Development Activities

Documentation

Source Code

Reference Simulations

Group Activities

User Guide

This page let you to answer some problems you can meet with ORCHIDEE. You will find several tutorials explaining how to install and run the model, how to debug, etc.

News

• [3551] 16/06/2016 Changes in ORCHIDEE_OL configurations
  • new default options : now soil freeezing and explicitsnow are default options. The soil depth for thermodynamics is now 90m. These options corresponds to what is set in the coupled configuraions LMDZOR_v6 and IPSLCM6.0.4
  • new albdo background file is used : albedo_bg_modisopt.nc
  • structure change : following options are removed from sechiba.card : ROUTING NEWHYDROL, OKCO2, IMPOSE_VEG, LAIMAP. Now the corresponding parameters can be changed directly in run.def.
  • switching on or of XIOS is done in orchiee_ol.card.
• 13/06/2016 Change to use XIOS2 by default in libIGCM configurations (J. Ghattas)
• 29/05/2015 Changed behaviour in reading the vegetation file PFTmap.nc (J. Ghattas)
• 11/02/2015 New method for manipulating run.def file in offline libIGCM configurations (J. Ghattas)
• 21/01/2015 Change to netcdf4p at obelix, LSCE cluster (J. Ghattas)

Technical Notes

• 2103/12 ​B. Guenet ​REPORT ON THE ROLE OF LITTER IN THE WATER FLUXES.pdf
• 2016/08 ​A. Ducharne Technical note on hydrol.f90 (in progress, updated on Dec 15, 2017)
• 2014/10 Notes on the coupling with LMDz Documentation/CouplingLMDZ
• See the list of parameters used by the model trunk version. See also the same list in ​orchidee.default in the latest version of the trunk
• Physical range of the parameters: ​Parameters Range Table
• Guide lines for the code structure in ORCHIDEE
• Introduction to ORCHIDEE configurations using libIGCM
• F. Cheruy slides for the atmosphere-surfaces coupling (from LMDZ training course 2018) ​https://forge.ipsl.jussieu.fr/orchidee/attachment/wiki/Documentation/UserGuide/Atmosphere%E2%80%93SurfaceFC_dopo.pdf

How to section

Installation/First run/Branch

• Login needed to access ORCHIDEE and work on the wiki (J. Ghattas)
• How to install ORCHIDEE with modipsl and libIGCM for offline use (J. Ghattas)
• How to install ORCHIDEE in coupled mode (J. Ghattas)
• How to install ORCHIDEE on my linux laptop or computer? (D.Solyga)
• How to run a simple test case with ORCHIDEE offline ? (J. Ghattas)
• How to submit a parallel job in a batch system (example at curie, ada and obelix) without libIGCM? (J. Ghattas)
• How to download and compile ORCHIDEE-DOFOCO and ORCHIDEE-CN-CAN? (M. McGrath)
• How to download, compile and run ORCHIDEE-CN-P & more information about the model (D. Goll)
• Install LMDZ at obelix? (J. Ghattas)
• Install and run at ciclad and ClimServ? (J. Ghattas)
• Compile methods : Standard makefiles and FCM (J. Ghattas)

svn

• Basic use of SVN​ (J. Ghattas)
• How to create a new branch or a personal version (J. Ghattas)
• Guidelines and help to commit on the trunk (or a branch) (J. Ghattas)
• How to keep a branch or personal version updated with the trunk or with another version (J. Ghattas)
• How to check the differences between a branch and a personal version? (M. McGrath)
• How to merge a branch to trunk (A. Jornet) ?
• Some more information about svn

libIGCM

• How to make a spinup analytic in OOL_SEC_STO? (J. Ghattas)
• How to loop over years with libIGCM (M. McGrath)
• How to prescribe the vegetation in a pixel? (S.Luyssaert)
• How to make use of a land cover map with libIGCM ?? (S.Luyssaert)
• How to make use of a land cover change maps with libIGCM ?? (A. Rajaud & S.Luyssaert)
• Change atmospheric CO2 scalar value (J. Ghattas)
• How to compare against Fluxnet data (M. McGrath)
• Is there a way to send all of my Orchidee output files to a different location? (J. Ryder)
• Is there a way to save all the output files when debugging with libIGCM?? (M. McGrath)
• Is there a way to specify different queues automatically with libIGCM? (M. McGrath)
• How to change the climate forcing with libIGCM? (M. McGrath)
• Possible ways to make headaches go away (M. McGrath)
• Launch a libIGCM job on Airain? (S.Luyssaert)
• Where to recover or how to manually rebuild a missing history file (S.Luyssaert)
• Error message cp: cannot stat (J. Ghattas)
• How to tell libIGCM to copy a new input file for ORCHIDEE (D. Goll, J. Ghattas)

History/output files

• Using XIOS
  • ​Presentation about XIOS in ORCHDIDEE, developers meeting 31 mars 2015 (J. Ghattas)
  • Using XIOS in ORCHIDEE_trunk configuration with libIGCM (J Ghattas)
  • Add a new output variable using XIOS (J Ghattas)

• Using IOIPSL
  • How to install ORCHIDEE without XIOS? (J. Ghattas)
  • How to understand the operators used to write the variables in the history files ? (F.Maignan)
  • How to add a variable to history files ? (S.Luyssaert)
  • How to easily change history output level for multiple variables in intersurf.f90?? (C.Yue)

netcdf

• How to check differences between netcdf files ? (S.Luyssaert)
• What's the quickest way to examine netCDF files? (J.Ryder)
• Use cdo commands to process netCDF files?
• Install and compile with another netCDF library ? (S.Luyssaert)

Debugging

• PRINTLEV : Control text output (J. Ghattas)
• How to solve a segmentation error ?(S.Luyssaert)
• How to find where the model is hanging ?(M. McGrath & S.Luyssaert)
• Extract a single pixel from a large restart file (M. McGrath)
• Debug a coupled LMDZOR run? (M. McGrath)
• How to use the debbugger IDB/Totalview
• Compilation flags

Profiling

• Run a profiling job in serial on obelix (M. McGrath)
• Run a profiling job in serial on Curie with intel vtune (A. Jornet)
• Run a profiling job in parallel on Curie with DDT Allinea Map (A. Jornet)

Parallelism

• Parallelization in ORCHIDEE and how to use OpenMP (A. Cozic, D.Solyga)
• How to run ORCHIDEE in parallel on Obelix ?? (D.Solyga)
• How to run ORCHIDEE with Vampir ? (D.Solyga)

Environments

• Running at Ada/IDRIS? (J. Ghattas)

Code

• How to add a new flag in ORCHIDEE ? (S.Luyssaert)

Coupling to LMDZ

• How to install ORCHIDEE in coupled mode (J. Ghattas)
• How to combine the above and install the DOFOCO branch, coupled, with the 11 layer hydrology/new physics/STOMATE ?? (J. Ryder)
• How do I set up a zoomed (and nudged) simulation (a.k.a. using a new LMDZOR grid) ? (M. McGrath and someone else?)
• How to set-up a preindustrial run with LMDZOR (DOFOCO) ? (S.Luyssaert and M. McGrath)
• How to set-up a present day run with LMDZOR (DOFOCO) ? (S.Luyssaert and M. McGrath)
• How to set-up a future run with LMDZOR (DOFOCO) ? (S.Luyssaert)
• How to perturb the initial conditions in LMDZOR ? (S.Luyssaert)
• What is important to know about using a new LMDZOR grid ? (M. McGrath)
• How to verify that the climate produced by your LMDZOR run is not terrible (ATLAS & TOA) ? (M. McGrath)
• How to launch a stand-alone ATLAS run to validate the climate (M. McGrath)
• How to set different output levels for the LMDZ ouput files (Y.Chen)

Forcing files

• How to run future simulations? (M. McGrath)
• How should be formatted the atmospheric forcing files for ORCHIDEE and how to verify if they are well read by the ORCHIDEE driver (M. Guimberteau)

Divers

• How to write a shell script ? (S.Luyssaert)
• How to use ferret to change the resolution of a file? (J.Otto & S.Luyssaert)
• How to use cdo to change the resolution of a file? (J.Barichivich & S.Luyssaert)
• How to rename many files at once? (S.Luyssaert)
• How to write a shell script for searching specific files and combining them together to a single file? (Y.Chen)
• Some information about regular expressions?
• Recurrent error messages
• ​How to create tickets (D.Solyga).
• ​Under development: How to run CliMAF atlas ORCHIDEE Obsolete!! Now see here : ​https://github.com/jservonnat/C-ESM-EP/wiki/The-C-ESM-EP-in-a-nutshell