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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

• Prepare
  • Login needed to access ORCHIDEE and work on the wiki (Last revision: 2020/01/03)
  • Set up environment before first time using a new machine: obelix, ciclad, climserv, irene, jean-zay (Last revision: 2020/03/19)
• Download and compile
  • Install and compile ORCHIDEE for offline use (Last revision: 2020/02/28)
  • How to install ORCHIDEE in coupled mode with LMDZ (Last revision: 2020/02/28)
  • How to install ORCHIDEE on a Linux PC (Ubuntu or Fedora distribution) (Last revision: 2020/02/28)
  • More about compile methods (Last revision: 2020/02/28)
• Run
  • Run a simple test case with ORCHIDEE offline (Last revision: 2020/03/19)
  • Run a parallel job in a batch system (example at curie, ada and obelix) without libIGCM (Last revision: 2020/03/03)
  • Run using libIGCM: see section libIGCM below
• Check list
  • Check list to prepare your simulation: configuration, input files, keywords, etc. (collective)

svn

• Basic use of SVN​ (Last revision: 2020/02/28)
• Various ways to get the code of an ORCHIDEE version with svn (Last revision: 2020/02/28)
• How to create a new branch or a personal version (Last revision: 2020/02/28)
• Guidelines and help to commit on the trunk (or a branch) (Last revision: 2020/02/28)
• How to keep a branch or personal version updated with the trunk or with another version (Last revision: 2020/02/28)
• How to compare two versions of ORCHIDEE (Last revision: 2020/02/28)
• How to add a new svn user (SVN administrators only) (Last revision: 2020/02/28)

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 (Last revision: 2020/03/19)
• Set up environment before first time using a new machine: obelix, ciclad, climserv, irene, jean-zay (Same link as in first section)
• Manipulation of parameter files in libIGCM configurations (Last revision: 2020/02/28)
• Spinup for Carbon-related variables: purpose and usages (Last revision: 2020/02/28)
  • How to loop over years with libIGCM (Last revision: 2020/02/28)
• How to prescribe the land cover? (Last revision: 2020/02/28)
• How to tell libIGCM to copy a new input file for ORCHIDEE (Last revision: 2020/02/28)
• Change atmospheric CO2 scalar value (Last revision: 2020/02/28)
• How to change the climate forcing with libIGCM? (Last revision: 2020/02/28)
• How to compare against Fluxnet data (Last revision: 2020/02/28)
• Is there a way to send all of my ORCHIDEE output files to a different location? (Last revision: 2020/02/28)
• Is there a way to specify different queues automatically with libIGCM? (Last revision: 2020/02/28)
• Where to recover or how to manually rebuild a missing history file (S.Luyssaert)
• Classical error message: cp cannot stat (Last revision: 2020/02/28)
• Classical error message: restopenin (Last revision: 2020/03/19)
• How to reduce the disk space usage and speed up your simulations (Last revision: 2020/02/28)

History/output files

• Using XIOS
  • ​Overview of XIOS in ORCHIDEE, Training of January 17, 2020 (Last revision: 2020/01/17)
  • Using XIOS in libIGCM configurations (Last revision: 2020/03/02)
  • Add a new output variable using XIOS (Last revision: 2020/03/02)
• Using IOIPSL
  • How to understand the operators used to write the variables in the history files using IOIPSL (Last revision: 2020/02/28)
  • How to add a variable to history files? (Last revision: 2020/02/28)
  • How to install ORCHIDEE without XIOS (Last revision: 2020/02/28)

netcdf

• How to check differences between netcdf files? (Las revision: 2020/02/28)
• How to manipulate/compare/examine netcdf files using cdo, nco or ncview? (Last revision: 2020/02/28)
• Is there something wrong with my netCDF library? (Last revision: 2020/02/28)

Debugging and profiling

• Using the compiler
  • How to get started debugging and compile with debug options (Last revision: 2020/02/28)
  • How to find a segmentation error or a floating invalid (Last revision: 2020/02/28)
  • How to find where the model is hanging?(Last revision: 2020/02/28)
  • Debug a coupled LMDZOR run (Last revision: 2020/02/28)
• Using options in ORCHIDEE
  • Control text output using variable PRINTLEV in run.def (Last revision: 2020/02/28)
  • Set the level of internal error checking (Last revision: 2020/03/19)
  • One plus One or the challenge of restartability (Last revision: 2020/02/28)
  • Extract a single pixel from a large restart file (Last revision: 2020/02/28)
  • Debug a coupled LMDZOR run (Last revision: 2020/02/28)
• Using additional software tools
  • Debugging with IDB (Last revision: 2019/05/02)
  • Debugging with Totalview (Last revision: 2019/05/02)
  • Debugging with DDT Allinea Map (Last revision: 2019/05/02)
  • Profiling with Valgrind (Last revision: 2019/09/19)
  • Profiling with Gprof (Last revision: 2019/09/30)
  • Profiling with Intel Vtune (Last revision: 2018/02/26)
  • Profiling with DDT Allinea Map (Last revision: 2014/04/18)
  • Profiling with Vampir? (Last revision: 2013/06/18)

Code

• Coding guidelines in ORCHIDEE (2020/03/19)
• How to add a new flag in ORCHIDEE? (2020/03/19)
• Parallelization in ORCHIDEE and how to use OpenMP (A. Cozic, D.Solyga)

Coupling to LMDZ

• How to install ORCHIDEE in coupled mode with LMDZ (link towards same page as in first section, Last revision: 2020/02/28)
• 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 perturb the initial conditions in LMDZOR? (S.Luyssaert)
• What is important to know about using a new LMDZOR grid? (Last revision: 2020/02/28)
• 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 offline simulations? (2020/03/19)
• How to format and how to verify atmospheric forcing files for ORCHIDEE offline driver (Last revision: 2020/02/28)

Divers

• How to write a shell script? (Last revision: 2020/02/28)
• How to use ferret to change the resolution of a file? (Last revision: 2020/03/19)
• How to use cdo to change the resolution of a file? (Last revision: 2020/03/19)
• How to rename many files at once? (Last revision: 2020/03/19)
• How to write a shell script to search specific files and combine them together to a single file? (Last revision: 2020/03/19)
• Classical error message: restopenin
• Classical error message: XIOS
• ​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 (Last revision: 2020/02/28)

Archived

• Load and compile another netCDF library for libIGCM (Last revision: 2016/11/20)
• How to set-up a preindustrial run with LMDZOR (DOFOCO)? (Last revision: 2016/11/26)
• How to set-up a present day run with LMDZOR (DOFOCO)? (Last revision: 2016/11/27)
• How to set-up a future run with LMDZOR (DOFOCO)? (Last revision: 2016/11/27)

To be removed

• Install LMDZ at obelix for run with libIGCM? (J. Ghattas)
• Running at Ada/IDRIS? (J. Ghattas)
• How to download and compile ORCHIDEE-DOFOCO and ORCHIDEE-CN-CAN? (M. McGrath)
• 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)
• How to combine the above and install the DOFOCO branch, coupled, with the 11 layer hydrology/new physics/STOMATE?? (J. Ryder)
• ​https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic
• Is there a way to save all the output files when debugging with libIGCM?? (M. McGrath)
• How to merge a branch to trunk (A. Jornet) ?
• 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)
• Setup for single grid simulations (avoid server mode)? (D Goll)