Changes between Version 21 and Version 22 of Documentation/UserGuide/CheckList


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Timestamp:
2020-05-31T20:14:22+02:00 (4 years ago)
Author:
aducharne
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  • Documentation/UserGuide/CheckList

    v21 v22  
    1 = Check list to prepare your simulation: configuration, input files, keywords, etc. = 
     1= Step by step guidelines to prepare your simulation: configuration, input files, keywords, etc. = 
    22[[PageOutline]] 
    33 
    4 First Author: A. Ducharne in 2019/01/22 
    5 With contributions from J. Ghattas, P. Peylin, F. Maignan, M. MacGrath, B. Guenet 
     4First Author: A. Ducharne in 2019/01/22\\ 
     5With contributions from J. Ghattas, P. Peylin, F. Maignan, M. MacGrath, B. Guenet\\ 
     6Reviwed by P. Arboleda in May 2020 
    67 
    78The goal of this howto is to sum up what you should not forget to run a simulation (for students and even for more experienced users).  
    … …  
    1314== 1) On which machine do I want to run? 
    1415 
    15 It can be at TGCC(irene), LSCE(obelix), IDRIS(ada), IPSL mesocentre(ciclad/climserv), anywhere libIGCM is maintained by the IPSL team. You first need to obtain a login. At TGCC and IDRIS, you need to be part of an existing project or set up a new one to obtain a login. You need to contribute to the annual request for computing resources and the annual report of consumed cpu time for the previous year.  
     16 
     17''' 1a) On a machine maintained by the IPSL team''' 
     18 
     19It can be at TGCC (irene), LSCE (obelix), IDRIS (jean-zay), IPSL mesocentre (ciclad/climserv), anywhere libIGCM is maintained by the IPSL team. You first need to obtain a login. At TGCC and IDRIS, you need to be part of an existing project or set up a new one to obtain a login. You need to contribute to the annual request for computing resources and the annual report of consumed cpu time for the previous year.  
    1620 
    1721Before starting to install the model, you must set up the proper environment (paths, modules).  
    1822 
    1923Read more here, which covers all the standard platforms supported by the IPSL:  https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocBenv 
     24 
     25''' 1b) Else you're pretty much on you own''' 
    2026 
    2127You can also run on your local **linux** machine, but in this case, you will have to manage your running environment yourself: libraries, compiler, etc. Find some information [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocBenv#HowtousetheIPSLmodelsandtoolswithalocalPC here], in addition to some of the links below (Installation and compilation). Please note that if you choose this option you may receive less support from the orchidee group. Except for specific reason this option is not recommended. 
    … …  
    3541''' 2b) Code options not decided by a revision''' 
    3642 
    37 The code of ORCHIDEE includes many "code" options, i.e. options to execute some parts of the code or not. These options are controlled by some configuration files, mostly config.card and PARAM/run.def (see 4a). While these depend in general on which branch of ORCHIDEE you are using, the following are in the trunk: 
     43The code of ORCHIDEE includes many "code" options, i.e. options to execute some parts of the code or not. These options are controlled by some configuration files, mostly config.card and PARAM/run.def (see 4a). Since these options are not hard-coded, you can change them without recompiling. But they condition your result, and you need to know them to explain your model version. 
     44 
     45These options depend in general on the branch of ORCHIDEE you are using. As a (non exhaustive) example, the following ones are in the CMIP6 trunk (now tagged 2.0): 
    3846- old or new driver (for offline simulations, to deal with meteorological input files) ***how is it set? 
    3947- use the module stomate, which has vegetation that grows and responds to climatic conditions (STOMATE_OK_STOMATE, defined in config.card or PARAM/run.def) 
    … …  
    6068In the configuration directory, "OOL" in a directory title refers to "ORCHIDEE offline", "SEC" refers to the SEChiba module in charge of the water and energy cycles, and "STO" refers to the STOmate model controlling vegetation and nutrient cycles.  OOL_SEC_STO, therefore, means the configuration is designed to use meteorological forcing files to drive the water, energy, and nutrient cycles.  OOL_SEC, on the other hand, does not include dynamic vegetation or nutrient cycles. 
    6169 
    62 '''4a) The simplest option if you use libIGCM is to use a predefined configuration''' (in modipsl/config/ORCHIDEE_OL/). 
    63 Each of the subdirectories constains the required elements to run a particular offline simulation: 
    64 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/config.card config.card] => to choose the name, length, restart of your simulation (link to more details) 
    65 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/PARAM/run.def PARAM/run.def] => to choose the options of your simulation, via the "keywords". These keywords can be flag (y or n to activate them or not) or they can be parameters values that you can change without recompiling the model. The number of these keywords is huge, and it has a large effect on the outcome of your simulation. The default values depend on the revision (see 2). 
    66 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/COMP/orchidee_ol.card COMP/orchidee_ol.card] => defines the meteorological forcing files and xml files (the latter of which are only used with XIOS...ORCHIDEE can also be run [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/DeactivateXIOS without XIOS], though it is not recommended)   
    67 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/COMP/sechiba.card COMP/sechiba.card] => defines the other input files, and some important user option for sechiba: 
     70'''4a) The simplest option if you use libIGCM is to use a predefined configuration''' 
     71 
     72They were defined for the [wiki:ReferenceSimulations reference simulations], each corresponding to a different [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#Contentsofthesubmissiondirectory submission directory] in modipsl/config/ORCHIDEE_OL/: 
     73- ENSEMBLE to run an ensemble of 1D simulations at FLUXNET sites ([wiki:Documentation/UserGuide/FLUXNETValidation more details]) 
     74- SPINUP_ANALYTIC_FG1, OOL_SEC_STO_FG1trans, OOL_SEC_STO_FG2, which are designed to be used one after the other to run a simulation with CRU-NCEP atmospheric forcing and the long spinup required for the carbon cycle ([wiki:Documentation/UserGuide/SpinUpCarbon#StandardprotocolforCarbon-relatedvariables more details])  
     75- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3 OOL_SEC_STO_FG3], for a run without spin-up (default restart state) under the WFDEI_GPCC atmospheric forcing 
     76 
     77Each of the submission directory contains the required elements to run a particular offline simulation:  
     78 
     79- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/config.card config.card]=> to choose the name, length, restart of your simulation ([https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#config.card more details]) 
     80- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/PARAM/run.def PARAM/run.def] => to choose the options of your simulation, via the "keywords". These keywords can be flag (y or n to activate them or not) or they can be parameters values that you can change without recompiling the model. The number of these keywords is huge, and it has a large effect on the outcome of your simulation. The default values depend on the revision (see 2). More details on [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#PARAMdirectory run.def] and see 4c for a list of keywords. 
     81- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/COMP/orchidee_ol.card COMP/orchidee_ol.card] => defines the meteorological forcing files and xml files (the latter of which are only used with XIOS; ORCHIDEE can also be run [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/DeactivateXIOS without XIOS], though it is not recommended)   
     82- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/COMP/sechiba.card COMP/sechiba.card] => defines the other input files, and some important user option for sechiba: 
    6883    * do we change the vegetation map every year of not (VEGET_UPDATE)? 
    6984    * frequency of the output and name of the corresponding output files 
    70     * the last part of the file is about post-processing *** is there an howto to explain this?  
    71 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/COMP/stomate.card COMP/stomate.card] => defines some important user option for stomate: 
     85    * the last part of the file is about [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Running#Simulation-Postprocessing post-processing]  
     86- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/COMP/stomate.card COMP/stomate.card] => defines some important user option for stomate: 
    7287    * do we use the analytical spinup? (SPINUP_ANALYTIC, see wiki:Documentation/UserGuide/SpinUpCarbon) 
    7388    * frequency of the output and name of the corresponding output files 
    74     * the last part of the file is about post-processing *** is there an howto to explain this?  
     89    * the last part of the file is about [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Running#Simulation-Postprocessing post-processing] 
    7590 
    7691'''4b) To create your own configuration,''' the simplest way is to modify an existing configuration: copy the corresponding directory with a new name in your modipsl/config/ORCHIDEE_OL/ and change what you want.