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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, compilation and basic run === * Prepare * ''' [wiki:Documentation/UserGuide/DifferentLogin Login needed to access ORCHIDEE and work on the wiki] '''(Last revision: 2020/01/03) * ''' [wiki:Documentation/UserGuide/BeforeUsingNewPlatform Set up environment before first time using a new machine: obelix, ciclad, climserv, irene, jean-zay] ''' (Last revision: 2020/02/28) * Download and compile * ''' [wiki:Documentation/UserGuide/InstallingORCHIDEEBasic Install and compile ORCHIDEE for offline use] '''(Last revision: 2020/02/28) * ''' [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: 2020/02/28) * Run * ''' [wiki:Documentation/UserGuide/TestCase1 Run a simple test case with ORCHIDEE offline] '''(Last revision: 2020/01/19) * ''' [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#libIGCM Run using libIGCM: see section libIGCM below]''' * Check list * ''' [wiki:Documentation/UserGuide/CheckList Check list to prepare your simulation: configuration, input files, keywords, etc.]''' (collective) === svn === * ''' [attachment:svn10minandORCH_20200228.pdf Basic use of SVN] ''' (Last revision: 2020/02/28) * ''' [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]''' * ''' [wiki:Documentation/UserGuide/ManipulationDefFile Manipulation of parameter files in libIGCM configurations] ''' (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/FLUXNETValidation How to compare against Fluxnet data] ''' (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/ReBuild Where to recover or how to manually rebuild a missing history file] ''' (S.Luyssaert) * ''' [wiki:Documentation/UserGuide/ErrorMessageCopy Classical error message: cp cannot stat]''' (Last revision: 2020/02/28) * ''' [wiki:/Documentation/UserGuide/MinimizeDiscUsage How to reduce the disk space usage and speed up your simulations] ''' (Last revision: 2020/02/28) * ''' [wiki:Documentation/UserGuide/LMDZatObelix Install LMDZ at obelix for run with libIGCM] ''' (J. Ghattas) * ''' [wiki:Documentation/UserGuide/SpinUpCarbon Spinup for Carbon-related variables: purpose and usages]''' (Last revision: 2020/02/28) * ''' [wiki:Documentation/UserGuide/LoopIGCM How to loop over years with libIGCM] ''' (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) === netcdf === * ''' [wiki:Documentation/UserGuide/DifferencesNetcdf How to check differences between netcdf files?]''' (2020/02/28) * ''' [wiki:Documentation/UserGuide/DifferencesNetcdf How to manipulate/compare/examine netcdf files using cdo, nco or ncview?]''' (Last revision: 2020/02/28) * ''' [wiki:Documentation/UserGuide/WrongNetcdfLib Is there something wrong with my netCDF library?] ''' (Last revision: 2020/02/28) === Debugging and profiling === * ''' [wiki:Documentation/UserGuide/flags How to get started debugging and compile with debug options]''' (Last revision: 2020/02/28) * ''' [wiki:Documentation/UserGuide/Printlev Control text output using variable PRINTLEV in run.def]''' (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/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) * ''' [wiki:Documentation/UserGuide/restartability One plus One or the challenge of restartability]''' (Last revision: 2020/02/28) * ''' [wiki:Documentation/UserGuide/IDB How to use the debbugger IDB/Totalview/DDT]''' * ''' [wiki:Documentation/UserGuide/valgrind Finding memory bugs with Valgrind]''' (M. !McGrath) * ''' [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) === 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) * ''' [wiki:Documentation/UserGuide/ParallelCoding Parallelization in ORCHIDEE and how to use OpenMP] ''' (A. Cozic, D.Solyga) === Coupling to LMDZ === * ''' [wiki:Documentation/UserGuide/LMDZOR How to install ORCHIDEE in coupled mode with LMDZ] '''(link towards same page as in first section, Last revision: 2020/02/28) * ''' [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 perturb the initial conditions in LMDZOR?]''' (S.Luyssaert) * ''' [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?]''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/NewForcingVerif How to format and how to verify atmospheric forcing files for ORCHIDEE offline driver]''' (Last revision: 2020/02/28) === Divers === * ''' [wiki:Documentation/UserGuide/ShellScript How to write a shell script?]''' (Last revision: 2020/02/28) * ''' [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 * ''' [wiki:/Documentation/UserGuide/CompareRunDefs How to compare used_run_def files from different model versions] ''' (Last revision: 2020/02/28) === Archived === * ''' [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) === To be removed === * ''' [wiki:Documentation/UserGuide/IDRIS Running at Ada/IDRIS] ''' (J. Ghattas) * ''' [wiki:Documentation/UserGuide/ORCHIDEEDOFOCOInstall How to download and compile ORCHIDEE-DOFOCO and ORCHIDEE-CN-CAN] ''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/ParallelObelix How to run ORCHIDEE in parallel on Obelix?] ''' (D.Solyga) * ''' [wiki:Documentation/UserGuide/RunAtCicladAndClimserv Install and run on ESPRI mesocenter: Ciclad and ClimServ] ''' (J. Ghattas) * ''' [wiki:Documentation/UserGuide/HistoryLevel How to easily change history output level for multiple variables in intersurf.f90?] ''' (C.Yue) * ''' [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) * ''' [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic] * ''' [wiki:Documentation/UserGuide/DebuglibIGCM Is there a way to save all the output files when debugging with libIGCM?] ''' (M. !McGrath) * ''' [wiki:Documentation/UserGuide/mergebranch How to merge a branch to trunk (A. Jornet) ] ''' * ''' [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/SiteScaleXIOS Setup for single grid simulations (avoid server mode)] ''' (D Goll)