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= 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.
* ''' [wiki:Documentation/UserGuide/UseXIOS2asDefault 13/06/2016 Change to use XIOS2 by default in libIGCM configurations]''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/ReadingPFTmap 29/05/2015 Changed behaviour in reading the vegetation file PFTmap.nc] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/ManipulationDefFile 11/02/2015 New method for manipulating run.def file in offline libIGCM configurations] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/ObleixNetcdf4p 21/01/2015 Change to netcdf4p at obelix, LSCE cluster] '''(J. Ghattas)
== Technical Notes ==
* 2103/12 [http://forge.ipsl.jussieu.fr/orchidee/raw-attachment/wiki/Documentation/REPORT%20ON%20THE%20ROLE%20OF%20LITTER%20IN%20THE%20WATER%20FLUXES.pdf B. Guenet REPORT ON THE ROLE OF LITTER IN THE WATER FLUXES.pdf]
* 2016/08 [http://forge.ipsl.jussieu.fr/orchidee/attachment/wiki/Documentation/UserGuide/eqs_hydrol.pdf A. Ducharne Technical note on hydrol.f90] (in progress, third version)
* 2014/10 F. Wang: Notes on the coupling with LMDz [wiki:Documentation/CouplingLMDZ]
* [wiki:Documentation/OrchideeParameters See the list of parameters] used by the model trunk version. See also the same list in [http://forge.ipsl.jussieu.fr/orchidee/browser/trunk/ORCHIDEE/orchidee.default orchidee.default] in the latest version of the trunk
* Physical range of the parameters: [https://docs.google.com/spreadsheets/d/1DYVvvqxVoXFAqA_M_hvkd-Ooru6ZQ32Lz2oa8oKKA5E/edit#gid=1984497631 Parameters Range Table]
* [wiki:Documentation#CodingGuidelines Guide lines for the code structure in ORCHIDEE]
* [Documentation/UserGuide/Config Introduction to ORCHIDEE configurations using libIGCM]
= How to section =
=== !Installation/First run/Branch ===
* ''' [wiki:Documentation/UserGuide/DifferentLogin Login needed to access ORCHIDEE and work on the wiki] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/InstallingORCHIDEEBasic How to install ORCHIDEE with modipsl and libIGCM for offline use] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/LMDZOR How to install ORCHIDEE in coupled mode] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/InstallingORCHIDEE How to install ORCHIDEE on my linux laptop or computer?] '''(D.Solyga)
* ''' [wiki:Documentation/UserGuide/TestCase1 How to run a simple test case with ORCHIDEE offline ?] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/TestCaseBatch How to submit a parallel job in a batch system (example at curie, ada and obelix) without libIGCM?] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/ORCHIDEEDOFOCOInstall How to download and compile ORCHIDEE-DOFOCO and ORCHIDEE-CN-CAN] ''' (M. !McGrath)
* ''' [wiki:DevelopmentActivities/ORCHIDEE-CNP How to download, compile and run ORCHIDEE-CN-P & more information about the model] ''' (D. Goll)
* ''' [wiki:Documentation/UserGuide/LMDZatObelix Install LMDZ at obelix] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/RunAtCicladAndClimserv Install and run at ciclad and ClimServ] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/CompileMethods Compile methods : Standard makefiles and FCM] ''' (J. Ghattas)
=== svn ===
* ''' [attachment:svn10min_Ghattas_20140612.pdf Basic use of SVN] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/svnBranchePerso How to create a new branch or a personal version] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/CommitOnTrunk Guidelines and help to commit on the trunk (or a branch)] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/svnKeepUpdated How to keep a branch or personal version updated with the trunk or with another version] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/svnmerge How to check the differences between a branch and a personal version?] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/mergebranch How to merge a branch to trunk (A. Jornet) ] '''
* ''' [wiki:Documentation/UserGuide/svnmore Some more information about svn] '''
=== libIGCM ===
* ''' [wiki:Documentation/UserGuide/SpinupInJobBasic How to make a spinup analytic in OOL_SEC_STO] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/LoopIGCM How to loop over years with libIGCM] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/ImposeVegetation How to prescribe the vegetation in a pixel?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/LandCoverMap How to make use of a land cover map with libIGCM ?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/LandCoverChanges How to make use of a land cover change maps with libIGCM ?]''' (A. Rajaud & S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/ChangeCO2 Change atmospheric CO2 scalar value]''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/FLUXNETValidation How to compare against Fluxnet data] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/OutputFiles Is there a way to send all of my Orchidee output files to a different location?] ''' (J. Ryder)
* ''' [wiki:Documentation/UserGuide/DebuglibIGCM Is there a way to save all the output files when debugging with libIGCM?] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/ChangeQueue Is there a way to specify different queues automatically with libIGCM?] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/ChangeCForcing How to change the climate forcing with libIGCM?] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/IGCMheadaches Possible ways to make headaches go away] ''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/RunAirain Launch a libIGCM job on Airain] ''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/ReBuild Where to recover or how to manually rebuild a missing history file] ''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/ErrorMessageCopy Error message cp: cannot stat]''' (J. Ghattas)
* ''' [wiki:/Documentation/UserGuide/AddNewInputFiles How to tell libIGCM to copy a new input file for ORCHIDEE] ''' (D. Goll, J. Ghattas)
=== History/output files ===
* Using XIOS
* ''' [https://forge.ipsl.jussieu.fr/orchidee/attachment/wiki/GroupActivities/Meetings/Developer/xios_in_orchidee_31mars2015_Ghattas_update4nov2015.pdf Presentation about XIOS in ORCHDIDEE, developers meeting 31 mars 2015] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/XIOSinConfig Using XIOS in ORCHIDEE_trunk configuration with libIGCM] ''' (J Ghattas)
* ''' [wiki:Documentation/UserGuide/XIOSaddVar Add a new output variable using XIOS] ''' (J Ghattas)
* Using IOIPSL
* ''' [wiki:Documentation/UserGuide/DeactivateXIOS How to install ORCHIDEE without XIOS?] ''' (J. Ghattas)
* ''' [wiki:Documentation/UserGuide/HistoryOperators How to understand the operators used to write the variables in the history files ?] ''' (F.Maignan)
* ''' [wiki:Documentation/UserGuide/VariableHistory How to add a variable to history files ?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/HistoryLevel How to easily change history output level for multiple variables in intersurf.f90?] ''' (C.Yue)
=== netcdf ===
* ''' [wiki:Documentation/UserGuide/DifferencesNetcdf How to check differences between netcdf files ?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/StudyNetCDF What's the quickest way to examine netCDF files?] ''' (J.Ryder)
* ''' [wiki:Documentation/UserGuide/CDO Use cdo commands to process netCDF files?] '''
* ''' [wiki:Documentation/UserGuide/InstallLibrary Install and compile with another netCDF library ?] ''' (S.Luyssaert)
=== Debugging ===
* ''' [wiki:Documentation/UserGuide/Printlev PRINTLEV : Control text output]''' (J. Ghattas)
* ''' [wiki:Documentation/SegmentationFault How to solve a segmentation error ?]'''(S.Luyssaert)
* ''' [wiki:Documentation/HangCrash How to find where the model is hanging ?]'''(M. !McGrath & S.Luyssaert)
* ''' [wiki:Documentation/ExtractPixel Extract a single pixel from a large restart file]''' (M. !McGrath)
* ''' [wiki:Documentation/DebugCoupled Debug a coupled LMDZOR run?]''' (M. !McGrath)
* ''' [wiki:Documentation/UserGuide/IDB How to use the debbugger IDB/Totalview]'''
* ''' [wiki:Documentation/UserGuide/flags Compilation flags]'''
=== Profiling ===
* ''' [wiki:Documentation/ProfileValgrind Run a profiling job in serial on obelix]''' (M. !McGrath)
* ''' [wiki:Documentation/ProfileVtune Run a profiling job in serial on Curie with intel vtune]''' (A. Jornet)
* ''' [wiki:Documentation/ProfileDDTmap Run a profiling job in parallel on Curie with DDT Allinea Map]''' (A. Jornet)
=== Parallelism ===
* ''' [wiki:Documentation/UserGuide/ParallelCoding Parallelization in ORCHIDEE and how to use OpenMP] ''' (A. Cozic, D.Solyga)
* ''' [wiki:Documentation/UserGuide/ParallelObelix How to run ORCHIDEE in parallel on Obelix ?] ''' (D.Solyga)
* ''' [wiki:Documentation/UserGuide/OrchideeVampir How to run ORCHIDEE with Vampir ?] ''' (D.Solyga)
=== Environments ===
* ''' [wiki:Documentation/UserGuide/IDRIS Running at Ada/IDRIS] ''' (J. Ghattas)
=== Code ===
* ''' [wiki:Documentation/UserGuide/NewFlag How to add a new flag in ORCHIDEE ?]''' (S.Luyssaert)
=== Coupling to LMDZ ===
* ''' [wiki:Documentation/UserGuide/LMDZOR How to install ORCHIDEE in coupled mode] '''(J. Ghattas)
* ''' [wiki:Documentation/UserGuide/CoupledDofoco How to combine the above and install the DOFOCO branch, coupled, with the 11 layer hydrology/new physics/STOMATE ?] ''' (J. Ryder)
* ''' [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/PreIndSim How to set-up a preindustrial run with LMDZOR (DOFOCO) ?]''' (S.Luyssaert and M. !McGrath)
* ''' [wiki:Documentation/UserGuide/PresentDay How to set-up a present day run with LMDZOR (DOFOCO) ?]''' (S.Luyssaert and M. !McGrath)
* ''' [wiki:Documentation/UserGuide/FutureTime How to set-up a future run with LMDZOR (DOFOCO) ?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/Perturb How to perturb the initial conditions in LMDZOR ?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/NewGrid What is important to know about using a new LMDZOR grid ?] ''' (M. !McGrath)
* ''' [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 simulations?]''' (M. !McGrath)
=== Divers ===
* ''' [wiki:Documentation/UserGuide/ShellScript How to write a shell script ?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/Ferret How to use ferret to change the resolution of a file?]''' (J.Otto & S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/CDO How to use cdo to change the resolution of a file?]''' (J.Barichivich & S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/ReName How to rename many files at once?]''' (S.Luyssaert)
* ''' [wiki:Documentation/UserGuide/ShellScriptFind How to write a shell script for searching specific files and combining them together to a single file?]''' (Y.Chen)
* ''' [wiki:Documentation/UserGuide/RegularExpression Some information about regular expressions]'''
* ''' [wiki:Documentation/UserGuide/ErrorMessages Recurrent error messages]'''
* ''' [http://dods.ipsl.jussieu.fr/orchidee/WIKI/TUTORIALS/Tickets.pdf How to create tickets]''' (D.Solyga).
* ''' [https://forge.ipsl.jussieu.fr/orchidee/browser/trunk/TOOLS/CliMAF_Atlas_ORCHIDEE/README Under development: How to run CliMAF atlas ORCHIDEE]'''