Progress 07/01/08 to 05/31/10
Outputs
OUTPUTS: Engineering graduate students at USU are engaged in this multi-disciplinary project designed to develop a full-scale computational fluid dynamics (CFD) model of a river with sediment transport. We collaborate with researchers from the USU Natural Resources department to obtain a realistic river topography, which we use to create a computational mesh with adequate resolution for Large-Eddy Simulation (LES). This process involves four major steps: 1. Design a computational mesh from field data; 2. Select an appropriate turbulence model; 3. Create a particle tracking algorithm to simulate the sediment transport; 4. Incorporate all parts into one overall computational simulation. We will make the developed solvers available after the validation phase. In our work we evaluated the mobilization and behavior of fine-grained quartz particles with silica grains, from a numerical simulation standpoint. The colloidal and shear forces were computed in accordance with established methods and validated with available literature. These, along with the drag and gravitational forces, were made manifest through their contributions to the momentum source terms associated with the Navier Stokes equations of motion. The use of OpenFOAM, and in particular, the Ico-LagrangianFoam solver, greatly facilitated the creation of the numerical algorithm. The results were validated against the experimental, visualization experiments of Cerda, and showed that the response of the fines particle, at close separation distances, was largely a function of the chemistry of the fluid medium. That is, for moderate to low levels of shear force, high values of pH and low values of electrolyte concentration constitute a repulsive response. Whereas, for low values of pH and high levels of electrolyte concentration, the attractive Van der Waals force dominates, and deposition is witnessed. We have tested the Weather Research Forecasting Model (WRF), coupled with the Community Land Model (CLM) version 3.5, on the USU high performance-computing cluster. The results indicate that the snow simulations are dramatically improved with this coupled model. Further analysis indicates that such improvement is the result of more realistic allocation of surface energy in CLM when compared to two land surface schemes embedded in the previous version of WRF. In addition, the improved snow simulation further reduces overestimated precipitation and a warm bias in WRF. Additional simulations indicate that topography plays an important role in snow modeling. CLM at 10 km resolution produces the most accurate snowpack simulations when compared to the simulations at coarser resolutions where the snowpack is underestimated. Moreover, we can see that CLM still can produce realistic snowpack simulations at 20 km resolution when the prescribed elevations in the model are replaced with the observed values, further indicating the important role of topography in snowpack simulations. PARTICIPANTS: Overall project coordinator, Jiming Jin, PI, snowpack simulations, Nate Benson, Co-PI, system manager, E. Garbi, M. Hradisky, P. Villanueva, A. Zabriskie - sediment transport simulations, K. Horne, J. McCulley - CGNS parallel I/O implementation, T. Johansen, S. Ripplinger - OpenFOAM, W. Frisby, T. Quist - system help; Lijuan Wen - Regional climate modeling. TARGET AUDIENCES: The findings from this project will give state water managers with informed knowledge about water availability in the western United States. PROJECT MODIFICATIONS: In addition to snow simulations over the western United States, we performed irrigation simulations over China on the USU HPC Cluster.
Impacts
The project was well-received and showed how computational fluid dynamic (CFD) tools can take advantage of parallel storage solutions through a parallel implementation of the CFD general notation system (CGNS). The current CGNS system provides a standardized and robust data format to the CFD community and has made it easier to exchange information between different tools in the CFD process. However, it lacks an implementation to take advantage of fast parallel storage systems. The HPC@USU project solves that problem and enables CFD developers to take advantage of parallel systems with little additional parallel programming effort. The team was encouraged by the panel of judges to continue this work because a large number of HPC users will be able to benefit from this library. The significant improvements of snow simulations in our regional climate model will greatly benefit agricultural water use forecasts in the western United States. The improved version of our regional climate model will give the climate community a better tool for climate research and forecasts. Through these presentations, the tools of HPC@USU have been advanced and disseminated to a much wider audience in the agricultural and life sciences fields, including the USU Colleges of Agriculture, Engineering, Science, Natural Resources, Water Laboratory, as well as SC09 conference attendees and USU Spring Runoff attendees through Utah and nation-wide.
Publications
- P. Wu, J. Jin, & X Zhao. 2010. Impact of climate change and irrigation technology advancement on agricultural water use in China. Climatic Change (in press).
- K. Horne, N. Benson, and T. Hauser. 2009. An Efficient and Flexible Parallel I/O Implementation for the CFD General Notation System, SC09 Storage Challenge finalist presentation. Hauser, T. 2009. Benchmarking serial and parallel CGNS I/O performance, in '47th AIAA Aerospace Sciences Meeting including The New Horizons Forum and Aerospace Exposition.'
- Hauser, T. 2008. Benchmarking the CGNS I/O Performance, in '46th AIAA Aerospace Sciences Meeting and Exhibit.'
- Hauser, T. & Allen, J. 2007. Numerical simulation of the behavior and mobilization of fine-grained quartz particles in porous media, in 'OpenFOAM International Conference.'
- Hauser, T., Allen, J. & Ripplinger, S. 2007. Numerical Simulation of the behavior and mobilization of fine-grained quartz particles in porous media, in '60th Annual Meeting of the Division of Fluid Dynamics.'
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Progress 07/01/08 to 06/30/09
Outputs
OUTPUTS: For this project, we evaluated the mobilization and behavior of fine-grained quartz particles with silica grains, from a numerical simulation standpoint. The colloidal and shear forces were computed in accordance with established methods and validated with available literature. These, along with the drag and gravitational forces, were made manifest through their contributions to the momentum source terms associated with the Navier Stokes equations of motion. The use of OpenFOAM, and in particular, the Ico-LagrangianFoam solver, greatly facilitated the creation of the numerical algorithm. The results were validated against the experimental, visualization experiments of Cerda, and showed that the response of the fines particle, at close separation distances, was largely a function of the chemistry of the fluid medium. That is, for moderate to low levels of shear force, high values of pH and low values of electrolyte concentration constitute a repulsive response. Whereas, for low values of pH and high levels of electrolyte concentration, the attractive Van der Waals force dominates, and deposition is witnessed. One important, often overlooked, issue for large, three dimensional time-dependent computational simulations is the input and output performance of the solver, especially for large time-dependent simulations. The development of the CFD General Notation System (CGNS) has brought a standardized and robust data format to the CFD community, enabling the exchange of information between the various stages of numerical simulations. Application of this standard data format to large parallel simulations is hindered by the reliance of most applications on the CGNS Mid-Level Library. This library has only supported serialized I/O. By moving to HDF5 as the recommended low-level data storage format, the CGNS standards committee has created the opportunity to support parallel I/O. We developed a parallel implementation of the CGNS Mid-Level Library and an I/O request-queuing approach to overcome some limitations of HDF5. We have tested the Weather Research Forecasting Model (WRF), coupled with the Community Land Model (CLM) version 3.5, on the USU high performance-computing cluster. The results indicate that the snow simulations are dramatically improved with this coupled model. Further analysis indicates that such improvement is the result of more realistic allocation of surface energy in CLM when compared to two land surface schemes embedded in the previous version of WRF. In addition, the improved snow simulation further reduces overestimated precipitation and a warm bias in WRF. Additional simulations indicate that topography plays an important role in snow modeling. CLM at 10 km resolution produces the most accurate snowpack simulations when compared to the simulations at coarser resolutions where the snowpack is underestimated. Moreover, we can see that CLM still can produce realistic snowpack simulations at 20 km resolution when the prescribed elevations in the model are replaced with the observed values, further indicating the important role of topography in snowpack simulations. PARTICIPANTS: Thomas Hauser, Jiming Jin, snowpack simulations, E. Garbi, M. Hradisky, P. Villanueva, A. Zabriskie - sediment transport simulations, K. Horne, J. McCulley - CGNS parallel I/O implementation, T. Johansen, S. Ripplinger - OpenFOAM, W. Frisby, T. Quist - system help; Lijuan Wen - Regional climate modeling. TARGET AUDIENCES: agricultural research community climate community PROJECT MODIFICATIONS: A new cluster computer was purchased with 64 nodes containing dual quad core AMD processors and a fast infiniband interconnect. This will better enable the proposed climate and fluid simulations, since our initial benchmarks reveal that we need much more computing power than initially estimated. We used the seed grant and symposium budget as approved by USDA to purchase the cluster. The cluster is now operational.
Impacts
As a result of our work, my student and I were selected as one of four finalists in the prestigious international Supercomputing Conference SC09 Storage Challenge. The project shows how computational fluid dynamic (CFD) tools can take advantage of parallel storage solutions through a parallel implementation of the CFD general notation system (CGNS). The current CGNS system provides a standardized and robust data format to the CFD community and has made it easier to exchange information between different tools in the CFD process. However, it lacks an implementation to take advantage of fast parallel storage systems. The HPC@USU project solves that problem and enables CFD developers to take advantage of parallel systems with little additional parallel programming effort. We presented our work at the November SC09 conference that has an acceptance rate of less than 20%. Our entry didn't win, but we were encouraged by the panel of judges to continue this work because a large number of HPC users will be able to benefit from our library.
Publications
- No publications reported this period
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