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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 [wiki:GroupActivities/Training the Orchidee Training courses]
=== Installation, compilation and basic run ===
* Prepare
* ''' [wiki:Documentation/UserGuide/DifferentLogin Login needed to access ORCHIDEE and work on the wiki] '''(Last revision: 2023/01/24)
* ''' [wiki:Documentation/UserGuide/BeforeUsingNewPlatform Set up environment before first time using a new machine: obelix, ciclad, climserv, irene, jean-zay] ''' (Last revision: 2020/03/19)
* Download and compile
* ''' [wiki:Documentation/UserGuide/InstallingORCHIDEEBasic Install and compile ORCHIDEE for offline use] '''(Last revision: 2022/01/28)
* ''' [wiki:Documentation/UserGuide/LMDZOR How to install ORCHIDEE in coupled mode with LMDZ] '''(Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/InstallingORCHIDEE How to install ORCHIDEE on a Linux PC (Ubuntu or Fedora distribution)] '''(Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/CompileMethods More about compile methods] ''' (Last revision: 2022/01/28)
* Run
* ''' [wiki:Documentation/UserGuide/TestCase1 Run a simple test case with ORCHIDEE offline using the trunk] '''(Last revision: 2022/01/17)
* ''' [wiki:Documentation/UserGuide/TestCaseORCH3 Run a simple test case with ORCHIDEE offline using ORCHIDEE_3] '''(Last revision: 2020/01/09)
* ''' [wiki:Documentation/UserGuide/TestCaseORCH2_0 Run a simple test case with ORCHIDEE offline using ORCHIDEE_2_0] '''(Last revision: 2022/01/17)
* ''' [wiki:Documentation/UserGuide/TestCaseBatch Run a parallel job in a batch system (example at curie, ada and obelix) without libIGCM] '''(Last revision: 2020/03/03)
* ''' [wiki:Documentation/UserGuide/TestCaselibIGCM Run a simple test using libIGCM]''' see also section ''Different ways to configure simulations with libIGCM'' below (Last revision: 2023/11/30)
* Check list
* ''' [wiki:Documentation/UserGuide/CheckList Step by step guidelines to prepare your simulation: configuration, input files, keywords, etc.]''' (collective, last updated: 2020/06/01, still in progress)
=== svn ===
* ''' [attachment:svn10minandORCH_jan2022.pdf Basic use of SVN] ''' (Last revision: 2022/01)
* ''' [wiki:Documentation/UserGuide/svnGetCode Various ways to get the code of an ORCHIDEE version with svn]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/svnBranchePerso How to create a new branch or a personal version] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/CommitOnTrunk Guidelines and help to commit on the trunk (or a branch)] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/svnKeepUpdated How to keep a branch or personal version updated with the trunk or with another version] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/svnmerge How to compare two versions of ORCHIDEE] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/svnmore 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 '''
* ''' [wiki:Documentation/UserGuide/Config Introduction to ORCHIDEE configurations using libIGCM]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/BeforeUsingNewPlatform Set up environment before first time using a new machine: obelix, ciclad, climserv, irene, jean-zay] ''' (Same link as in first section)
* ''' [wiki:Documentation/UserGuide/ManipulationDefFile Manipulation of parameter files in libIGCM configurations] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/SpinUpCarbon Spinup : why, how and how long? The answer depends on the ORCHIDEE component]''' (Last revision: 2020/04/01)
* ''' [wiki:Documentation/UserGuide/LoopIGCM How to loop over years with libIGCM] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ImposeVegetation How to prescribe the land cover?]''' (Last revision: 2020/02/28)
* ''' [wiki:/Documentation/UserGuide/AddNewInputFiles How to tell libIGCM to copy a new input file for ORCHIDEE] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ChangeCO2 Change atmospheric CO2 scalar value]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ChangeCForcing How to change the climate forcing with libIGCM?] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/RoutageHighres How to run with the hig hresolution routing scheme?] ''' (Last revision: 2022/07/28)
* ''' [wiki:Documentation/UserGuide/FLUXNETValidation Configuration ENSEMBLE to run ORCHIDEE at Fluxnet sites] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/OutputFiles Is there a way to send all of my ORCHIDEE output files to a different location?] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ChangeQueue Is there a way to specify different queues automatically with libIGCM?] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ErrorMessageCopy Classical error message: cp cannot stat]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ErrorMessages Classical error message: restopenin]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/MinimizeDiscUsage How to reduce the disk space usage and speed up your simulations] ''' (Last revision: 2020/02/28)
=== History/output files ===
* Using XIOS
* ''' [https://forge.ipsl.jussieu.fr/orchidee/raw-attachment/wiki/GroupActivities/Training/HowToConfigureOutputfiles_JGhattas_2020.pdf Overview of XIOS in ORCHIDEE, Training of January 17, 2020 ] ''' (Last revision: 2020/01/17)
* ''' [wiki:Documentation/UserGuide/XIOSinConfig Using XIOS in libIGCM configurations] ''' (Last revision: 2020/03/02)
* ''' [wiki:Documentation/UserGuide/XIOSaddVar Add a new output variable using XIOS] ''' (Last revision: 2020/03/02)
* Using IOIPSL
* ''' [wiki:Documentation/UserGuide/HistoryOperators How to understand the operators used to write the variables in the history files using IOIPSL] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/VariableHistory How to add a variable to history files?]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/DeactivateXIOS How to install ORCHIDEE without XIOS] ''' (Last revision: 2020/02/28)
* '''[wiki:Documentation/UserGuide/RiverDesc How to find river_desc.nc for some river discharge processing]''' (Last revision: 2020/05/20)
* ''' [https://github.com/jservonnat/C-ESM-EP/wiki/The-C-ESM-EP-in-a-nutshell How to look at simulation output using CliMAF to produce a C-ESM-EP atlas ]
=== netcdf ===
* ''' [wiki:Documentation/UserGuide/DifferencesNetcdf How to check differences between netcdf files?]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/StudyNetCDF How to manipulate/compare/examine netcdf files using cdo, nco or ncview?]''' (Last revision: 2020/05/11)
* ''' [wiki:Documentation/UserGuide/Ferret How to use ferret to change the resolution of a file?]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/WrongNetcdfLib Is there something wrong with my netCDF library?] ''' (Last revision: 2020/02/28)
=== Code ===
* ''' [wiki:Documentation/UserGuide/CodingGuidelines Coding guidelines in ORCHIDEE]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/NewFlag How to add a new flag in ORCHIDEE?]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/ParallelCoding Parallelization in ORCHIDEE and how to use OpenMP] ''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/ErrorMessagesXIOS Classical error message: XIOS]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/DoxygenDocumentation Use doxygen to generate subroutine call graphs and offline html-form documentation]''' (Last revision: 2022/06)
* ''' [wiki:Documentation/UserGuide/Internal/OpenTrusting How to run the Open Trusting]''' (First version: 2023/06/01, you need to login to see this page)
=== Debugging and profiling ===
* Using the compiler
* ''' [wiki:Documentation/UserGuide/flags How to get started debugging and compile with debug options]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/SegmentationFault How to find a segmentation error or a floating invalid ]'''(Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/HangCrash How to find where the model is hanging?]'''(Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/DebugCoupled Debug a coupled LMDZOR run]''' (Last revision: 2020/02/28)
* Using options in ORCHIDEE
* ''' [wiki:Documentation/UserGuide/Printlev Control text output using variable PRINTLEV in run.def]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ErrAct Set the level of internal error checking]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/restartability One plus One or the challenge of restartability]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/ExtractPixel Extract a single pixel from a large restart file]''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/DebugCoupled Debug a coupled LMDZOR run]''' (Last revision: 2020/02/28)
* Using additional software tools
* ''' [wiki:Documentation/UserGuide/IDB Debugging with IDB]''' (Last revision: 2019/05/02)
* ''' [wiki:Documentation/UserGuide/Totalview Debugging with Totalview]''' (Last revision: 2019/05/02)
* ''' [wiki:Documentation/UserGuide/DDTmap Debugging with DDT Allinea Map]''' (Last revision: 2019/05/02)
* ''' [wiki:Documentation/UserGuide/ProfileValgrind Profiling with Valgrind]''' (Last revision: 2019/09/19)
* ''' [wiki:Documentation/UserGuide/ProfileGprof Profiling with Gprof]''' (Last revision: 2019/09/30)
* ''' [wiki:Documentation/UserGuide/ProfileVtune Profiling with Intel Vtune]''' (Last revision: 2018/02/26)
* ''' [wiki:Documentation/UserGuide/ProfileDDTmap Profiling with DDT Allinea Map]''' (Last revision: 2014/04/18)
* ''' [wiki:Documentation/UserGuide/OrchideeVampir Profiling with Vampir?] ''' (Last revision: 2013/06/18)
=== Coupling to LMDZ ===
* ''' [wiki:Documentation/UserGuide/LMDZOR How to install ORCHIDEE in coupled mode with LMDZ] '''(Link towards same page as in first section)
* ''' [wiki:Documentation/UserGuide/SetupZoomEurope How do I set up a zoomed (and nudged) simulation (a.k.a. using a new LMDZOR grid)?] ''' (M. !McGrath and someone else?)
* ''' [wiki:Documentation/UserGuide/Perturb How to estimate the uncertainty of an LMDZOR run?]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/NewGrid What is important to know about using a new LMDZOR grid?] ''' (Last revision: 2020/02/28)
* ''' [wiki:Documentation/UserGuide/VerifyClimate How to verify that the climate produced by your LMDZOR run is not terrible (ATLAS & TOA)?] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/LaunchATLAS How to launch a stand-alone ATLAS run to validate the climate] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/SetDiffLevel How to set different output levels for the LMDZ ouput files]''' (Y.Chen)
=== Forcing files ===
* ''' [wiki:Documentation/UserGuide/FutureForcing How to run future offline simulations?]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/NewForcingVerif How to format and how to verify atmospheric forcing files for ORCHIDEE offline driver]''' (Last revision: 2020/02/28)
=== Useful shellscript examples ===
* ''' [wiki:Documentation/UserGuide/ShellScript How to write a shell script?]''' (Last revision: 2020/05/11)
* ''' [wiki:Documentation/UserGuide/ReName How to rename many files at once?]''' (Last revision: 2020/03/19)
* ''' [wiki:Documentation/UserGuide/ShellScriptFind How to write a shell script to search specific files and combine them together to a single file?]''' (Last revision: 2020/03/19)
* ''' [wiki:/Documentation/UserGuide/CompareRunDefs How to compare used_run_def files from different model versions] ''' (Last revision: 2020/02/28)
=== Q&A from orchidee-help
* '''[wiki:Documentation/UserGuide/UseNewDriver How to use the new driver?]''' (Last revision: 2020/06/01)
* '''[wiki:Documentation/UserGuide/UserDefinedSoilParameters How to impose user-defined soil parameters?]''' (Last revision: 2020/06/01)
* '''[wiki:Documentation/UserGuide/NoDrainage How to prevent drainage losses (w/o violating mass conservation)?]''' (Last revision: 2020/06/01)
* '''[wiki:Documentation/UserGuide/NoKsDecrease How to deactivate the decline of Ks with depth in hydrol.f90?]''' (Last revision: 2020/06/01)
* '''[wiki:Documentation/UserGuide/parallel_obelix Problem to run in parallel with several proc on obelix]''' (Last revision: 2020/06/16)
* '''[wiki:Documentation/UserGuide/RoutageSimple How to set up a run with routage simple]''' (Last revision: 2022/03/17)
* '''[wiki:Documentation/UserGuide/RoutageHighres How to set up a run with routage highres]''' (Under edition: 2022/07/15)
=== Propositions for additional pages
* Good practices to avoid using buggy code (e.g. use debug mode, check mass conservation, check 1+1=2) : proposed by D. Goll to be inserted in each page of the Debug section
=== Archived (old pages, partly outdated, but still useful with caution)===
* ''' [wiki:Documentation/UserGuide/InstallLibrary Load and compile another netCDF library for libIGCM] ''' (Last revision: 2016/11/20)
* ''' [wiki:Documentation/UserGuide/PreIndSim How to set-up a preindustrial run with LMDZOR (DOFOCO)?]''' (Last revision: 2016/11/26)
* ''' [wiki:Documentation/UserGuide/PresentDay How to set-up a present day run with LMDZOR (DOFOCO)?]''' (Last revision: 2016/11/27)
* ''' [wiki:Documentation/UserGuide/FutureTime How to set-up a future run with LMDZOR (DOFOCO)?]''' (Last revision: 2016/11/27)
* ''' [wiki:Documentation/UserGuide/ReBuild Where to recover or how to manually rebuild a missing history file] ''' (Last revision: 2015/03/23)