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}}} [[PageOutline]] = 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/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) * ''' [wiki:Documentation/UserGuide/CheckList Check list to prepare your simulation: configuration, input files, keywords, etc.]''' (collective) === svn === * ''' [attachment:svn10min_Ghattas_20140612.pdf Basic use of SVN] ''' (J. Ghattas) * ''' [wiki:Documentation/UserGuide/svnGetCode Various ways to get the code of an ORCHIDEE version with svn]''' (A. Ducharne) * ''' [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/Config Introduction to ORCHIDEE configurations using libIGCM]''' * ''' [wiki:Documentation/UserGuide/ManipulationDefFile Manipulation of parameter files in libIGCM configurations] ''' (J. Ghattas) * ''' [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) * ''' [wiki:/Documentation/UserGuide/MinimizeDiscUsage How to reduce the disc space usage] ''' (D. Goll) * ''' [wiki:/Documentation/UserGuide/CompareRunDefs How to compare used_run_def files from different model versions] ''' (S. Lussaert, L. Fairhead) === 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) * ''' [wiki:Documentation/UserGuide/SiteScaleXIOS Setup for single grid simulations (avoid server mode)] ''' (D Goll) * 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 and A.S. Lansø) * ''' [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/UserGuide/SegmentationFault How to solve a segmentation error ?]'''(S.Luyssaert) * ''' [wiki:Documentation/UserGuide/HangCrash How to find where the model is hanging ?]'''(M. !McGrath & S.Luyssaert) * ''' [wiki:Documentation/UserGuide/ExtractPixel Extract a single pixel from a large restart file]''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/DebugCoupled Debug a coupled LMDZOR run?]''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/IDB How to use the debbugger IDB/Totalview/DDT]''' * ''' [wiki:Documentation/UserGuide/flags How to get started debugging]''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/valgrind Finding memory bugs with Valgrind]''' (M. !McGrath) === Profiling === * ''' [wiki:Documentation/UserGuide/ProfileValgrind Run a profiling job in serial on obelix (Valgrind)]''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/ProfileGprof Run a profiling job in serial on obelix (gprof)]''' (A.S. Lansø and S. Luyssaert) * ''' [wiki:Documentation/UserGuide/ProfileVtune Run a profiling job in serial on Curie with intel vtune]''' (A. Jornet) * ''' [wiki:Documentation/UserGuide/ProfileDDTmap Run a profiling job in parallel on Curie with DDT Allinea Map]''' (A. Jornet) * ''' [wiki:Documentation/UserGuide/OrchideeVampir How to run ORCHIDEE with Vampir ?] ''' (D.Solyga) === 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) === Code === * ''' [wiki:Documentation/UserGuide/CodingGuidelines Coding guidelines in ORCHIDEE]''' (To be done) * ''' [wiki:Documentation/UserGuide/NewFlag How to add a new flag in ORCHIDEE ?]''' (S.Luyssaert) === Scientific issues === * ''' [wiki:Documentation/UserGuide/SpinUpCarbon Spin up for carbon related variables]''' (P. Peylin) === 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) * ''' [wiki:Documentation/UserGuide/NewForcingVerif 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 === * ''' [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]''' Obsolete!! Now see here : https://github.com/jservonnat/C-ESM-EP/wiki/The-C-ESM-EP-in-a-nutshell === To be removed === * ''' [wiki:Documentation/UserGuide/IDRIS Running at Ada/IDRIS] ''' (J. Ghattas)