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The vsoil-player software allows to run simulations from an existing model to produce results.

General use

Several models are available for use in the VSoil modelling platform. They are all supplied with functional configuration files representing different contexts (initial situations). These files allow the platform to be manipulated in relatively simple conditions, with ready-to-use models.

It is of course possible to use models not supplied with VSoil. They can come from other VSoil users or from the team in charge of developing the platform. Model export and import functions are available in all VSoil software to exchange models. They are described in the import/export user manual. There will be a tutorial on this subject soon: Export and import in VSoil.

Deporting calculations to a remote machine

By default, a model is run on the machine where the platform is installed. However, execution can be deported to a remote calculation server or cluster. It is also possible to choose an execution environment different from that of the user's machine. In this case, the model runs in the encapsulated environment of a container which has no side-effects with the host system. The model execution environment is defined and checked by the VSoil support team. Currently, VSoil uses Singularity software.

Refer to the user manual Using a VSoil model, chapter 1 "Configuration de l’exécution locale ou à distance" to learn more about activating remote run.

Once you have chosen a model, the machine on which to run it and its execution environment, you need to define its use. In VSoil, there are two possibility:
- simple execution, with a single initial situation or with a limited number of different initial situations (batch);
- statistical calculation, for sensitivity analysis or parameter estimation.

Simple execution

In the simple execution mode, an initial situation must be defined, both global (at model level) and specific to each module of the model. The global parameters include the description of the soil profile and the simulation dates. The modules have their own parameters, as well as initial values for some of their output variables that require them. Refer to the user manual Using a VSoil model to learn more about running a model with VSoil graphical interfaces.

When different initial situations exist, the 'batch' mode can be used to run the same model several times. In this case, VSoil makes it possible to parallelise the execution of these different situations, since each one is independent of the others. Refer to the user manual Méthodes statistiques et exécution de plusieurs simulations, chapter 4 "Exécution multiple d’un modèle" to learn more about running a model in batch mode.

Statistical calculation

The VSoil modelling platform is interfaced with the R statistics software environment. In particular, this allows the use of sensitivity analysis and parameter estimation methods, offered by dedicated R packages.

When a sensitivity analysis method is chosen by user, it needs to be configured. This involves choosing the parameters of the model defining the experimental design.

When a parameter estimation method is chosen, the parameters to be estimated must be selected. Next, user have to select the model output variables that will be used to calculate the deviation from the observed data. The latter must therefore also be supplied.

To interface with the R statistics software, the VSoil platform generates a script. This contains instructions that can be interpreted and executed using the Rscript command. The content of the script depends on the choices previously made by the user in the VSoil graphical interface. It is therefore the R software that drives the VSoil model: initialisation, execution, retrieval of results, etc. Results can be viewed in the VSoil graphical interface. Certain statistical methods allow parallel calculation. The platform do it as much as possible.

Refer to the user manual Méthodes statistiques et exécution de plusieurs simulations, in particular with chapter 5 and 6, to learn more on statistical calculation with VSoil graphical interfaces.

Connection to databases

The VSoil modelling platform is interfaced with databases. These are accessible in the graphical interfaces for configuring the initial situations of certain modules, predefined with this functionality. The Climatik database is currently available. It contains climatic data for the whole of France. Access is authorised to INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) staff for scientific research purposes. Access authorisation is also available on request from Agroclim service unit of the AgroEcoSystem department at the INRAE PACA Centre in Avignon.