ORCHIDEE

ORCHIDEE

This manual provides the information about the land-surface model ORCHIDEE (technical page for advanced users) from Institute Pierre Simone Laplace (IPSL). Its installation on the HPC of the CIMA called hydra.

Model description

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

Off-line atmospheric forcings

• Desdcribed here: ORforcings
  • Atmoshperic variables required by ORCHIDEE: LWdown, PSurf, Qair, Rainf, SWdown, Snowf, Tair, Wind_E, Wind_N
  • CRU-NCEP (v5.4, 0.5°): mixing CRU with NCEP: cruncep_halfdeg_[YYYY].nc at hydra (taking ${ORforcing}=/share/ORCHIDEE/data/IGCM/SRF):

${ORforcing}/METEO/CRU-NCEP/v5.4/halfdeg

Morphological forcings as data-base

Installed in CIMA's HPC hydra at

/share/DATA/ORCHIDEE/IGCM

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

PFT map

• • • • 13 PFT, percentage of each by grid-point (maxvegetfrac, see table for equivalencies of PFT)

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

• • • • PFTmap_IPCC_[YYYY].nc (0.5°, basic), a file per/year ESA-LUH2, v2 at:

${ORforcing}/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_2000.nc

• • • • carteveg5km.nc (Olson's global classification of 94 PFT, 5km transformation) No temporal evolution at:

${ORforcing}/PFTMAPS/

Global Olson vegetation at 5 km of resolution Homolosine projection

Soil characterisitcs

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

Additional

• • • LAI: on runs without stomate (otherwise, LAI is dynamic), one needs to provide climatologies of the LAI: 13 LAI values which evolves along time (monthly climatology) lai2D_[00/01/03].nc
    • Albedo: on runs without stomate (otherwise, albedo is dynamic) new maps only for the bare soil albedo at higher resolution to avoid the use of soilcolor from soils_param.nc. Fixed values for wet/dry background albedo. Or a new file
      • alb_bg_jrctip.nc: albedos climatologies retrieved from MODIS satellite JRC-TIP package
      • alb_bg_modisopt_2D.nc: Another non.climatological albedo from MODIS

${ORforcing}/albedo

• • • Routing: routing.nc: worldwide data-base of river basins at 0.5°: 1-8 direction, <89 point at the sea, ... (trip), riverID (basins), water retention (topoind), etc..., cartepente2d_15min.nc topography slope (0.25°)
    • Floodplains: floodplain.nc To account for maximum flooded area: lake, dam, swamp, saline, pond, irrig
    • Chemistry: orchidee_fertilizer_1995.nc with fertilization (for N₂) for rice and the others
    • Reference Temperature: To be used as a reference temperature for the soil (reftemp.nc)

• All ORCHIDEE configuration is controlled by run.def.: Domain, period, physics activation, sechiba/stomate, routing, floodplains, ... ORparameters
• I/O controlled by *.xml files from XIOS libraries
  • iodef.xml: main XIOS configuration
  • context_orchidee.xml: I/O global configuration for ORCHIDEE
  • field_def_orchidee.xml: definition of I/O variables (names, units, dimensions, long-name, ...)
  • file_def_orchidee.xml: 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

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...)

Running the model

ORCHDEE can run in a large variety of forms. Here is desribed a simple way to run a year of simulation

• Assuming a working directory ${WORKDIR} (e.g.: /home/lluis.fita/estudios/LUPA). Creation of the running folder

$ mkdir -p tests/control 
$ cd tests/control

• Writting of a simple run.def with stomate and routing activated for the 1977 year (the meaning and default values of all parameters are available here

# Use XIOS for writing diagnostics file
# defulat = n
XIOS_ORCHIDEE_OK = y
#
START_DATE = 1977-01-01_00
END_DATE = 1978-01-01_00
TIME_LENGTH = 1Y
DT_SECHIBA = 1800

# Atmospheric forcing file
FORCING_FILE = atmos_forcing.nc

#
# South America
#
#WEST_EAST = -85., -31.
#SOUTH_NORTH = -57, 14.
LIMIT_WEST = -85.
LIMIT_EAST = -31.
LIMIT_SOUTH = -57.
LIMIT_NORTH = 14.
MERID_RES = 0.5
ZONAL_RES = 0.5

VEGET_YEAR=1

# Activation of stomate
STOMATE_OK_CO2= y
STOMATE_OK_STOMATE= y
STOMATE_OK_NCYCLE=FALSE

# For routing
RIVER_ROUTING = y
ROUTING_FILE = routing.nc
HYDROL_CWRR = y
DT_ROUTING = 86400
RIVER_DESC = y
RIVER_DESC_FILE = river_desc.nc
ROUTING_RIVERS = 50

# Debug standard output printing level
PRINTLEV = 0

• Linking atomspheric forcing files (0.5° CRU-NCEP v5.4 files)

$ ln -s /share/ORCHIDEE/data/IGCM/SRF/METEO/CRU-NCEP/v5.4/halfdeg/cruncep_halfdeg_1977.nc ./atmos_forcing.nc

• Linking the routing data-base

$ ln -s /share/ORCHIDEE/data/IGCM/SRF/routing.nc ./

• Linking the topographical slope

$ ln -s /share/ORCHIDEE/data/IGCM/SRF/cartepente2d_15min.nc ./

• Linking the morphological files

$ ln -s /share/ORCHIDEE/data/IGCM/SRF/soils_param.nc ./ 
$ ln -s /share/ORCHIDEE/data/IGCM/SRF/PFTmap_IPCC_1850.nc ./PFTmap.nc

• Getting the XIOS files

$ cp /share/modipsl/modeles/ORCHIDEE/src_xml/*xml ./

• Edit the file_def_orchidee.xml to define output frequency and level of of output (remove all the _AUTO_)

$ vim file_def_orchidee.xml

• The final configuration gets:

$ 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="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.">

• Linking the ORCHIDEE executable

$ ln -s [INSTALLDIR]/modipsl/bin/orchidee_ol ./

• Getting the PBS scheduling job to run ORCHIDEE

$ cp /share/ORCHIDEE/run_or.pbs ./

• Launching the model

$ qsub run_or.pbs

• If everything went fine, one should have (at least)

orout/sechiba_history.nc  orout/sechiba_history_4dim.nc  stomate_history.nc

• • sechiba_history.nc, sechiba_history_4dim.nc, stomate_history.nc: Outputs (optional, only when stomate is activated)
  • sechiba_rest_out.nc, stomate_restart.nc: restarts for sechiba<code> and <code>stomate (optional, only when stomate is activated)
  • out_orchidee_[nnnn]: standard output files for each process
  • river_desc.nc: output with river description (optional, only when routing is activated)

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 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 [land-atmosphere interaction and its modelling]. All the iformation is available in the wiki page OR1proc OR 1proc