scholarly journals The Oceanographic Multipurpose Software Environment

2016 ◽  
Author(s):  
Inti Pelupessy ◽  
Ben van Werkhoven ◽  
Arjen van Elteren ◽  
Jan Viebahn ◽  
Adam Candy ◽  
...  
Keyword(s):  
Numerical Experiments ◽  
High Performance ◽  
Rapid Development ◽  
Circulation Model ◽  
Simulation Models ◽  
Ocean Model ◽  
Propagation Model ◽  
Global Ocean ◽  
Global Circulation Model ◽  
Software Environment

Abstract. In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). This framework aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, OMUSE facilitates the design of numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales. Rapid development of simulation models is made possible through the creation of simple high-level scripts, with the low-level core part of the abstraction designed to deploy these simulations efficiently on heterogeneous high performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver, to the global circulation model POP. We discuss the types of the couplings that can be implemented using OMUSE and present example applications, that demonstrate the efficient and relatively straightforward model initialisation and coupling within OMUSE. These also include the concurrent use of data analysis tools on a running model. We also give examples of multi-scale and multi-physics simulations by embedding a regional ocean model into a global ocean model, and in coupling a surface wave propagation model with a coastal circulation model.

scholarly journals The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

2017 ◽  
Vol 10 (8) ◽  
pp. 3167-3187 ◽  
Author(s):  
Inti Pelupessy ◽  
Ben van Werkhoven ◽  
Arjen van Elteren ◽  
Jan Viebahn ◽  
Adam Candy ◽  
...  
Keyword(s):  
Numerical Experiments ◽  
High Performance ◽  
Rapid Development ◽  
Circulation Model ◽  
Simulation Models ◽  
Ocean Model ◽  
Propagation Model ◽  
Global Ocean ◽  
Global Circulation Model ◽  
Software Environment

Abstract. In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model.

Evaluating Effects of Observational Data Assimilation in General Ocean Circulation Model by Ensemble Kalman Filtering: Numerical Experiments with Synthetic Observations

2021 ◽  
pp. 50-66
Author(s):  
V. N. Stepanov ◽  
◽  
Yu. D. Resnyanskii ◽  
B. S. Strukov ◽  
A. A. Zelen’ko ◽  
...  
Keyword(s):  
Data Assimilation ◽  
Observational Data ◽  
Ocean Circulation ◽  
Numerical Experiments ◽  
Turbulent Viscosity ◽  
Bottom Topography ◽  
Synthetic Data ◽  
Circulation Model ◽  
Ocean Model ◽  
Global Ocean

The quality of simulation of model fields is analyzed depending on the assimilation of various types of data using the PDAF software product assimilating synthetic data into the NEMO global ocean model. Several numerical experiments are performed to simulate the ocean–sea ice system. Initially, free model was run with different values of the coefficients of horizontal turbulent viscosity and diffusion, but with the same atmospheric forcing. The model output obtained with higher values of these coefficients was used to determine the first guess fields in subsequent experiments with data assimilation, while the model results with lower values of the coefficients were assumed to be true states, and a part of these results was used as synthetic observations. The results are analyzed that are assimilation of various types of observational data using the Kalman filter included through the PDAF to the NEMO model with real bottom topography. It is shown that a degree of improving model fields in the process of data assimilation is highly dependent on the structure of data at the input of the assimilation procedure.

scholarly journals The GPU version of LICOM3 under HIP framework and its large-scale application

2020 ◽  
Author(s):  
Pengfei Wang ◽  
Jinrong Jiang ◽  
Pengfei Lin ◽  
Mengrong Ding ◽  
Junlin Wei ◽  
...  
Keyword(s):  
Graphics Processing Units ◽  
General Circulation ◽  
High Performance ◽  
Large Scale ◽  
Data Transfer ◽  
Circulation Model ◽  
Ocean General Circulation Model ◽  
Ocean Model ◽  
Global Ocean ◽  
Almost All

Abstract. A high-resolution (1/20°) global ocean general circulation model with Graphics processing units (GPUs) code implementations is developed based on the LASG/IAP Climate system Ocean Model version 3 (LICOM3) under Heterogeneous-compute Interface for Portability (HIP) framework. The dynamic core and physics package of LICOM3 are both ported to the GPU, and 3-dimensional parallelization is applied. The HIP version of the LICOM3 (LICOM3-HIP) is 42 times faster than what the same number of CPU cores dose, when 384 AMD GPUs and CPU cores are used. The LICOM3-HIP has excellent scalability; it can still obtain speedup of more than four on 9216 GPUs comparing to 384 GPUs. In this phase, we successfully performed a test of 1/20° LICOM3-HIP using 6550 nodes and 26200 GPUs, and at the grand scale, the model’s time to solution can still obtain an increasing, about 2.72 simulated years per day (SYPD). The high performance was due to putting almost all of computation processes inside GPUs, and thus greatly reduces the time cost of data transfer between CPUs and GPUs. At the same time, a 14-year spin-up integration following the phase 2 of Ocean Model Intercomparison Project (OMIP-2) protocol of surface forcing has been conducted, and the preliminary results have been evaluated. We found that the model results have little differences from the CPU version. Further comparison with observations and lower-resolution LICOM3 results suggests that the 1/20° LICOM3-HIP can not only reproduce the observations, but also produce much smaller scale activities, such as submesoscale eddies and frontal scales structures.

scholarly journals Multi-grid algorithm for passive tracer transport in the NEMO ocean circulation model: a case study with the NEMO OGCM (version 3.6)

2020 ◽  
Vol 13 (11) ◽  
pp. 5465-5483
Author(s):  
Clément Bricaud ◽  
Julien Le Sommer ◽  
Gurvan Madec ◽  
Christophe Calone ◽  
Julie Deshayes ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Ocean Circulation ◽  
Circulation Model ◽  
Ocean Model ◽  
Ocean Dynamics ◽  
Global Ocean ◽  
Passive Tracer ◽  
Tracer Transport ◽  
Ocean Circulation Model ◽  
Grid Algorithm

Abstract. Ocean biogeochemical models are key tools for both scientific and operational applications. Nevertheless the cost of these models is often expensive because of the large number of biogeochemical tracers. This has motivated the development of multi-grid approaches where ocean dynamics and tracer transport are computed on grids of different spatial resolution. However, existing multi-grid approaches to tracer transport in ocean modelling do not allow the computation of ocean dynamics and tracer transport simultaneously. This paper describes a new multi-grid approach developed for accelerating the computation of passive tracer transport in the Nucleus for European Modelling of the Ocean (NEMO) ocean circulation model. In practice, passive tracer transport is computed at runtime on a grid with coarser spatial resolution than the hydrodynamics, which reduces the CPU cost of computing the evolution of tracers. We describe the multi-grid algorithm, its practical implementation in the NEMO ocean model, and discuss its performance on the basis of a series of sensitivity experiments with global ocean model configurations. Our experiments confirm that the spatial resolution of hydrodynamical fields can be coarsened by a factor of 3 in both horizontal directions without significantly affecting the resolved passive tracer fields. Overall, the proposed algorithm yields a reduction by a factor of 7 of the overhead associated with running a full biogeochemical model like PISCES (with 24 passive tracers). Propositions for further reducing this cost without affecting the resolved solution are discussed.

scholarly journals An Epidemic Model of Computer Worms with Time Delay and Variable Infection Rate

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Yu Yao ◽  
Qiang Fu ◽  
Wei Yang ◽  
Ying Wang ◽  
Chuan Sheng
Keyword(s):  
Time Delay ◽  
Infection Rate ◽  
Numerical Experiments ◽  
Rapid Development ◽  
Nonlinear Process ◽  
Existence Condition ◽  
Propagation Model ◽  
Positive Equilibrium ◽  
Worm Propagation ◽  
Security Issues

With rapid development of Internet, network security issues become increasingly serious. Temporary patches have been put on the infectious hosts, which may lose efficacy on occasions. This leads to a time delay when vaccinated hosts change to susceptible hosts. On the other hand, the worm infection is usually a nonlinear process. Considering the actual situation, a variable infection rate is introduced to describe the spread process of worms. According to above aspects, we propose a time-delayed worm propagation model with variable infection rate. Then the existence condition and the stability of the positive equilibrium are derived. Due to the existence of time delay, the worm propagation system may be unstable and out of control. Moreover, the threshold τ0 of Hopf bifurcation is obtained. The worm propagation system is stable if time delay is less than τ0. When time delay is over τ0, the system will be unstable. In addition, numerical experiments have been performed, which can match the conclusions we deduce. The numerical experiments also show that there exists a threshold in the parameter a, which implies that we should choose appropriate infection rate β(t) to constrain worm prevalence. Finally, simulation experiments are carried out to prove the validity of our conclusions.

First results from coupling the Parallel Ice Sheet Model with the Modular Ocean Model via an Antarctic ice-shelf cavity module

2021 ◽  
Author(s):  
Moritz Kreuzer ◽  
Ronja Reese ◽  
Willem Huiskamp ◽  
Stefan Petri ◽  
Torsten Albrecht ◽  
...  
Keyword(s):  
Time Scales ◽  
General Circulation ◽  
Ice Sheet ◽  
Circulation Model ◽  
Ocean Model ◽  
Global Ocean ◽  
Ice Shelf ◽  
Antarctic Ice Sheet ◽  
First Results ◽  
The Antarctic

<p>The past and future evolution of the Antarctic Ice Sheet is largely controlled by interactions between the ocean and floating ice shelves. To investigate these interactions, coupled ocean and ice sheet model configurations are required. Previous modelling studies have mostly relied on high resolution configurations, limiting these studies to individual glaciers or regions over short time scales of decades to a few centuries. To study global and long term interactions, we developed a framework to couple the dynamic ice sheet model PISM with the global ocean general circulation model MOM5 via the ice-shelf cavity module PICO. Since ice-shelf cavities are not resolved by MOM5, but parameterized with the box model PICO, the framework allows the ice sheet and ocean model to be run at resolution of 16 km and 3 degrees, respectively. We present first results from our coupled setup and discuss stability, feedbacks, and interactions of the Antarctic Ice Sheet and the global ocean system on millennial time scales.</p>

scholarly journals Impact of Parameterized Internal Wave Drag on the Semidiurnal Energy Balance in a Global Ocean Circulation Model

2016 ◽  
Vol 46 (5) ◽  
pp. 1399-1419 ◽  
Author(s):  
Maarten C. Buijsman ◽  
Joseph K. Ansong ◽  
Brian K. Arbic ◽  
James G. Richman ◽  
Jay F. Shriver ◽  
...  
Keyword(s):  
Internal Wave ◽  
Ocean Circulation ◽  
Deep Water ◽  
Mode Conversion ◽  
Circulation Model ◽  
Wave Drag ◽  
Ocean Model ◽  
Internal Tides ◽  
Global Ocean ◽  
Numerical Dissipation

AbstractThe effects of a parameterized linear internal wave drag on the semidiurnal barotropic and baroclinic energetics of a realistically forced, three-dimensional global ocean model are analyzed. Although the main purpose of the parameterization is to improve the surface tides, it also influences the internal tides. The relatively coarse resolution of the model of ~8 km only permits the generation and propagation of the first three vertical modes. Hence, this wave drag parameterization represents the energy conversion to and the subsequent breaking of the unresolved high modes. The total tidal energy input and the spatial distribution of the barotropic energy loss agree with the Ocean Topography Experiment (TOPEX)/Poseidon (TPXO) tidal inversion model. The wave drag overestimates the high-mode conversion at ocean ridges as measured against regional high-resolution models. The wave drag also damps the low-mode internal tides as they propagate away from their generation sites. Hence, it can be considered a scattering parameterization, causing more than 50% of the deep-water dissipation of the internal tides. In the near field, most of the baroclinic dissipation is attributed to viscous and numerical dissipation. The far-field decay of the simulated internal tides is in agreement with satellite altimetry and falls within the broad range of Argo-inferred dissipation rates. In the simulation, about 12% of the semidiurnal internal tide energy generated in deep water reaches the continental margins.

scholarly journals The GPU version of LASG/IAP Climate System Ocean Model version 3 (LICOM3) under the heterogeneous-compute interface for portability (HIP) framework and its large-scale application

2021 ◽  
Vol 14 (5) ◽  
pp. 2781-2799
Author(s):  
Pengfei Wang ◽  
Jinrong Jiang ◽  
Pengfei Lin ◽  
Mengrong Ding ◽  
Junlin Wei ◽  
...  
Keyword(s):  
General Circulation ◽  
Large Scale ◽  
Vertical Direction ◽  
Circulation Model ◽  
Ocean General Circulation Model ◽  
Ocean Model ◽  
Climate System ◽  
Global Ocean ◽  
Processing Unit ◽  
Model Version

Abstract. A high-resolution (1/20∘) global ocean general circulation model with graphics processing unit (GPU) code implementations is developed based on the LASG/IAP Climate System Ocean Model version 3 (LICOM3) under a heterogeneous-compute interface for portability (HIP) framework. The dynamic core and physics package of LICOM3 are both ported to the GPU, and three-dimensional parallelization (also partitioned in the vertical direction) is applied. The HIP version of LICOM3 (LICOM3-HIP) is 42 times faster than the same number of CPU cores when 384 AMD GPUs and CPU cores are used. LICOM3-HIP has excellent scalability; it can still obtain a speedup of more than 4 on 9216 GPUs compared to 384 GPUs. In this phase, we successfully performed a test of 1/20∘ LICOM3-HIP using 6550 nodes and 26 200 GPUs, and on a large scale, the model's speed was increased to approximately 2.72 simulated years per day (SYPD). By putting almost all the computation processes inside GPUs, the time cost of data transfer between CPUs and GPUs was reduced, resulting in high performance. Simultaneously, a 14-year spin-up integration following phase 2 of the Ocean Model Intercomparison Project (OMIP-2) protocol of surface forcing was performed, and preliminary results were evaluated. We found that the model results had little difference from the CPU version. Further comparison with observations and lower-resolution LICOM3 results suggests that the 1/20∘ LICOM3-HIP can reproduce the observations and produce many smaller-scale activities, such as submesoscale eddies and frontal-scale structures.

scholarly journals A nested Atlantic-Mediterranean Sea general circulation model for operational forecasting

Ocean Science ◽  
2009 ◽  
Vol 5 (4) ◽  
pp. 461-473 ◽  
Author(s):  
P. Oddo ◽  
M. Adani ◽  
N. Pinardi ◽  
C. Fratianni ◽  
M. Tonani ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
General Circulation Model ◽  
Ocean Circulation ◽  
General Circulation ◽  
Circulation Model ◽  
Ocean Model ◽  
Global Ocean ◽  
Lateral Boundary ◽  
The Mediterranean ◽  
The Impact

Abstract. A new numerical general circulation ocean model for the Mediterranean Sea has been implemented nested within an Atlantic general circulation model within the framework of the Marine Environment and Security for the European Area project (MERSEA, Desaubies, 2006). A 4-year twin experiment was carried out from January 2004 to December 2007 with two different models to evaluate the impact on the Mediterranean Sea circulation of open lateral boundary conditions in the Atlantic Ocean. One model considers a closed lateral boundary in a large Atlantic box and the other is nested in the same box in a global ocean circulation model. Impact was observed comparing the two simulations with independent observations: ARGO for temperature and salinity profiles and tide gauges and along-track satellite observations for the sea surface height. The improvement in the nested Atlantic-Mediterranean model with respect to the closed one is particularly evident in the salinity characteristics of the Modified Atlantic Water and in the Mediterranean sea level seasonal variability.

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