Reuse of process-based models: Automatic transformation into many programming languages and simulation platforms

Midingoyi Cyrille Ahmed, Pradal Christophe, Athanasiadis Ioannis, Donatelli Marcello, Enders Andreas, Fumagalli Davide, Garcia Frédérick, Holzworth Dean, Hoogenboom Gerrit, Porter Cheryl, Raynal Hélène, Thorburn Peter J., Martre Pierre. 2020. Reuse of process-based models: Automatic transformation into many programming languages and simulation platforms. In Silico Plants, 3 (1):diaa007 : -20.

Résumé : The diversity of plant and crop process-based modeling platforms in terms of implementation language, software design, and architectural constraints limits the reusability of the model components outside the platform in which they were originally developed, making model reuse a persistent issue. To facilitate the intercomparison and improvement of process-based models and the exchange of model components, several groups in the field joined to create the Agricultural Model Exchange Initiative (AMEI). AMEI proposes a centralized framework for exchanging and reusing model components. It provides a modular and declarative approach to describe the specification of unit models and their composition. A model algorithm is associated with each model specification, which implements its mathematical behavior. This paper focuses on the expression of the model algorithm independently of the platform specificities, and how the model algorithm can be seamlessly integrated into different platforms. We define CyML, a Cython-derived language with minimum specifications to implement model component algorithms. We also propose CyMLT, an extensible source-to-source transformation system that transforms CyML source code into different target languages such as Fortran, C#, C++, Java and Python, and into different programming paradigms. CyMLT is also able to generate model components to target modeling platforms such as DSSAT, BioMA, Record, SIMPLACE and OpenAlea. We demonstrate our reuse approach with a simple unit model and the capacity to extend CyMLT with other languages and platforms. The approach we present here will help to improve the reproducibility, exchange and reuse of process-based models.

Mots-clés Agrovoc : modélisation des cultures, modèle de simulation

Mots-clés complémentaires : Langage de programmation

Mots-clés libres : Source transformation, Model reuse, Transpiler, Software reuse, Crop model

Classification Agris : U10 - Informatique, mathématiques et statistiques
F01 - Culture des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement européennes : European Commission

Programme de financement européen : H2020

Projets sur financement : (EU) Data Driven Precision Agriculture Services and Skill Acquisition

Auteurs et affiliations

• Midingoyi Cyrille Ahmed, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0009-0000-4411-7989
• Pradal Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2555-761X - auteur correspondant
• Athanasiadis Ioannis, Wageningen University and Research Centre (NLD)
• Donatelli Marcello, CREA (ITA)
• Enders Andreas, Universität Bonn (DEU)
• Fumagalli Davide, IES (ITA)
• Garcia Frédérick, INRAE (FRA)
• Holzworth Dean, CSIRO (AUS)
• Hoogenboom Gerrit, University of Florida (USA)
• Porter Cheryl, University of Florida (USA)
• Raynal Hélène, INRAE (FRA)
• Thorburn Peter J., CSIRO (AUS)
• Martre Pierre, INRAE (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/596723/)

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