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User Guide to ORCHIDEE

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. You can also find information among the presentations done during the Orchidee Training courses

Installation, compilation and basic run

• Login needed to access ORCHIDEE and work on the wiki (last revised 2020/01/03)
• Set up environment before first time using a new machine: obelix, ciclad, climserv, irene, jean-zay (to be created)
• Install and compile ORCHIDEE for offline use (J. Ghattas)
• Install and compile ORCHIDEE in coupled mode (J. Ghattas)
• How to install ORCHIDEE on a Linux PC (Ubuntu or Fedora distribution) (D.Solyga)
• More about compile methods (J. Ghattas)
• Run a simple test case with ORCHIDEE offline (last revised 2020/01/03)
• Run a parallel job in a batch system (example at curie, ada and obelix) without libIGCM (J. Ghattas)
• Run using libIGCM: see section libIGCM below
• Check list to prepare your simulation: configuration, input files, keywords, etc. (collective)

svn

• Basic use of SVN​ (J. Ghattas)
• Various ways to get the code of an ORCHIDEE version with svn (A. Ducharne)
• How to create a new branch or a personal version (Last revised 2020/02/28)
• Guidelines and help to commit on the trunk (or a branch) (Last revised 2020/02/28)
• 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

Different ways to configure simulations with libIGCM

• ​Official documentation about libIGCM by the Plateforme groupe at IPSL Climate Modelling Centre ​http://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc
• Introduction to ORCHIDEE configurations using libIGCM
• Manipulation of parameter files in libIGCM configurations (J. Ghattas)
• 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)
• How to tell libIGCM to copy a new input file for ORCHIDEE (D. Goll, J. Ghattas)
• 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)
• Classical error message: cp cannot stat (J. Ghattas)
• How to reduce the disc space usage (D. Goll)
• Install LMDZ at obelix for run with libIGCM? (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)
  • Setup for single grid simulations (avoid server mode)? (D Goll)
• 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)

netcdf

• How to check differences between netcdf files ? (S.Luyssaert and A.S. Lansø)
• 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 and profiling

• Control text output using variable PRINTLEV in run.def (J. Ghattas)
• How to compile in debug mode (to be created)? (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 get started debugging (M. McGrath)
• one plus one challenge (A.S. Lanso)

• How to use the debbugger IDB/Totalview/DDT
• Finding memory bugs with Valgrind (M. McGrath)
• Run a profiling job in serial on obelix (Valgrind) (M. McGrath)
• Run a profiling job in serial on obelix (gprof) (A.S. Lansø and S. Luyssaert)
• 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)
• How to run ORCHIDEE with Vampir ? (D.Solyga)

Parallelism

• Parallelization in ORCHIDEE and how to use OpenMP (A. Cozic, D.Solyga)

Code

• Coding guidelines in ORCHIDEE (To be done)
• How to add a new flag in ORCHIDEE ? (S.Luyssaert)

Scientific issues

• Spin up for carbon related variables (P. Peylin)

Coupling to LMDZ

• Install and compile ORCHIDEE in coupled mode (link towards same page as in first section)
• 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
• How to compare used_run_def files from different model versions (S. Lussaert, L. Fairhead)

To be removed

• Running at Ada/IDRIS? (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)
• How to run ORCHIDEE in parallel on Obelix ?? (D.Solyga)
• Install and run on ESPRI mesocenter: Ciclad and ClimServ? (J. Ghattas)
• How to easily change history output level for multiple variables in intersurf.f90?? (C.Yue)