Articles | Volume 9, issue 11
Geosci. Model Dev., 9, 4209–4225, 2016
https://doi.org/10.5194/gmd-9-4209-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Geosci. Model Dev., 9, 4209–4225, 2016
https://doi.org/10.5194/gmd-9-4209-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Development and technical paper 22 Nov 2016
Development and technical paper | 22 Nov 2016
P-CSI v1.0, an accelerated barotropic solver for the high-resolution ocean model component in the Community Earth System Model v2.0
Xiaomeng Huang et al.
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Qingyang Xiao, Yixuan Zheng, Guannan Geng, Cuihong Chen, Xiaomeng Huang, Huizheng Che, Xiaoye Zhang, Kebin He, and Qiang Zhang
Atmos. Chem. Phys., 21, 9475–9496, https://doi.org/10.5194/acp-21-9475-2021, https://doi.org/10.5194/acp-21-9475-2021, 2021
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We used both statistical methods and a chemical transport model to assess the contribution of meteorology and emissions to PM2.5 during 2000–2018. Both methods revealed that emissions dominated the long-term PM2.5 trend with notable meteorological effects ranged up to 37.9 % of regional annual average PM2.5. The meteorological contribution became more beneficial to PM2.5 control in southern China but more unfavorable in northern China during the studied period.
Zhuang Liu, Yi Zhang, Xiaomeng Huang, Jian Li, Dong Wang, Mingqing Wang, and Xing Huang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2020-158, https://doi.org/10.5194/gmd-2020-158, 2020
Revised manuscript not accepted
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This paper describes several techniques for the parallelization and performance optimization of
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Xiaomeng Huang, Xing Huang, Dong Wang, Qi Wu, Yi Li, Shixun Zhang, Yuwen Chen, Mingqing Wang, Yuan Gao, Qiang Tang, Yue Chen, Zheng Fang, Zhenya Song, and Guangwen Yang
Geosci. Model Dev., 12, 4729–4749, https://doi.org/10.5194/gmd-12-4729-2019, https://doi.org/10.5194/gmd-12-4729-2019, 2019
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We designed a simple computing library (OpenArray) to decouple ocean modelling and parallel computing. OpenArray provides 12 basic operators featuring user-friendly interfaces and an implicit parallelization ability. Based on OpenArray, we implement a practical ocean model with an enhanced readability and an excellent scalable performance. OpenArray may signal the beginning of a new frontier in future ocean modelling through ingesting basic operators and cutting-edge computing techniques.
Allison H. Baker, Yong Hu, Dorit M. Hammerling, Yu-heng Tseng, Haiying Xu, Xiaomeng Huang, Frank O. Bryan, and Guangwen Yang
Geosci. Model Dev., 9, 2391–2406, https://doi.org/10.5194/gmd-9-2391-2016, https://doi.org/10.5194/gmd-9-2391-2016, 2016
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Software quality assurance is critical to detecting errors in large, complex climate simulation codes. We focus on ocean model simulation data in the context of an ensemble-based statistical consistency testing approach developed for atmospheric data. Because ocean and atmosphere models have differing characteristics, we develop a new statistical tool to evaluate ocean model simulation data that provide a simple, subjective, and systematic way to detect errors and instil model confidence.
S. Xu, X. Huang, L.-Y. Oey, F. Xu, H. Fu, Y. Zhang, and G. Yang
Geosci. Model Dev., 8, 2815–2827, https://doi.org/10.5194/gmd-8-2815-2015, https://doi.org/10.5194/gmd-8-2815-2015, 2015
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In this paper, we redesign the mpiPOM with GPUs. Specifically, we first convert the model from its original Fortran form to a new CUDA-C version, POM.gpu-v1.0. Then we optimize the code on each of the GPUs, the communications between the GPUs, and the I/O between the GPUs and the CPUs.
We show that the performance of the new model on a workstation containing 4 GPUs is comparable to that on a powerful cluster with 408 standard CPU cores, and it reduces the energy consumption by a factor of 6.8.
X. M. Huang, W. C. Wang, H. H. Fu, G. W. Yang, B. Wang, and C. Zhang
Geosci. Model Dev., 7, 93–103, https://doi.org/10.5194/gmd-7-93-2014, https://doi.org/10.5194/gmd-7-93-2014, 2014
Qingyang Xiao, Yixuan Zheng, Guannan Geng, Cuihong Chen, Xiaomeng Huang, Huizheng Che, Xiaoye Zhang, Kebin He, and Qiang Zhang
Atmos. Chem. Phys., 21, 9475–9496, https://doi.org/10.5194/acp-21-9475-2021, https://doi.org/10.5194/acp-21-9475-2021, 2021
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We used both statistical methods and a chemical transport model to assess the contribution of meteorology and emissions to PM2.5 during 2000–2018. Both methods revealed that emissions dominated the long-term PM2.5 trend with notable meteorological effects ranged up to 37.9 % of regional annual average PM2.5. The meteorological contribution became more beneficial to PM2.5 control in southern China but more unfavorable in northern China during the studied period.
Genevieve Jay Brett, Daniel B. Whitt, Matthew C. Long, Frank Bryan, Kate Feloy, and Kelvin J. Richards
Biogeosciences, 18, 3123–3145, https://doi.org/10.5194/bg-18-3123-2021, https://doi.org/10.5194/bg-18-3123-2021, 2021
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We quantify one form of uncertainty in modeled 21st-century changes in phytoplankton growth. The supply of nutrients from deep to surface waters decreases in the warmer future ocean, but the effect on phytoplankton growth also depends on changes in available light, how much light and nutrient the plankton need, and how fast they can grow. These phytoplankton properties can be summarized as a biological timescale: when it is short, future growth decreases twice as much as when it is long.
Sheri Mickelson, Alice Bertini, Gary Strand, Kevin Paul, Eric Nienhouse, John Dennis, and Mariana Vertenstein
Geosci. Model Dev., 13, 5567–5581, https://doi.org/10.5194/gmd-13-5567-2020, https://doi.org/10.5194/gmd-13-5567-2020, 2020
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Every generation of MIP exercises introduces new layers of complexity and an exponential growth in the amount of data requested. CMIP6 required us to develop a new tool chain and forced us to change our methodologies. The new methods discussed in this paper provided us with an 18 times faster speedup over our existing methods. This allowed us to meet our deadlines and we were able to publish more than half a million data sets on the Earth System Grid Federation (ESGF) for the CMIP6 project.
Shaoqing Zhang, Haohuan Fu, Lixin Wu, Yuxuan Li, Hong Wang, Yunhui Zeng, Xiaohui Duan, Wubing Wan, Li Wang, Yuan Zhuang, Hongsong Meng, Kai Xu, Ping Xu, Lin Gan, Zhao Liu, Sihai Wu, Yuhu Chen, Haining Yu, Shupeng Shi, Lanning Wang, Shiming Xu, Wei Xue, Weiguo Liu, Qiang Guo, Jie Zhang, Guanghui Zhu, Yang Tu, Jim Edwards, Allison Baker, Jianlin Yong, Man Yuan, Yangyang Yu, Qiuying Zhang, Zedong Liu, Mingkui Li, Dongning Jia, Guangwen Yang, Zhiqiang Wei, Jingshan Pan, Ping Chang, Gokhan Danabasoglu, Stephen Yeager, Nan Rosenbloom, and Ying Guo
Geosci. Model Dev., 13, 4809–4829, https://doi.org/10.5194/gmd-13-4809-2020, https://doi.org/10.5194/gmd-13-4809-2020, 2020
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Science advancement and societal needs require Earth system modelling with higher resolutions that demand tremendous computing power. We successfully scale the 10 km ocean and 25 km atmosphere high-resolution Earth system model to a new leading-edge heterogeneous supercomputer using state-of-the-art optimizing methods, promising the solution of high spatial resolution and time-varying frequency. Corresponding technical breakthroughs are of significance in modelling and HPC design communities.
Zhuang Liu, Yi Zhang, Xiaomeng Huang, Jian Li, Dong Wang, Mingqing Wang, and Xing Huang
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2020-158, https://doi.org/10.5194/gmd-2020-158, 2020
Revised manuscript not accepted
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This paper describes several techniques for the parallelization and performance optimization of
an unstructured-mesh global atmospheric model. The purpose of this research is to facilitate the rapid iterative model development. These techniques are general and can be used for other parallel modeling on unstructured meshes.
Xiaomeng Huang, Xing Huang, Dong Wang, Qi Wu, Yi Li, Shixun Zhang, Yuwen Chen, Mingqing Wang, Yuan Gao, Qiang Tang, Yue Chen, Zheng Fang, Zhenya Song, and Guangwen Yang
Geosci. Model Dev., 12, 4729–4749, https://doi.org/10.5194/gmd-12-4729-2019, https://doi.org/10.5194/gmd-12-4729-2019, 2019
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We designed a simple computing library (OpenArray) to decouple ocean modelling and parallel computing. OpenArray provides 12 basic operators featuring user-friendly interfaces and an implicit parallelization ability. Based on OpenArray, we implement a practical ocean model with an enhanced readability and an excellent scalable performance. OpenArray may signal the beginning of a new frontier in future ocean modelling through ingesting basic operators and cutting-edge computing techniques.
Li Liu, Cheng Zhang, Ruizhe Li, Bin Wang, and Guangwen Yang
Geosci. Model Dev., 11, 3557–3586, https://doi.org/10.5194/gmd-11-3557-2018, https://doi.org/10.5194/gmd-11-3557-2018, 2018
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C-Coupler2 is a new version of C-Coupler with a series of new enhancements. It is ready for use to develop various coupled or nested models. It has passed a number of test cases involving model coupling and nesting, and with various MPI process layouts between component models, and has already been used in several real coupled models. Its source code can be downloaded from https://github.com/C-Coupler-Group/c-coupler-lib.
Daniel J. Milroy, Allison H. Baker, Dorit M. Hammerling, and Elizabeth R. Jessup
Geosci. Model Dev., 11, 697–711, https://doi.org/10.5194/gmd-11-697-2018, https://doi.org/10.5194/gmd-11-697-2018, 2018
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The Community Earth System Model Ensemble Consistency Test (CESM-ECT) suite was developed as an alternative to requiring bitwise identical output for quality assurance. We extend the CESM-ECT suite with an inexpensive and robust test for ensemble consistency that is applied to Community Atmospheric Model output after only nine model time steps. The new ultra-fast test facilitates CESM development, porting, and optimization efforts, and complements the original suite of tools.
Allison H. Baker, Dorit M. Hammerling, Sheri A. Mickelson, Haiying Xu, Martin B. Stolpe, Phillipe Naveau, Ben Sanderson, Imme Ebert-Uphoff, Savini Samarasinghe, Francesco De Simone, Francesco Carbone, Christian N. Gencarelli, John M. Dennis, Jennifer E. Kay, and Peter Lindstrom
Geosci. Model Dev., 9, 4381–4403, https://doi.org/10.5194/gmd-9-4381-2016, https://doi.org/10.5194/gmd-9-4381-2016, 2016
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We apply lossy data compression to output from the Community Earth System Model Large Ensemble Community Project. We challenge climate scientists to examine features of the data relevant to their interests and identify which of the ensemble members have been compressed, and we perform direct comparisons on features critical to climate science. We find that applying lossy data compression to climate model data effectively reduces data volumes with minimal effect on scientific results.
Allison H. Baker, Yong Hu, Dorit M. Hammerling, Yu-heng Tseng, Haiying Xu, Xiaomeng Huang, Frank O. Bryan, and Guangwen Yang
Geosci. Model Dev., 9, 2391–2406, https://doi.org/10.5194/gmd-9-2391-2016, https://doi.org/10.5194/gmd-9-2391-2016, 2016
Short summary
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Software quality assurance is critical to detecting errors in large, complex climate simulation codes. We focus on ocean model simulation data in the context of an ensemble-based statistical consistency testing approach developed for atmospheric data. Because ocean and atmosphere models have differing characteristics, we develop a new statistical tool to evaluate ocean model simulation data that provide a simple, subjective, and systematic way to detect errors and instil model confidence.
S. Xu, X. Huang, L.-Y. Oey, F. Xu, H. Fu, Y. Zhang, and G. Yang
Geosci. Model Dev., 8, 2815–2827, https://doi.org/10.5194/gmd-8-2815-2015, https://doi.org/10.5194/gmd-8-2815-2015, 2015
Short summary
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In this paper, we redesign the mpiPOM with GPUs. Specifically, we first convert the model from its original Fortran form to a new CUDA-C version, POM.gpu-v1.0. Then we optimize the code on each of the GPUs, the communications between the GPUs, and the I/O between the GPUs and the CPUs.
We show that the performance of the new model on a workstation containing 4 GPUs is comparable to that on a powerful cluster with 408 standard CPU cores, and it reduces the energy consumption by a factor of 6.8.
A. H. Baker, D. M. Hammerling, M. N. Levy, H. Xu, J. M. Dennis, B. E. Eaton, J. Edwards, C. Hannay, S. A. Mickelson, R. B. Neale, D. Nychka, J. Shollenberger, J. Tribbia, M. Vertenstein, and D. Williamson
Geosci. Model Dev., 8, 2829–2840, https://doi.org/10.5194/gmd-8-2829-2015, https://doi.org/10.5194/gmd-8-2829-2015, 2015
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Climate simulation codes are especially complex, and their ongoing state of development requires frequent software quality assurance to both
preserve code quality and instil model confidence. To formalize and simplify this previously subjective and expensive process, we
have developed a new tool for evaluating climate consistency.
The tool has proven its utility in detecting errors in software and hardware
environments and providing rapid feedback to model developers.
X. M. Huang, W. C. Wang, H. H. Fu, G. W. Yang, B. Wang, and C. Zhang
Geosci. Model Dev., 7, 93–103, https://doi.org/10.5194/gmd-7-93-2014, https://doi.org/10.5194/gmd-7-93-2014, 2014
K. Misumi, K. Lindsay, J. K. Moore, S. C. Doney, F. O. Bryan, D. Tsumune, and Y. Yoshida
Biogeosciences, 11, 33–55, https://doi.org/10.5194/bg-11-33-2014, https://doi.org/10.5194/bg-11-33-2014, 2014
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Geosci. Model Dev., 14, 4319–4333, https://doi.org/10.5194/gmd-14-4319-2021, https://doi.org/10.5194/gmd-14-4319-2021, 2021
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Model predictions always contain uncertainty. But in some cases, such as weather forecasting or climate modeling, chaotic unpredictability increases the difficulty to say exactly how much uncertainty there is. We combine two recently proposed mathematical methods to show how the uncertainty can be analyzed in models that are simplifications of true weather models. The results can be extended in the future to show how forecasts from large-scale models can be improved.
Alexander Schaaf, Miguel de la Varga, Florian Wellmann, and Clare E. Bond
Geosci. Model Dev., 14, 3899–3913, https://doi.org/10.5194/gmd-14-3899-2021, https://doi.org/10.5194/gmd-14-3899-2021, 2021
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Uncertainty is an inherent property of any model of the subsurface. We show how geological topology information – how different regions of rocks in the subsurface are connected – can be used to train uncertain geological models to reduce uncertainty. More widely, the method demonstrates the use of probabilistic machine learning (Bayesian inference) to train structural geological models on auxiliary geological knowledge that can be encoded in graph structures.
Matthew Ozon, Aku Seppänen, Jari P. Kaipio, and Kari E. J. Lehtinen
Geosci. Model Dev., 14, 3715–3739, https://doi.org/10.5194/gmd-14-3715-2021, https://doi.org/10.5194/gmd-14-3715-2021, 2021
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Experimental research has provided large amounts of high-quality data on aerosol over the last 2 decades. However, inference of the process rates (e.g., the rates at which particles are generated) is still typically done by simple curve-fitting methods and does not assess the credibility of the estimation. The devised method takes advantage of the Bayesian framework to not only retrieve the state of the observed aerosol system but also to estimate the process rates (e.g., growth rate).
Colton J. Conroy and Einat Lev
Geosci. Model Dev., 14, 3553–3575, https://doi.org/10.5194/gmd-14-3553-2021, https://doi.org/10.5194/gmd-14-3553-2021, 2021
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Lava flows present a natural hazard to communities around volcanoes and are usually slow-moving (< 1-5 cm/s). Lava flows during the 2018 eruption of Kilauea volcano, Hawai’i, however, reached speeds as high as 11 m/s. To investigate these dynamics we develop a new lava flow computer model that incorporates a nonlinear expression for the fluid viscosity. Model results indicate that the lava flows at Site 8 of the eruption displayed shear thickening behavior due to the flow's high bubble content.
Antti Hellsten, Klaus Ketelsen, Matthias Sühring, Mikko Auvinen, Björn Maronga, Christoph Knigge, Fotios Barmpas, Georgios Tsegas, Nicolas Moussiopoulos, and Siegfried Raasch
Geosci. Model Dev., 14, 3185–3214, https://doi.org/10.5194/gmd-14-3185-2021, https://doi.org/10.5194/gmd-14-3185-2021, 2021
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Yumeng Chen, Konrad Simon, and Jörn Behrens
Geosci. Model Dev., 14, 2289–2316, https://doi.org/10.5194/gmd-14-2289-2021, https://doi.org/10.5194/gmd-14-2289-2021, 2021
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Mesh adaptivity can reduce overall model error by only refining meshes in specific areas where it us necessary in the runtime. Here we suggest a way to integrate mesh adaptivity into an existing Earth system model, ECHAM6, without having to redesign the implementation from scratch. We show that while the additional computational effort is manageable, the error can be reduced compared to a low-resolution standard model using an idealized test and relatively realistic dust transport tests.
Sylvain Mailler, Romain Pennel, Laurent Menut, and Mathieu Lachâtre
Geosci. Model Dev., 14, 2221–2233, https://doi.org/10.5194/gmd-14-2221-2021, https://doi.org/10.5194/gmd-14-2221-2021, 2021
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Representing the advection of thin polluted plumes in numerical models is a challenging task since these models usually tend to excessively diffuse these plumes in the vertical direction. This numerical diffusion process is the cause of major difficulties in representing such dense and thin polluted plumes in numerical models. We propose here, and test in an academic framework, a novel method to solve this problem through the use of an antidiffusive advection scheme in the vertical direction.
Daniel Otoo and David Hodgetts
Geosci. Model Dev., 14, 2075–2095, https://doi.org/10.5194/gmd-14-2075-2021, https://doi.org/10.5194/gmd-14-2075-2021, 2021
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The forward stratigraphic simulation method is used to predict lithofacies, porosity, and permeability in a reservoir model. The objective of using this approach is to enhance subsurface property modelling through geologic realistic 3-D stratigraphic patterns.
Results show realistic stratigraphic sequences. Given this, we can derive spatial and geometric data as secondary data to constrain property simulation in a reservoir model. The approach can reduce the uncertainty of property modelling.
Kang Pan, Mei Qi Lim, Markus Kraft, and Epaminondas Mastorakos
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2021-47, https://doi.org/10.5194/gmd-2021-47, 2021
Revised manuscript accepted for GMD
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A new moving point source (MPS) model was developed to simulate the dispersion of emissions generated by the moving ships. Compared to the commonly used line source (LS) or fixed point source (FPS) model, the MPS model predicted more realistic emission distribution generated from the moving ships and matched reasonably with the measurements. Therefore, the MPS model provides an alternative for the environmental society to evaluate the pollutant dispersion contributed from the moving ships.
Denise Degen and Mauro Cacace
Geosci. Model Dev., 14, 1699–1719, https://doi.org/10.5194/gmd-14-1699-2021, https://doi.org/10.5194/gmd-14-1699-2021, 2021
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In this work, we focus on improving the understanding of subsurface processes with respect to interactions with climate dynamics. We present advanced, open-source mathematical methods that enable us to investigate the influence of various model properties on the final outcomes. By relying on our approach, we have been able to showcase their importance in improving our understanding of the subsurface and highlighting the current shortcomings of currently adopted models.
Rostislav Kouznetsov
Geosci. Model Dev., 14, 377–389, https://doi.org/10.5194/gmd-14-377-2021, https://doi.org/10.5194/gmd-14-377-2021, 2021
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Resetting of non-significant figures (precision trimming) enables efficient data compression and helps to avoid excessive use of storage space and network bandwidth while having well-constrained distortion to the data. The paper analyses accuracy losses and artifacts caused by trimming methods and by the widely used linear packing method. The paper presents several methods with implementation, evaluation, and illustrations and includes subroutines directly usable in geoscientific models.
Annika Günther, Johannes Gütschow, and Mairi Louise Jeffery
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2020-392, https://doi.org/10.5194/gmd-2020-392, 2021
Revised manuscript accepted for GMD
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The mitigation components of the Nationally Determined Contributions (NDCs) under the Paris Agreement are essential in our fight against climate change. Regular updates with increased ambition are requested, to limit global warming to 1.5–2 °C. The new and easy to be updated open-source tool NDCmitiQ can be used to quantify the NDCs' mitigation targets and construct resulting emissions pathways. In use cases, we show target uncertainties from missing clarity, data, and methodological challenges.
Axel Peytavin, Bruno Sainte-Rose, Gael Forget, and Jean-Michel Campin
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2020-385, https://doi.org/10.5194/gmd-2020-385, 2021
Revised manuscript accepted for GMD
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We present a new algorithm developed at The Ocean Cleanup to update ocean plastic models based on measurements collected in the field to improve future cleaning operations. Prepared in collaboration with MIT researchers, this initial study presents its use in several test cases in which two observers in a simulated flow field record regular observations to update a plastic forecast. We demonstrate this improves the prediction, even with inaccurate knowledge of the water flows driving plastic.
Bertrand Bessagnet, Laurent Menut, and Maxime Beauchamp
Geosci. Model Dev., 14, 91–106, https://doi.org/10.5194/gmd-14-91-2021, https://doi.org/10.5194/gmd-14-91-2021, 2021
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This paper presents a new interpolator useful for geophysics applications. It can explore N-dimensional meshes, grids or look-up tables. The code accepts irregular but structured grids. Written in Fortran, it is easy to implement in existing codes and very fast and portable. We have compared it with a Python library. Python is convenient but suffers from portability and is sometimes not optimized enough. As an application case, this method is applied to atmospheric sciences.
Oksana Guba, Mark A. Taylor, Andrew M. Bradley, Peter A. Bosler, and Andrew Steyer
Geosci. Model Dev., 13, 6467–6480, https://doi.org/10.5194/gmd-13-6467-2020, https://doi.org/10.5194/gmd-13-6467-2020, 2020
Anna Wirbel and Alexander Helmut Jarosch
Geosci. Model Dev., 13, 6425–6445, https://doi.org/10.5194/gmd-13-6425-2020, https://doi.org/10.5194/gmd-13-6425-2020, 2020
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We present an open-source numerical tool to simulate the free-surface evolution of gravity-driven flows (e.g. glaciers) constrained by bed topography. No ad hoc post-processing is required to enforce positive ice thickness and mass conservation. We utilise finite elements, define benchmark tests, and showcase glaciological examples. In addition, we provide a thorough analysis of the applicability and robustness of different spatial stabilisation and time discretisation methods.
Emmanuel Wyser, Yury Alkhimenkov, Michel Jaboyedoff, and Yury Y. Podladchikov
Geosci. Model Dev., 13, 6265–6284, https://doi.org/10.5194/gmd-13-6265-2020, https://doi.org/10.5194/gmd-13-6265-2020, 2020
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In this work, we present an efficient and fast material point method (MPM) implementation in MATLAB. We first discuss the vectorization strategies to adapt this numerical method to a MATLAB implementation. We report excellent agreement of the solver compared with classical analysis among the MPM community, such as the cantilever beam problem. The solver achieves a performance gain of 28 compared with a classical iterative implementation.
Steven J. Phipps, Jason L. Roberts, and Matt A. King
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2020-382, https://doi.org/10.5194/gmd-2020-382, 2020
Revised manuscript accepted for GMD
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Simplified schemes, known as parameterisations, are sometimes used to describe physical processes within numerical models. However, the values of the parameters are uncertain. This introduces uncertainty into the model outputs. We develop a simple approach to identify plausible ranges for model parameters. Using a model of the Antarctic Ice Sheet, we find that the value of one parameter can depend on the values of others. We conclude that a single optimal set of parameter values does not exist.
Lauri Tuppi, Pirkka Ollinaho, Madeleine Ekblom, Vladimir Shemyakin, and Heikki Järvinen
Geosci. Model Dev., 13, 5799–5812, https://doi.org/10.5194/gmd-13-5799-2020, https://doi.org/10.5194/gmd-13-5799-2020, 2020
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This paper presents general guidelines on how to utilise computer algorithms efficiently in order to tune weather models so that they would produce better forecasts. The main conclusions are that the computer algorithms work most efficiently with a suitable cost function, certain forecast length and ensemble size. We expect that our results will facilitate the use of algorithmic methods in the tuning of weather models.
Tarandeep S. Kalra, Neil K. Ganju, and Jeremy M. Testa
Geosci. Model Dev., 13, 5211–5228, https://doi.org/10.5194/gmd-13-5211-2020, https://doi.org/10.5194/gmd-13-5211-2020, 2020
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The paper covers the description of a 3-D open-source model that dynamically couples the biophysical interactions between submerged aquatic vegetation (SAV), hydrodynamics (currents, waves), sediment dynamics, and nutrient loading. Based on SAV growth model, SAV can use growth or dieback while contributing and sequestering nutrients from the water column (modifying the biological environment) and subsequently affect the hydrodynamics and sediment transport (modifying the physical environment).
Xiaoshuang Li, Richard Garth James Bellerby, Jianzhong Ge, Philip Wallhead, Jing Liu, and Anqiang Yang
Geosci. Model Dev., 13, 5103–5117, https://doi.org/10.5194/gmd-13-5103-2020, https://doi.org/10.5194/gmd-13-5103-2020, 2020
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We have developed an ANN model to predict pH using 11 cruise datasets from 2013 to 2017,
demonstrated its reliability using three cruise datasets during 2018 and applied it to
retrieve monthly pH for the period 2000 to 2016 on the East China Sea shelf using the
ANN model in combination with input variables from the Changjiang biology Finite-Volume
Coastal Ocean Model. This approach may be a valuable tool for understanding the seasonal
variation of pH in poorly observed regions.
Christopher Subich, Pierre Pellerin, Gregory Smith, and Frederic Dupont
Geosci. Model Dev., 13, 4379–4398, https://doi.org/10.5194/gmd-13-4379-2020, https://doi.org/10.5194/gmd-13-4379-2020, 2020
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This work presents a semi-Lagrangian advection module for the NEMO (OPA) ocean model. Semi-Lagrangian advection transports fluid properties (temperature, salinity, velocity) between time steps by following fluid motion and interpolating from upstream locations of fluid parcels.
This method is commonly used in atmospheric models to extend time step size, but it has not previously been applied to operational ocean models. Overcoming this required a new approach for solid boundaries (coastlines).
Jouni Susiluoto, Alessio Spantini, Heikki Haario, Teemu Härkönen, and Youssef Marzouk
Geosci. Model Dev., 13, 3439–3463, https://doi.org/10.5194/gmd-13-3439-2020, https://doi.org/10.5194/gmd-13-3439-2020, 2020
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We describe a new computer program that is able produce maps of carbon dioxide or other quantities based on data collected by satellites that orbit the Earth. When working with such data there is often too much data in one area and none in another. The program is able to describe the fields even when data is not available. To be able to do so, new computational methods were developed. The program is also able to describe how uncertain the estimated carbon dioxide or other fields are.
Olivier Pannekoucke and Ronan Fablet
Geosci. Model Dev., 13, 3373–3382, https://doi.org/10.5194/gmd-13-3373-2020, https://doi.org/10.5194/gmd-13-3373-2020, 2020
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Learning physics from data using a deep neural network is a challenge that requires an appropriate but unknown network architecture. The package introduced here helps to design an architecture by translating known physical equations into a network, which the experimenter completes to capture unknown physical processes. A test bed is introduced to illustrate how this learning allows us to focus on truly unknown physical processes in the hope of making better use of data and digital resources.
Dmitry Sidorenko, Sergey Danilov, Nikolay Koldunov, Patrick Scholz, and Qiang Wang
Geosci. Model Dev., 13, 3337–3345, https://doi.org/10.5194/gmd-13-3337-2020, https://doi.org/10.5194/gmd-13-3337-2020, 2020
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Computation of barotropic and meridional overturning streamfunctions for models formulated on unstructured meshes is commonly preceded by interpolation to a regular mesh. This operation destroys the original conservation, which can be then be artificially imposed to make the computation possible. An elementary method is proposed that avoids interpolation and preserves conservation in a strict model sense.
Xavier Couvelard, Florian Lemarié, Guillaume Samson, Jean-Luc Redelsperger, Fabrice Ardhuin, Rachid Benshila, and Gurvan Madec
Geosci. Model Dev., 13, 3067–3090, https://doi.org/10.5194/gmd-13-3067-2020, https://doi.org/10.5194/gmd-13-3067-2020, 2020
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Within the framework of the Copernicus Marine Environment Monitoring Service (CMEMS), an objective is to demonstrate the contribution of coupling the high-resolution analysis and forecasting system with a wave model. This study describes the necessary steps and discusses the various choices made for coupling a wave model and an oceanic model for global-scale applications.
Rohitash Chandra, Danial Azam, Arpit Kapoor, and R. Dietmar Müller
Geosci. Model Dev., 13, 2959–2979, https://doi.org/10.5194/gmd-13-2959-2020, https://doi.org/10.5194/gmd-13-2959-2020, 2020
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Forward landscape and sedimentary basin evolution models pose a major challenge in the development of efficient inference and optimization methods. Bayesian inference provides a methodology for estimation and uncertainty quantification of free model parameters. In this paper, we present an application of a surrogate-assisted Bayesian parallel tempering method where that surrogate mimics a landscape evolution model. We use the method for parameter estimation and uncertainty quantification.
Juliette Mignot, Carlos Mejia, Charles Sorror, Adama Sylla, Michel Crépon, and Sylvie Thiria
Geosci. Model Dev., 13, 2723–2742, https://doi.org/10.5194/gmd-13-2723-2020, https://doi.org/10.5194/gmd-13-2723-2020, 2020
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The most robust representation of climate is usually obtained by averaging a large number of simulations, thereby cancelling individual model errors. Here, we work towards an objective way of selecting the least biased models over a certain region, based on physical parameters. This statistical method based on a neural classifier and multi-correspondence analysis is illustrated here for the Senegalo-Mauritanian region, but it could potentially be developed for any other region or process.
Mathieu Gravey and Grégoire Mariethoz
Geosci. Model Dev., 13, 2611–2630, https://doi.org/10.5194/gmd-13-2611-2020, https://doi.org/10.5194/gmd-13-2611-2020, 2020
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Stochastic simulations are key tools to generate complex spatial structures uses as input in geoscientific models. In this paper, we present a new open-source tool that enables to simulate complex structures in a straightforward and efficient manner, based on analogues. The method is tested on a variety of use cases to demonstrate the generality of the framework.
Gong Cheng, Per Lötstedt, and Lina von Sydow
Geosci. Model Dev., 13, 2245–2258, https://doi.org/10.5194/gmd-13-2245-2020, https://doi.org/10.5194/gmd-13-2245-2020, 2020
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A full Stokes subgrid scheme in two dimensions for the grounding line migration problem is presented in the open-source finite-element framework Elmer/ICE. This method can achieve comparable results to previous research using a more than 20 times larger mesh size, which can be used to improve the efficiency in marine ice sheet simulations.
Colin Grudzien, Marc Bocquet, and Alberto Carrassi
Geosci. Model Dev., 13, 1903–1924, https://doi.org/10.5194/gmd-13-1903-2020, https://doi.org/10.5194/gmd-13-1903-2020, 2020
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All scales of a dynamical physical process cannot be resolved accurately in a multiscale, geophysical model. The behavior of unresolved scales of motion are often parametrized by a random process to emulate their effects on the dynamically resolved variables, and this results in a random–dynamical model. We study how the choice of a numerical discretization of such a system affects the model forecast and estimation statistics, when the random–dynamical model is unbiased in its parametrization.
Theo Baracchini, Philip Y. Chu, Jonas Šukys, Gian Lieberherr, Stefan Wunderle, Alfred Wüest, and Damien Bouffard
Geosci. Model Dev., 13, 1267–1284, https://doi.org/10.5194/gmd-13-1267-2020, https://doi.org/10.5194/gmd-13-1267-2020, 2020
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Lake physical processes occur at a wide range of spatiotemporal scales. 3D hydrodynamic lake models are the only information source capable of solving those scales; however, they still need observations to be calibrated and to constrain their uncertainties. The optimal combination of a 3D hydrodynamic model, in situ measurements, and remote sensing observations is achieved through data assimilation. Here we present a complete data assimilation experiment for lakes using open-source tools.
Negin Nazarian, E. Scott Krayenhoff, and Alberto Martilli
Geosci. Model Dev., 13, 937–953, https://doi.org/10.5194/gmd-13-937-2020, https://doi.org/10.5194/gmd-13-937-2020, 2020
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We present an update to the Multi-Layer Urban Canopy Model by revisiting the parameterization of length scales based on high-resolution and validated large-eddy simulations. Additionally, the inclusion of dispersive fluxes in the parameterization schemes are also discussed. The results demonstrate that updated parameterizations improve the accuracy of the vertical exchange of momentum in the street canyon.
Thomas H. Gibson, Lawrence Mitchell, David A. Ham, and Colin J. Cotter
Geosci. Model Dev., 13, 735–761, https://doi.org/10.5194/gmd-13-735-2020, https://doi.org/10.5194/gmd-13-735-2020, 2020
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Galerkin finite element discretizations for atmospheric modeling often require the solution of ill-conditioned, saddle point equations which can be efficiently solved using a hybridized method. By extending Firedrake's domain-specific abstraction, we provide a mechanism for the rapid implementation of hybridization methods for a wide class of methods. In this paper, we show that hybridization is an effective alternative to traditional block solvers for simulating geophysical flows.
Murat Gunduz, Emin Özsoy, and Robinson Hordoir
Geosci. Model Dev., 13, 121–138, https://doi.org/10.5194/gmd-13-121-2020, https://doi.org/10.5194/gmd-13-121-2020, 2020
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The Bosphorus exchange is of critical importance for hydrodynamics and hydroclimatology of the Black Sea. In this study, we report on the development of a medium-resolution circulation model of the Black Sea, making use of surface atmospheric forcing with high space and time resolution, climatic river fluxes and strait exchange, enabled by adding elementary details of strait and coastal topography and seasonal hydrology specified in an artificial box on the Marmara Sea side.
Ewan Pinnington, Tristan Quaife, Amos Lawless, Karina Williams, Tim Arkebauer, and Dave Scoby
Geosci. Model Dev., 13, 55–69, https://doi.org/10.5194/gmd-13-55-2020, https://doi.org/10.5194/gmd-13-55-2020, 2020
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We present LAVENDAR, a mathematical method for combining observations with models of the terrestrial environment. Here we use it to improve estimates of crop growth in the UK Met Office land surface model. However, the method is model agnostic, requires no modification to the underlying code and can be applied to any part of the model. In the example application we improve estimates of maize yield by 74 % by assimilating observations of leaf area, crop height and photosynthesis.
Xavier Delaunay, Aurélie Courtois, and Flavien Gouillon
Geosci. Model Dev., 12, 4099–4113, https://doi.org/10.5194/gmd-12-4099-2019, https://doi.org/10.5194/gmd-12-4099-2019, 2019
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This research aimed at finding a compression method suitable for the ground processing of CFOSAT and SWOT satellite datasets. Lossless algorithms did not allow enough compression. That is why we began studying lossy alternatives. This work introduces the digit rounding algorithm which reduces the volume of scientific datasets keeping only the significant digits in each sample value. The number of digits kept is relative to each sample so that both small and high values are similarly preserved.
Richard Scalzo, David Kohn, Hugo Olierook, Gregory Houseman, Rohitash Chandra, Mark Girolami, and Sally Cripps
Geosci. Model Dev., 12, 2941–2960, https://doi.org/10.5194/gmd-12-2941-2019, https://doi.org/10.5194/gmd-12-2941-2019, 2019
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Producing 3-D models of structures under the Earth's surface based on sensor data is a key problem in geophysics (for example, in mining exploration). There may be multiple models that explain the data well. We use the open-source Obsidian software to look at the efficiency of different methods for exploring the model space and attaching probabilities to models, leading to less biased results and a better idea of how sensor data interact with geological assumptions.
Anna Denvil-Sommer, Marion Gehlen, Mathieu Vrac, and Carlos Mejia
Geosci. Model Dev., 12, 2091–2105, https://doi.org/10.5194/gmd-12-2091-2019, https://doi.org/10.5194/gmd-12-2091-2019, 2019
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This work is dedicated to a new model that reconstructs the surface ocean partial pressure of carbon dioxide (pCO2) over the global ocean on a monthly 1°×1° grid. The model is based on a feed-forward neural network and represents the nonlinear relationships between pCO2 and the ocean drivers. Reconstructed pCO2 has a satisfying accuracy compared to independent observational data and shows a good agreement in seasonal and interannual variability with three existing mapping methods.
Alexey Androsov, Vera Fofonova, Ivan Kuznetsov, Sergey Danilov, Natalja Rakowsky, Sven Harig, Holger Brix, and Karen Helen Wiltshire
Geosci. Model Dev., 12, 1009–1028, https://doi.org/10.5194/gmd-12-1009-2019, https://doi.org/10.5194/gmd-12-1009-2019, 2019
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We present a description of a coastal ocean circulation model designed to work on variable-resolution meshes made of triangular and quadrilateral cells. This hybrid mesh functionality allows for higher numerical performance and less dissipative solutions.
Kai-Lan Chang, Owen R. Cooper, J. Jason West, Marc L. Serre, Martin G. Schultz, Meiyun Lin, Virginie Marécal, Béatrice Josse, Makoto Deushi, Kengo Sudo, Junhua Liu, and Christoph A. Keller
Geosci. Model Dev., 12, 955–978, https://doi.org/10.5194/gmd-12-955-2019, https://doi.org/10.5194/gmd-12-955-2019, 2019
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We developed a new method for combining surface ozone observations from thousands of monitoring sites worldwide with the output from multiple atmospheric chemistry models. The result is a global surface ozone distribution with greater accuracy than any single model can achieve. We focused on an ozone metric relevant to human mortality caused by long-term ozone exposure. Our method can be applied to studies that quantify the impacts of ozone on human health and mortality.
Colin M. Zarzycki, Christiane Jablonowski, James Kent, Peter H. Lauritzen, Ramachandran Nair, Kevin A. Reed, Paul A. Ullrich, David M. Hall, Mark A. Taylor, Don Dazlich, Ross Heikes, Celal Konor, David Randall, Xi Chen, Lucas Harris, Marco Giorgetta, Daniel Reinert, Christian Kühnlein, Robert Walko, Vivian Lee, Abdessamad Qaddouri, Monique Tanguay, Hiroaki Miura, Tomoki Ohno, Ryuji Yoshida, Sang-Hun Park, Joseph B. Klemp, and William C. Skamarock
Geosci. Model Dev., 12, 879–892, https://doi.org/10.5194/gmd-12-879-2019, https://doi.org/10.5194/gmd-12-879-2019, 2019
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We summarize the results of the Dynamical Core Model Intercomparison Project's idealized supercell test case. Supercells are storm-scale weather phenomena that are a key target for next-generation, non-hydrostatic weather prediction models. We show that the dynamical cores of most global numerical models converge between approximately 1 and 0.5 km grid spacing for this test, although differences in final solution exist, particularly due to differing grid discretizations and numerical diffusion.
Christian Kühnlein, Willem Deconinck, Rupert Klein, Sylvie Malardel, Zbigniew P. Piotrowski, Piotr K. Smolarkiewicz, Joanna Szmelter, and Nils P. Wedi
Geosci. Model Dev., 12, 651–676, https://doi.org/10.5194/gmd-12-651-2019, https://doi.org/10.5194/gmd-12-651-2019, 2019
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We present a novel finite-volume dynamical core formulation considered for future numerical weather prediction at ECMWF. We demonstrate that this formulation can be competitive in terms of solution quality and computational efficiency to the proven spectral-transform dynamical core formulation currently operational at ECMWF, while providing a local, more scalable discretization, conservative and monotone advective transport, and flexible meshes.
Ramadan Abdelaziz, Broder J. Merkel, Mauricio Zambrano-Bigiarini, and Sreejesh Nair
Geosci. Model Dev., 12, 167–177, https://doi.org/10.5194/gmd-12-167-2019, https://doi.org/10.5194/gmd-12-167-2019, 2019
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The paper presents a robust tool to estimate the thermodynamic surface complexation parameter for the sorption of uranium(VI) onto quartz surfaces. The optimization package hydroPSO R is coupled with the geochemical speciation code PHREEQC. hydroPSO used the m parameter estimation tool for geochemical modeling with PHREEQC. Coupled hydroPSO with PHREEQC proved to be a robust tool to estimate surface complexation constants for uranium(VI) species on quartz.
Miguel de la Varga, Alexander Schaaf, and Florian Wellmann
Geosci. Model Dev., 12, 1–32, https://doi.org/10.5194/gmd-12-1-2019, https://doi.org/10.5194/gmd-12-1-2019, 2019
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GemPy is an open-source Python-based 3-D structural geological modeling software, which allows the implicit (i.e. automatic) creation of complex geological models from interface and orientation data. GemPy is implemented in the programming language Python, making use of a highly efficient underlying library, Theano, for efficient code generation that performs automatic differentiation. This enables the link to probabilistic machine-learning and Bayesian inference frameworks.
Tianfeng Chai, Ariel Stein, and Fong Ngan
Geosci. Model Dev., 11, 5135–5148, https://doi.org/10.5194/gmd-11-5135-2018, https://doi.org/10.5194/gmd-11-5135-2018, 2018
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While model predictions depend on release parameters, model uncertainties in inverse modeling should also vary with the source terms. In this paper, model uncertainties that will change with the source terms are introduced in a weak-constraint inverse modeling system. Tests using HYSPLIT model and CAPTEX observations show that adding such model uncertainty terms improves release rate estimates. A cost function normalization scheme introduced to avoid spurious solutions proves to be effective.
Christopher J. Skinner, Tom J. Coulthard, Wolfgang Schwanghart, Marco J. Van De Wiel, and Greg Hancock
Geosci. Model Dev., 11, 4873–4888, https://doi.org/10.5194/gmd-11-4873-2018, https://doi.org/10.5194/gmd-11-4873-2018, 2018
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Landscape evolution models are computer models used to understand how the Earth’s surface changes over time. Although designed to look at broad changes over very long time periods, they could potentially be used to predict smaller changes over shorter periods. However, to do this we need to better understand how the models respond to changes in their set-up – i.e. their behaviour. This work presents a method which can be applied to these models in order to better understand their behaviour.
Gary L. Russell, David H. Rind, and Jeffrey Jonas
Geosci. Model Dev., 11, 4637–4656, https://doi.org/10.5194/gmd-11-4637-2018, https://doi.org/10.5194/gmd-11-4637-2018, 2018
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This paper presents the Fortran 90 source code for one-layer model GISS:IB on an icosahedral grid. The model solves the shallow water equations on the sphere using three symmetric horizontal components of angular momentum instead of velocity. One-layer shallow water models are a basic building block used in complex global weather and climate models.
Istvan Z. Reguly, Daniel Giles, Devaraj Gopinathan, Laure Quivy, Joakim H. Beck, Michael B. Giles, Serge Guillas, and Frederic Dias
Geosci. Model Dev., 11, 4621–4635, https://doi.org/10.5194/gmd-11-4621-2018, https://doi.org/10.5194/gmd-11-4621-2018, 2018
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We present the VOLNA-OP2 tsunami simulation code, built on the OP2 library. It is unique among such solvers in its support for several high-performance computing platforms: CPUs, the Intel Xeon Phi, and GPUs. This is achieved in a way that the scientific code is kept separate from various parallel implementations, enabling easy maintainability. Scalability and efficiency are demonstrated on three supercomputers built with CPUs, Xeon Phi's, and GPUs.
Joakim Beck, Sören Wolfers, and Gerald P. Roberts
Geosci. Model Dev., 11, 4383–4397, https://doi.org/10.5194/gmd-11-4383-2018, https://doi.org/10.5194/gmd-11-4383-2018, 2018
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Seismic hazard assessment requires records of earthquake recurrence with many slip events. Current data from paleoseismology on individual faults are sparse and do not provide stable estimates of earthquake recurrence. We propose a statistical model-based method to study timings of earthquakes over the past few millennia. The results agree with historical earthquakes for faults in the Italian Apennines, and can aid future studies of fault interactions over multiple earthquake cycles.
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Short summary
Refining model resolution is helpful for representing climate processes. With resolution increasing, the computational cost will become very huge. We designed a new solver to accelerate the high-resolution ocean simulation so as to reduce the computational cost and make full use of the computing resource of supercomputers. Our results show that the simulation speed of the improved ocean component with 0.1° resolution achieves 10.5 simulated years per wall-clock day on 16875 CPU cores.
Refining model resolution is helpful for representing climate processes. With resolution...
