How to run a simple test case with ORCHIDEE

Author: J. Ghattas
Last revision: 2020/01/19, J. Ghattas, update done after inclusion of branch CN-CAN in the trunk
Last revision: 2020/06/26, F. Maignan, output_level="X" (noticed by E. Dupont)

Objectives

Prepare and run a simple test case for ORCHIDEE trunk without using any script. All input files needed are listed on this page. This page is adapted for the use of ORCHIDEE trunk revision 6614 or later version. If you need to prepare a test case for ORCHIDEE_3, go to the following page: TestCaseORCH3

This page describes how to prepare the run directory and run ORCHIDEE interactively, i.e. to launch directly in the terminal without passing through the batch system. You can also run using a job and launch on the batch system, for that case go to the following page: Documentation/UserGuide/TestCaseBatch.

Prepare input files

You need the following files :

• executable orchidee_ol
• forcing_file.nc and other netcdf input files
• xml files to configure output using XIOS
• run.def, orchidee.def and orchidee_pft.def parameter files to set up the simulation

Create a directory where you will run the model and copy input files as follow.

Executable orchidee_ol

Install and compile the model to get the executable orchidee_ol. Read more here: wiki:Documentation/UserGuide/InstallingORCHIDEEBasic

Input netcdf files

File in shared repository	File name expected by ORCHIDEE
${R_IN}/SRF/METEO/CRU-NCEP/v5.3.2/twodeg/cruncep_twodeg_${year}.nc	forcing_file.nc
${R_IN}/SRF/PFTMAPS/CMIP6/ESA-LUH2v2/historical/15PFT.v2/PFTmap_${year}.nc	PFTmap.nc
${R_IN}/SRF/SOIL/soils_param.nc	soils_param.nc
${R_IN}/SRF/SOIL/soil_bulk_and_ph.nc	soil_bulk_and_ph.nc
${R_IN}/SRF/cartepente2d_15min.nc	cartepente2d_15min.nc
${R_IN}/SRF/reftemp.nc	reftemp.nc
${R_IN}/SRF/ROUTING/routing.nc	routing.nc
${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/synthetic/historical/Nfer_pasture_${year}.nc	nfert_pasture.nc
${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/synthetic/historical/Nfer_cropland_${year}.nc	nfert_cropland.nc
${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/manure/historical/Nmanure_pasture_${year}.nc	nmanure_pasture.nc
${R_IN}/SRF/NITROGEN/N_FERTILISATION/NMIP/manure/historical/Nmanure_cropland_${year}.nc	nmanure_cropland.nc
${R_IN}/SRF/NITROGEN/N_DEPOSITION/CCMI_ndep/historical/CCMI_ndep_nhx_${year}.nc	ndep_nhx.nc
${R_IN}/SRF/NITROGEN/N_DEPOSITION/CCMI_ndep/historical/CCMI_ndep_noy_${year}.nc	ndep_noy.nc
${R_IN}/SRF/NITROGEN/BNF/bnf_1850.nc	bnf.nc

where

• R_IN=/prodigfs/ipslfs/igcmg/IGCM at ciclad/climserv
• R_IN=/home/orchideeshare/igcmg/IGCM at obelix
• IDRIS, TGCC see ORCHIDEE training courses or ​http://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/ComputingCenters
• or download using wget, replace R_IN by ​https://vesg.ipsl.upmc.fr/thredds/catalog/IPSLFS/igcmg/IGCM
• replace ${year} by the year of your choice between 1901-2010

xml files for running with XIOS

Note: If you do not compile with XIOS, you do not need to copy these files but you need to adapt run.def to activate output with IOIPSL, see further below.

The xml files controls the output of the model if you use XIOS. XIOS is the default instead of IOIPSL since rev 3115 in the trunk. Moreover, since rev 3839, only XIOS/trunk revision 965 (XIOS2) or later can be used.

• Copy all the xml files from the "modeles" directory ORCHIDEE/src_xml to your run directory: iodef.xml, context_orchidee.xml, context_input_orchidee.xml, field_def_orchidee.xml and file_def_orchidee.xml.

• Edit file_def_orchidee.xml to change every instance of "_AUTO_" (3 for each output file)
  • output_level="_AUTO_" into output_level="X" where X is an integer between 0-11
  • output_freq="_AUTO_" into output_freq="1mo" or output_freq="1d" par example
  • enabled="_AUTO_" into enabled="true" or enabled="false"
  • do any other change as you wish to adapt the output to your needs

• Edit field_def_orchidee.xml only if you changed the ORCHDEE source code.

Parameter files

Copy following parameter files from experiment set up OOL_SEC_STO2 into your run folder and modify all occurrences of AUTO as follow:

• modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/run.def

  TIME_LENGTH = 1D
  TIME_SKIP = 0
  DRIVER_reset_time = n
  RESTART_FILEIN = NONE
  ATM_CO2 = 350.
  

• modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/orchidee.def

  SECHIBA_restart_in = NONE
  STOMATE_RESTART_FILEIN = NONE
  XIOS_ORCHIDEE_OK = y
  SECHIBA_HISTFILE2 = n
  WRITE_STEP = 0
  WRITE_STEP2 = 0 
  STOMATE_HIST_DT = 0
  STOMATE_IPCC_HIST_DT = 0
  RIVER_DESC = n
  VEGET_UPDATE = 0Y
  SPINUP_ANALYTIC = n
  SPINUP_PERIOD = 0
  STOMATE_OK_STOMATE = y 
  NINPUT_UPDATE = 0Y
  STOMATE_IMPOSE_CN = n
  

• modipsl/config/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/orchidee_pft.def_15pft.1ac
  • rename the file as orchidee_pft.def, no changes in the file

Check you environment and launch the model

To run the model you first need to load the same netcdf library as the one used for the compilation. This depends on the machine you work at. If you use one of the predefined IPSL machines (irene, jeanzay, obelix or ciclad/climserv), source the file in the folder ORCHIDEE_OL/ARCH:

source modipsl/config/ORCHIDEE_OL/ARCH/arch.env

For other machines, make sure you use the same environment as the one used during compilation.

Once you've get all input files, launch the model in the same directory :

./orchidee_ol > out_orchidee_ol 2>&1

Other methods to set up a run directory

If you run with libIGCM, set up a normal job using the command ./../../../libIGMC/ins_job but add exit in the main Job after following:

  echo
  echo "#######################################"
  echo "#      DIR BEFORE RUN EXECUTION       #"
  echo "#######################################"
  echo
  ls -lrt

  exit

Launch the job and the go to the run directory where you'll find all input netcdf files and parameter files. You can work directly in this run directory to make simpler test cases.

Note: at obelix, set RUN_DIR_PATH in the main job so the run directory will be accessible.

Another way to do it from a run you've already finished with libIGCM is to look at the Script_Output_* file. Inside this file libIGCM lists all the files that it copies to the run directory (look for the commands where the commands IGCM_sys_Cp and IGCM_sys_Get appear in the Script_Output_* file). If you copy those files manually to a new directory, you should be able to launch the exact same simulation but you first need to change all occurrences of AUTO as in the above part of this page.