= Check list to prepare your simulation: configuration, input files, keywords, etc. = [[PageOutline]] First Author: A. Ducharne in 2019/01/22 With contributions from J. Ghattas, P. Peylin, F. Maignan, M. MacGrath, B. Guenet The 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). The examples of this page are focused on offline simulations with [http://forge.ipsl.jussieu.fr/libigcm/wiki/WikiStart libIGCM] ("infrastructure développée à l'IPSL pour accéder, lancer et enchaîner simulation et post-traitements pour une simulation type"). Links to particular files are given for [browser:tags/ORCHIDEE_2_0/ tag2.0] (created in March 2018 for CMIPv1). This checklist is also valid in other cases (LMDZOR, no libIGCM), although the details won't hold. == 1) On which machine do I want to run? 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. Before starting to install the model, you must set up the proper environment (paths, modules). Read more here, which covers all the standard platforms supported by the IPSL: https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocBenv You 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. == 2) Which code do I want to run? ''' 2a) Choosing a revision''' The best way is to use svn to download a referenced version of the code (trunk, tag, branch, perso). By using SVN, you can easily change between model versions (more information on SVN is found [https://forge.ipsl.jussieu.fr/orchidee/attachment/wiki/Documentation/UserGuide/svn10min_Ghattas_20140612.pdf in this PDF]), as well as incorporate bug fixes and updates from others. In this case, each version is referenced by a revision number, which corresponds to different source code, but also to potentially different "keywords" and their default values (more in 4). Therefore, only tests between identical revisions can be expected to be identical. Some revisions are "tagged" (e.g., ORCHIDEE 2.0). A tagged revision is considered stable and does not change. Other revisions are likely undergoing continual development and modification, with occasional commits breaking them. Branches are "forks" from the main code (referred to as the "trunk"), in which developers are adding new features. It takes significant effort and knowledge of the code base to merge some of these features, which means not every feature is present in every revision of ORCHIDEE. Selecting a revision and branch should therefore take into account the research questions you are trying to address. These pages contain further information on the [https://forge.ipsl.jussieu.fr/orchidee/wiki/SourceCode trunk] as well as the [https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities branches]. The ORCHIDEE model is flexible, with many features controlled by input files. The model also requires additional information (e.g., spatial and temporal extents) and input data (often called, "forcing files," including meteorological forcing data) in order to run. The collection of input files that direct model behavior are referred to as the configuration. More information on configurations is found below. ADVICE: If you want to run two versions of ORCHIDEE (e.g. a new development and the reference version it originates from), you are strongly advised to create two different directories (e.g. NEW/modipsl/... and REF/modipsl/...). It's also the case of you want to run two simulations with same code but for hard-coded parameters (but in this case, it is often better to take advantage of the "externalization" feature and define the parameters as keywords that can be defined in your PARAM/run.def, see 4a, 4d). ''' 2b) Code options not decided by a revision''' 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: - old or new driver (for offline simulations, to deal with meteorological input files) ***how is it set? - 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) - activate the dynamic global vegetation model (DGVM), where the fraction of a grid cell covered by vegetation changes with climatic conditions (STOMATE_OK_DGVM in PARAM/run.def) - allow vegetation to burn in fires (FIRE_DISABLE in PARAM/run.def) - dynamic nitrogen cycle, where nitrogen scarcity can limit vegetation growth (STOMATE_IMPOSE_CN in PARAM/run.def) - activate soil_freezing, etc... *** complete the list, give the keywords NOTE: not all of these components can be activated at the same time and still give reliable results. It's important to test the configuration you select. == 3) Installation and compilation Read here about to download ORCHIDEE for offline (i.e., driven by separate meteorological forcing files) use: [wiki:Documentation/UserGuide/InstallingORCHIDEEBasic] The same method is used for offline and coupled configurations, where "coupled" typically refers to coupling ORCHIDEE to an atmospheric model that generates meteorological data at every time step. Find the full documentation about installation and using of IPSL-cmc coupled models [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc here]. or go directly to a brief description of the [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocHconfigBlmdzorv6 LMDZOR_v6 configuration] (LMDZ coupled to ORCHIDEE). Always recompile your code if you make changes in the fortran code. Further information on compiling ORCHIDEE can be found [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/CompileMethods here]. Information for downloading the [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/ORCHIDEEDOFOCOInstall CAN] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP CNP] branches of ORCHIDEE also exists and can likely be modified for any branch, but note that permission to access branches is generally restricted. == 4) Configuration of your simulation ORCHIDEE output is controlled by separate modules, referred to as XIOS ([[https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP here] PDF] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/XIOSinConfig webpage]) and IOIPSL. These modules greatly improve reading and writing data for large simulations, although the benefits may not be seen for single pixel, single CPU runs. In 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. '''4a) The simplest option if you use libIGCM is to use a predefined configuration''' (in modipsl/config/ORCHIDEE_OL/). Each of the subdirectories constains the required elements to run a particular offline simulation: - [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) - [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). - [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) - [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: * do we change the vegetation map every year of not (VEGET_UPDATE)? * frequency of the output and name of the corresponding output files * the last part of the file is about post-processing *** is there an howto to explain this? - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/COMP/stomate.card COMP/stomate.card] => defines some important user option for stomate: * do we use the analytical spinup? (SPINUP_ANALYTIC, see wiki:Documentation/UserGuide/SpinUpCarbon) * frequency of the output and name of the corresponding output files * the last part of the file is about post-processing *** is there an howto to explain this? '''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. ADVICE: Create a new directory in your modipsl/config/ORCHIDEE_OL/ for each different run you want to keep in the end. It's the case for instance if you want to run one ORCHIDEE with different parameter sets using the keywords to define the parameters. '''4c) More on keywords''' Give definition (externalized parameters), and explain the ones to be careful with after the merge to CN. *** Explain more, links '''4d) Spinup and initialization''' A simulation requires initial conditions, which are defined by section #D-- Restarts - in [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/config.card config.card]. There are two options: Restart = n ("from scratch" with arbitrary initial values) vs. Restart = y (we use state variables from a pre-existing simulation as initial conditions; only works if the two simulations have the same horizontal and vertical resolution, and the same processes thus state variables). In both cases, we usually need some warmup or spinup, unless we are just pursuing a simulation. Read more on the ways to set up your spinup on [wiki:Documentation/UserGuide/SpinUpCarbon Spinup : why, how and how long? The answer depends on the ORCHIDEE component]. It is also possible to do an [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic analytical spinup] that is faster. == 5) Run your simulation libIGCM is the environment that makes it easier to run simulations: gathering the required input files, copying them to the run directory, running the simulation, and then storing the output, in particular for multiple year simulations where you would otherwise have to manually copy restart files and name them appropriately. The libIGCM section on the [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide HowTo] has additional information about manipulating libIGCM in special cases. It is possible to run [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCase1 simple offline test cases] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/TestCaseBatch larger parallel jobs] without libIGCM. This can be useful when you are debugging your code. Job, queues, etc. [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocFsimu][[BR]] LSCE specific: batch system & jobs submission [https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php] If your simulation crashes : - guidelines to understand the problem [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/CheckDebug] - if debugging is required, look at the the Debugging section on the [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide HowTo], starting with the [wiki:Documentation/UserGuide/flags introductory page on debug flags]. == 6) How to get some help Step 1: Documentation and howto pages, training sessions, ... Step 2: Ask your supervisor or close collaborators Step 3: orchidee-help == 7) Analyse your results If your simulation(s) have run, you probably want to look at it(them)... - Model outputs are in netcdf format. You can find here (wiki:Documentation/UserGuide/StudyNetCDF) some information on how to look at netcdf data - Basic checks (global mean values compared to reference simulations and observations; water conservation and twbr, etc.) - Some tools to evaluate to model are available such as CLIMAF ([https://github.com/jservonnat/C-ESM-EP/wiki/The-C-ESM-EP-in-a-nutshell How to run C-ESM-EP atlas using CliMAF]). You can also have access to intermonitoring tools developed at IPSL (http://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Running#Monitoringandintermonitoring) == 8) How to archive your developments? If your developments proved interesting, the ORCHIDEE community would be happy to benefit from them: - Presentation of your results (share your report or paper, invite the group to your seminar/defense, present a talk an ORCHIDEE weekly of DEV meeting) - Backup your development via svn on a branch or perso directory - For inclusion in the trunk, this has to be proposed to the ORCHIDEE-Project group