba4" name="sechiba_interp_diag" output_level="3" output_freq="1d" enabled=".TRUE.">
<file id="stomate1" name="stomate_history" output_level="10" output_freq="1d" enabled=".TRUE.">
<file id="stomate2" name="stomate_ipcc_history" output_level="1" output_freq="1mo" enabled=".FALSE.">
<file id="stomate3" name="stomate_history_4dim" output_level="11" output_freq="1d" enabled=".TRUE.">
<file id="stomate4" name="stomate_fixed_dia" output_level="4" output_freq="1d" enabled=".FALSE.">
</pre>
Linking the ORCHIDEE executable
<pre>$ ln -s $INSTALLDIR/modipsl/bin/orchideedriver_prod ./orchideedriver
$ ln -s /share/ORCHIDEE/modipsl/bin/xios_server_prod.exe ./xios.exe
</pre>

Getting the PBS scheduling job to run ORCHIDEE
<pre>$ cp /share/ORCHIDEE/launch_orchidee.pbs ./</pre>

Launching the model
<pre>$ qsub launch_orchidee.pbs</pre>

There is a problem with the meteorological forcing data <code>IGCM/SRF/METEO/WFDE5_CRU_GPCC/v1/WFDE5_CRU_GPCC_[nnnn].nc</code>, its time axis is units are: <code>'hours since 1900-01-01 00:00:00'</code>. But this gives an <code>IOIPSL</code> error from <code>flinopen_work</code> subroutine from <code>IOIPSL/src/flincom.f90</code> (lines #586-600):
<pre style="Fortran">
!---
!-- 5.1 Find the time axis. Prefered method is the 'timestep since'
!---
gdtmaf_id = -1
gdtt_id = -1
old_id = -1
DO iv=1,ncnbva(fid_out)
name=''
iret = NF90_INQUIRE_VARIABLE (fid, iv, name=name)
units=''
iret = NF90_GET_ATT (fid, iv, 'units', units)
IF (INDEX(units,'seconds since') > 0) gdtmaf_id = iv
IF (INDEX(units,'timesteps since') > 0) gdtt_id = iv
IF (INDEX(name, 'tstep') > 0 .OR. INDEX(name,'time') > 0 ) old_id = iv
ENDDO
</pre>
Therefore, axis time units have to changed to <code>'seconds since 1900-01-01 00:00:00'</code>


If everything went fine, one should have (at least)
=== single file output ===
<pre>orout/sechiba_history.nc orout/sechiba_history_4dim.nc stomate_history.nc</pre>
* <code>sechiba_history.nc</code>, <code>sechiba_history_4dim.nc</code>, <code>stomate_history.nc</code>: Outputs (optional, only when stomate is activated)
* <code>sechiba_rest_out.nc</code>, <code>stomate_restart.nc</code>: restarts for <code>sechiba<code> and <code>stomate</code> (optional, only when stomate is activated)
* <code>out_orchidee_[nnnn]</code>: standard output files for each process
* <code>river_desc.nc</code>: output with river description (optional, only when routing is activated)

=== multiple file output ===
In case we run without XIOS, each processor will produce an output file. We need to use the <code>rebuild</code> utility for that
<pre style="sell">
sechiba_history_[nnnn].nc, sechiba_interp_diag_[nnnn].nc, stomate_history_[nnnn].nc, stomate_history_4dim_[nnnn].nc
$ /share/ORCHIDEE/modipsl/modeles/IOIPSL/bin/rebuild -h

"rebuild"
rebuild a model_file from several input files.
Each input file contains the model_data for a domain.

Usage :
rebuild [-h]
rebuild [-v level] [-f] -o output_file_name input_file_names

Options :
-h : help
-v O/1/2/3 : verbose mode (verbosity increasing with level)
-f : executing mode
(execute the program even if the number of input files
is not equal to the total number of domains)
</pre>
We reconstruct:
<pre style="shell">
/share/ORCHIDEE/modipsl/modeles/IOIPSL/bin/rebuild -o sechiba_history.nc sechiba_history_????.nc
</pre>

== Running the model in DCAO's computational lab ==
Follow this link [[runORDCAO]] to set-up the runs in the machines of DCAO's computational laboratory

= OR4L: L. Fita's work-flow management for ORCHIDEE =
ORCHIDEE should be run with [http://forge.ipsl.jussieu.fr/libigcm libIGCM] which is a work-flow management for ORCHIDEE developed at the IPSL.

However, L. Fita developed an independent simpler and less potent work-flow called OR4L. See how it works in this wiki page [[ORCHIDEE/OR4L OR4L]]

= OR_1proc: DCAO's 1-proc work-flow management for ORCHIDEE =
DCAO's computational lab machines are 1 processors standard machines. A new work-flow management has been created for such cases. Mostly related to the UMI & DCAO course of [[http://www.cima.fcen.uba.ar/UMI/wrk/modelado-2019.php land-atmosphere interaction and its modelling]]. All the iformation is available in the wiki page [[OR1proc OR 1proc]]

Wikicima - Contribuciones del usuario [es]

ORCHIDEE