User Guide

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News

• 11/02/2015 New method for manipulating run.def file in offline libIGCM configurations (J. Ghattas)
• 21/01/2015 Change to netcdf4p at obelix, LSCE cluster (J. Ghattas)

How to page

This page let you to answer some problems you can meet with ORCHIDEE. You will find some tutorials explaining how to install and run the model, how to debug,etc.

Questions asked

Installation/First run/Branch

• How to install ORCHIDEE with modipsl and libIGCM for offline use (J. Ghattas)
• How to install ORCHIDEE in coupled mode : LMDZOR_v5 and LMDZOR_v5.2 ? (J. Ghattas)
• How to install ORCHIDEE on my linux laptop or computer? (D.Solyga)
• How to run a simple test case with ORCHIDEE offline ? (J. Ghattas)
• How to submit a parallel job in a batch system (example at curie, ada and obelix) without libIGCM? (J. Ghattas)
• How to download and compile ORCHIDEE-DOFOCO (M. McGrath)
• Install LMDZ at obelix (J. Ghattas)
• Compile methods : Standard makefiles and FCM (J. Ghattas)

svn

• Basic use of SVN​ (J. Ghattas)
• How to create a new branch or a personal version (J. Ghattas)
• How to keep a branch or personal version updated with the trunk (J. Ghattas)
• How to check the differences between a branch and a personal version? (M. McGrath)
• Some more information about svn

libIGCM

• How to make a spinup analytic in OOL_SEC_STO (J. Ghattas)
• How to loop over years with libIGCM (M. McGrath)
• How to prescribe the vegetation in a pixel? (S.Luyssaert)
• 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)
• Change atmospheric CO2 scalar value (J. Ghattas)
• How to compare against Fluxnet data (M. McGrath)
• Is there a way to send all of my Orchidee output files to a different location? (J. Ryder)
• Is there a way to save all the output files when debugging with libIGCM? (M. McGrath)
• Is there a way to specify different queues automatically with libIGCM? (M. McGrath)
• How to change the climate forcing with libIGCM? (M. McGrath)
• Possible ways to make headaches go away (M. McGrath)
• Launch a libIGCM job on Airain (S.Luyssaert)
• Where to recover or how to manually rebuild a missing history file (S.Luyssaert)
• Error message cp: cannot stat (J. Ghattas)

History files

• How to understand the operators used to write the variables in the history files ? (F.Maignan)
• How to add a variable to history files ? (S.Luyssaert)
• How to easily change history output level for multiple variables in intersurf.f90? (C.Yue)

netcdf

• How to check differences between netcdf files ? (S.Luyssaert)
• What's the quickest way to examine netCDF files? (J.Ryder)
• Use cdo commands to process netCDF files?
• Install and compile with another netCDF library ? (S.Luyssaert)

Debugging

• How to solve a segmentation error ?(S.Luyssaert)
• How to find where the model is hanging ?(M. McGrath & S.Luyssaert)
• Extract a single pixel from a large restart file (M. McGrath)
• Debug a coupled LMDZOR run? (M. McGrath)
• Run a profiling job in serial on obelix (M. McGrath)
• How to use the debbugger IDB

Parallelism

• Parallelization in ORCHIDEE and how to use OpenMP (A. Cozic, D.Solyga)
• How to run ORCHIDEE in parallel on Obelix ? (D.Solyga)
• How to run ORCHIDEE with Vampir ? (D.Solyga)

Environments

• Running at Ada/IDRIS (J. Ghattas)

Code

• How to add a new flag in ORCHIDEE ? (S.Luyssaert)

Coupling to LMDz

• How to install ORCHIDEE in coupled mode : LMDZOR_v5 and LMDZOR_v5.2 ? (J. Ghattas)
• How to combine the above and install the DOFOCO branch, coupled, with the 11 layer hydrology/new physics/STOMATE ? (J. Ryder)
• 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 set-up a preindustrial run with LMDZOR (DOFOCO) ? (S.Luyssaert and M. McGrath)
• How to set-up a present day run with LMDZOR (DOFOCO) ? (S.Luyssaert and M. McGrath)
• What is important to know about using a new LMDZOR grid ? (M. McGrath)
• 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 simulations? (M. McGrath)

Divers

• How to write a shell script ? (S.Luyssaert)
• How to use ferret to change the resolution of a file? (J.Otto & S.Luyssaert)
• How to use cdo to change the resolution of a file? (J.Barichivich & S.Luyssaert)
• How to rename many files at once? (S.Luyssaert)
• How to write a shell script for searching specific files and combining them together to a single file? (Y.Chen)
• Some information about regular expressions

Tutorial list

• How to create tickets ? (D.Solyga). If you have an wiki account, you can create tickets. To know more about it, look the following tutorial ​here
• First steps with ORCHIDEE on LSCE machines (ORCHIDEE training day) (D.Solyga, N.Vuichard) : ​The tutorial in PDF

Coding Guidelines

• Coding guidelines document in the Documentation page / Coding guidelines section

This document is the follow-up of the former discussion page:

• Fortran standards and style guide (J.Ryder) This is a working document, so feel free to comment or edit

More about ORCHIDEE configurations using libIGCM

see here [Documentation/UserGuide/Config] (old page Scripts)