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@article{grooms2021diffusion,
title = {Diffusion-{Based} {Smoothers} for {Spatial} {Filtering} of {Gridded} {Geophysical} {Data}},
volume = {13},
copyright = {© 2021 The Authors. Journal of Advances in Modeling Earth Systems published by Wiley Periodicals LLC on behalf of American Geophysical Union.},
issn = {1942-2466},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002552},
doi = {10.1029/2021MS002552},
abstract = {We describe a new way to apply a spatial filter to gridded data from models or observations, focusing on low-pass filters. The new method is analogous to smoothing via diffusion, and its implementation requires only a discrete Laplacian operator appropriate to the data. The new method can approximate arbitrary filter shapes, including Gaussian filters, and can be extended to spatially varying and anisotropic filters. The new diffusion-based smoother's properties are illustrated with examples from ocean model data and ocean observational products. An open-source Python package implementing this algorithm, called gcm-filters, is currently under development.},
language = {en},
number = {9},
journal = {Journal of Advances in Modeling Earth Systems},
author = {Grooms, I. and Loose, N. and Abernathey, R. and Steinberg, J. M. and Bachman, S. D. and Marques, G. and Guillaumin, A. P. and Yankovsky, E.},
year = {2021},
keywords = {coarse graining, data analysis, spatial filtering},
pages = {e2021MS002552},
}
@article{hoyer2017xarray,
title={xarray: ND labeled arrays and datasets in Python},
author={Hoyer, Stephan and Hamman, Joe},
journal={Journal of Open Research Software},
volume={5},
number={1},
year={2017},
publisher={Ubiquity Press},
doi={10.5334/jors.148}
}
@article{rocklin_dask_2015,
title = {Dask: {Parallel} {Computation} with {Blocked} algorithms and {Task} {Scheduling}},
shorttitle = {Dask},
url = {http://conference.scipy.org/proceedings/scipy2015/matthew_rocklin.html},
doi = {10.25080/majora-7b98e3ed-013},
urldate = {2021-11-05},
journal = {Proceedings of the 14th Python in Science Conference},
author = {Rocklin, Matthew},
year = {2015},
note = {Conference Name: Proceedings of the 14th Python in Science Conference},
pages = {126--132},
file = {Full Text PDF:/Users/noraloose/Zotero/storage/A3H5QUZ6/Rocklin - 2015 - Dask Parallel Computation with Blocked algorithms.pdf:application/pdf;Snapshot:/Users/noraloose/Zotero/storage/DP4JWDBB/matthew_rocklin.html:text/html},
}
@misc{dask,
title = {Dask: Library for dynamic task scheduling},
author = {{Dask Development Team}},
year = {2016},
url = {https://dask.org},
}
@misc{mom5,
title = {MOM 5: The Modular Ocean Model},
author = {{MOM 5 Development Team}},
year = {2012},
url = {https://github.com/mom-ocean/MOM5},
}
@misc{mom6,
title = {MOM 6: The Modular Ocean Model},
author = {{MOM 6 Development Team}},
url = {https://github.com/NOAA-GFDL/MOM6},
}
@manual{pop2,
title = {The Parallel Ocean Program (POP) reference manual},
year = {2010},
author = {Smith, R. and Jones, P. and Briegleb, B. and Bryan, F. and Danabasoglu, G. and Dennis, J. and Dukowicz, J. and Eden, C. and Fox-Kemper, B. and Gent, P. and Hecht, M. and Jayne, S. and Jochum, M. and Large, W. and Lindsay, K., Maltrud, M. and Norton, N. and Peacock, S. and Vertenstein, M. and Yeager, S.},
url = {http://www.cesm.ucar.edu/models/cesm1.0/pop2/doc/sci/POPRefManual.pdf},
}
@manual{pop2-cesm,
title = {POP2-CESM},
author = {{POP2-CESM Development Team}},
url = {https://github.com/ESCOMP/POP2-CESM},
}
@InProceedings{ matthew_rocklin-proc-scipy-2015,
author = { Matthew Rocklin },
title = { Dask: Parallel Computation with Blocked algorithms and Task Scheduling },
booktitle = { Proceedings of the 14th Python in Science Conference },
pages = { 130 - 136 },
year = { 2015 },
editor = { Kathryn Huff and James Bergstra }
}
@ARTICLE{2020SciPy-NMeth,
author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and
Haberland, Matt and Reddy, Tyler and Cournapeau, David and
Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and
Bright, Jonathan and {van der Walt}, St{\'e}fan J. and
Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and
Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and
Kern, Robert and Larson, Eric and Carey, C J and
Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and
{VanderPlas}, Jake and Laxalde, Denis and Perktold, Josef and
Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and
Harris, Charles R. and Archibald, Anne M. and
Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and
{van Mulbregt}, Paul and {SciPy 1.0 Contributors}},
title = {{{SciPy} 1.0: Fundamental Algorithms for Scientific
Computing in Python}},
journal = {Nature Methods},
year = {2020},
volume = {17},
pages = {261--272},
adsurl = {https://rdcu.be/b08Wh},
doi = {10.1038/s41592-019-0686-2},
}
@Article{ harris2020array,
title = {Array programming with {NumPy}},
author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
van der Walt and Ralf Gommers and Pauli Virtanen and David
Cournapeau and Eric Wieser and Julian Taylor and Sebastian
Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
Travis E. Oliphant},
year = {2020},
month = sep,
journal = {Nature},
volume = {585},
number = {7825},
pages = {357--362},
doi = {10.1038/s41586-020-2649-2},
publisher = {Springer Science and Business Media {LLC}},
url = {https://doi.org/10.1038/s41586-020-2649-2}
}
@inproceedings{cupy2017learningsys,
author = "Okuta, Ryosuke and Unno, Yuya and Nishino, Daisuke and Hido, Shohei and Loomis, Crissman",
title = "CuPy: A NumPy-Compatible Library for NVIDIA GPU Calculations",
booktitle = "Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems (NIPS)",
year = "2017",
url = "http://learningsys.org/nips17/assets/papers/paper_16.pdf"
}
@Article{Hunter2007,
title = {Matplotlib: A 2D graphics environment},
author = {Hunter, J. D.},
journal = {Computing in Science \& Engineering},
volume = {9},
number = {3},
pages = {90--95},
year = {2007},
doi = {10.1109/MCSE.2007.55}
}
@article{adcroft2019MOM6,
author = {Adcroft, Alistair and Anderson, Whit and Balaji, V. and Blanton, Chris and Bushuk, Mitchell and Dufour, Carolina O. and Dunne, John P. and Griffies, Stephen M. and Hallberg, Robert and Harrison, Matthew J. and Held, Isaac M. and Jansen, Malte F. and John, Jasmin G. and Krasting, John P. and Langenhorst, Amy R. and Legg, Sonya and Liang, Zhi and McHugh, Colleen and Radhakrishnan, Aparna and Reichl, Brandon G. and Rosati, Tony and Samuels, Bonita L. and Shao, Andrew and Stouffer, Ronald and Winton, Michael and Wittenberg, Andrew T. and Xiang, Baoqiang and Zadeh, Niki and Zhang, Rong},
title = {The GFDL Global Ocean and Sea Ice Model OM4.0: Model Description and Simulation Features},
journal = {Journal of Advances in Modeling Earth Systems},
volume = {11},
number = {10},
pages = {3167-3211},
keywords = {ocean circulation model, CORE, hybrid coordinates},
doi = {10.1029/2019MS001726},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019MS001726},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019MS001726},
abstract = {Abstract We document the configuration and emergent simulation features from the Geophysical Fluid Dynamics Laboratory (GFDL) OM4.0 ocean/sea ice model. OM4 serves as the ocean/sea ice component for the GFDL climate and Earth system models. It is also used for climate science research and is contributing to the Coupled Model Intercomparison Project version 6 Ocean Model Intercomparison Project. The ocean component of OM4 uses version 6 of the Modular Ocean Model and the sea ice component uses version 2 of the Sea Ice Simulator, which have identical horizontal grid layouts (Arakawa C-grid). We follow the Coordinated Ocean-sea ice Reference Experiments protocol to assess simulation quality across a broad suite of climate-relevant features. We present results from two versions differing by horizontal grid spacing and physical parameterizations: OM4p5 has nominal 0.5° spacing and includes mesoscale eddy parameterizations and OM4p25 has nominal 0.25° spacing with no mesoscale eddy parameterization. Modular Ocean Model version 6 makes use of a vertical Lagrangian-remap algorithm that enables general vertical coordinates. We show that use of a hybrid depth-isopycnal coordinate reduces the middepth ocean warming drift commonly found in pure z* vertical coordinate ocean models. To test the need for the mesoscale eddy parameterization used in OM4p5, we examine the results from a simulation that removes the eddy parameterization. The water mass structure and model drift are physically degraded relative to OM4p5, thus supporting the key role for a mesoscale closure at this resolution.},
year = {2019}
}
@manual{Cartopy,
author = {{Met Office}},
title = {Cartopy: a cartographic python library with a matplotlib interface},
year = {2010 - 2015},
address = {Exeter, Devon },
url = {http://scitools.org.uk/cartopy}
}
@article{adcroft_mitgcm_2018,
title = {MITgcm {User} {Manual}},
doi = {1721.1/117188},
journal = {Zenodo},
author = {Adcroft, A. and J.M. Campin and S. Dutkiewicz and C. Evangelinos and D. Ferreira and G. Forget and B. Fox-Kemper and P. Heimbach and C. Hill and E. Hill and H. Hill and O. Jahn and M. Losch and J. Marshall and G. Maze and D. Menemenlis and A. Molod},
year = {2018},
}
@software{mitgcm,
author = {Jean-Michel Campin and
Patrick Heimbach and
Martin Losch and
Gael Forget and
edhill3 and
Alistair Adcroft and
amolod and
Dimitris Menemenlis and
dfer22 and
Chris Hill and
Oliver Jahn and
Jeff Scott and
stephdut and
Matt Mazloff and
Baylor Fox-Kemper and
antnguyen13 and
Ed Doddridge and
Ian Fenty and
Michael Bates and
AndrewEichmann-NOAA and
Timothy Smith and
Torge Martin and
Jonathan Lauderdale and
Ryan Abernathey and
samarkhatiwala and
hongandyan and
Bruno Deremble and
dngoldberg and
Pascal Bourgault and
raphael dussin},
title = {MITgcm/MITgcm: checkpoint67z},
month = jun,
year = 2021,
publisher = {Zenodo},
version = {checkpoint67z},
doi = {10.5281/zenodo.4968496},
url = {https://doi.org/10.5281/zenodo.4968496}
}