Journal cover Journal topic
Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
https://doi.org/10.5194/gmd-2017-167
© Author(s) 2017. This work is distributed under
the Creative Commons Attribution 4.0 License.
Model description paper
19 Jul 2017
Review status
This discussion paper is a preprint. It is a manuscript under review for the journal Geoscientific Model Development (GMD).
Parcels v0.9: prototyping a Lagrangian Ocean Analysis framework for the petascale age
Michael Lange1 and Erik van Sebille2,3 1Grantham Institute & Department of Earth Science and Engineering, Imperial College London, UK
2Institute for Marine and Atmospheric research Utrecht, Utrecht University, Utrecht, Netherlands
3Grantham Institute & Department of Physics, Imperial College London, UK
Abstract. As Ocean General Circulation Models (OGCMs) move into the petascale age, where the output from global high-resolution model runs can be of the order of hundreds of terabytes in size, tools to analyse the output of these models will need to scale up too. Lagrangian Ocean Analysis, where virtual particles are tracked through hydrodynamic fields, is an increasingly popular way to analyse OGCM output, by mapping pathways and connectivity of biotic and abiotic particulates. However, the current software stack of Lagrangian Ocean Analysis codes is not dynamic enough to cope with the increasing complexity, scale and need for customisation of use-cases. Furthermore, most community codes are developed for stand-alone use, making it a nontrivial task to integrate virtual particles at runtime of the OGCM. Here, we introduce the new Parcels code, which was designed from the ground up to be sufficiently scalable to cope with petascale computing. We highlight its API design that combines flexibility and customisation with the ability to optimise for HPC workflows, following the paradigm of domain-specific languages. Parcels is primarily written in Python, utilising the wide range of tools available in the scientific Python ecosystem, while generating low-level C-code and using Just-In-Time compilation for performance-critical computation. We show a worked-out example of its API, and validate the accuracy of the code against seven idealised test cases. This version 0.9 of Parcels is focussed on laying out the API, with future work concentrating on optimisation, efficiency and at-runtime coupling with OGCMs.

Citation: Lange, M. and van Sebille, E.: Parcels v0.9: prototyping a Lagrangian Ocean Analysis framework for the petascale age, Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-167, in review, 2017.
Michael Lange and Erik van Sebille
Michael Lange and Erik van Sebille

Model code and software

Parcels v0.9: prototyping a Lagrangian Ocean Analysis framework for the petascale age
E. van Sebille, M. Lange, J. Scutt Phillips, J. Kronborg, Thomas-95, nathanieltarshish, and D. A. Ham
https://doi.org/10.5281/zenodo.823562
Scripts to create Figures of Parcels v0.9 manuscript
E. van Sebille
https://doi.org/10.5281/zenodo.823994
Michael Lange and Erik van Sebille

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Short summary
Here, we present version 0.9 of Parcels, (Probably A Really Computationally Efficient Lagrangian Simulator). Parcels is an experimental prototype code aimed at exploring novel approaches for Lagrangian tracking of virtual ocean particles in the petascale age. The modularity, flexibility and scalability will allow the code to be used to track water, nutrients, microbes, plankton, plastic and even fish.
Here, we present version 0.9 of Parcels, (Probably A Really Computationally Efficient Lagrangian...
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