Progress 07/15/06 to 07/14/08
Outputs
OUTPUTS: The Center for High Performance Computing (HPC@USU) hosted its first two-day symposium on Opportunities for High Performance Computing in Agricultural and Life Sciences. Keynote speaker Dr. Colien Hefferan, USDA administrator of CSREES, spoke of the need for HPC capabilities in all elements of scientific research to remain competitive and enhance research. She noted many researchers rely on outdated techniques learned decades ago in graduate school, but to remain competitive today requires the use of new tools for tracking, monitoring and computing analysis. HPC offers these capabilities and efficiencies, Hefferan stated, and praised the research investment of HPC@USU. The symposium also had the following presentations: The Cornell Computational Agriculture Initiative: HPC Solutions to Agricultural Problems, Harold M. van Es, Int'l Professor of Crop & Soil Sciences, Cornell University; Applications of HPC in plant breeding, conservation, and genetics; Steven R. Larson, Research Geneticist, Forage & Range Research Lab, USU; Vision of HPC in Agriculture and Life Sciences, Rodney J. Brown, Dean, College of Agriculture & Biology, BYU; Simulation of Large Scale Spatial Evolutionary Processes, Mark P. Miller, Assistant Professor, Biology Department & HPC@USU; Application of HPC in Geophysics, William P. Johnson, Professor Geology & Geophysics. University of Utah Panel Discussions: Opportunities for HPC in Agricultural Research transcript - Rodney J. Brown, Dean College of Agriculture & Biology, BYU Moderator - Colien Hefferan, Administrator CSREES - Harold M. van Es, Int'l Professor, Corp & Soil Sciences Cornell University - William P. Johnson, Professor Geology & Geophysics, University of Utah - Steven R. Larson, Research Geneticist, Forage & Range Research Lab, USU; Bringing HPC to New Research Communities ppt transcript - Linda Callahan, Executive Director Cornell Theory Center Moderator - Frank Williams, Director Arctic Region Supercomputing Center - John Hanks, System Administrator HPC@USU - Mark P. Miller, Biology Department & HPC@USU. Workshops and tutorials: Scientific Computing 101 - Mark Miller & Sarah Moody, Visualization 101 - Michal Hardisky & Sarah Moody pdf; Parallel Computing 101 - Mark Perl, Mark Miller, & Sarah Moody pdf; We also developed the spatial genetics infrastructure and the pore scale simulation code. Two conference presentations were presented about the pore scale transport code. We created a new visualization environment together with a large storage and backup facility. PARTICIPANTS: Thomas Hauser - PI, organizer of the ACRES symposium; Mark Miller - Co-PI, development of the spatial genetics simulation infrastructure; John Hanks - system administrator, installation and development of the storage, network and visualization infrastructure; Jeffrey Allen - graduate student, postdoctoral researcher, development of the pore scale simulation code in OpenFOAM; Barbara Sidwell - office assistant, coorganization of the ACRES symposium, assisting the PI; Sarah Moody - graduate student, tutorials on scientific computing; Daniel Schauerhamer - graduate student, particle simulations; Sandeep Buddala - graduate student, development of packed column algorithms to achieve prescribed porosity; Todd Johansen - graduate student, optimization; Kari Johnson - student, optimization and development of the spatial genetics simulation code; Scott Nielson -student, assisting John Hanks in storage infrastructure; and Scott Ripplinger - student, additional models in the pore scale simulation code. TARGET AUDIENCES: Aricultural and life science students and researchers. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
- Increase the awareness of agricultural researchers and students about high performance computing through tutorials. - Enable new research through development of a storage and stereo visualization environment. - One is a new spatial genetics simulation code which is an example of how to efficiently develop scientific programs and make use of the hpc infrastructure for other similar problems. - Simulation code to study small particle transport on a pore scale level.
Publications
- Hauser, T., J. Allen 2007. foamDSCM - a DSMC solver for rarefied flow applications based. 1st International OpenFoam Conference.
- Hauser, T. and J.B. Allen 2007. Numerical simulation of the behavior and mobilization of fine-grained quartz particles in porous media with OpenFOAM. 1st International OpenFoam Conference.
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Progress 07/15/06 to 07/14/07
Outputs
1. Simulation of spatial genetic processes. Although challenges associated with understanding mechanisms of introgression between crop and wild plant varieties appears daunting, we note that the principle evolutionary mechanisms associated with the discipline of population genetics is well equipped to address this phenomenon. In population genetics, factors such as genetic drift, gene flow, mutation, and natural selection work in concert to determine the long term fates of genetic variants within populations and species. We have implemented a procedure to start simulations to answer some of these questions. 2. Pore scale simulations. We implemented a numerical code for numerical simulations in order to evaluate the mobilization and behavior of fine grained, quartz particles with silica grains within an aqueous solution. The colloidal and shear forces were computed in accordance with established methods and validated with available literature. These, along with the drag
and net 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 IcoLagrangianFoam solver, greatly facilitated the creation of the numerical algorithm. The results were validated from the empirical, 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 constituted a repulsive response. Whereas, for low values of pH and high levels of electrolyte concentration, the attractive Van der Waals force dominated, and particle deposition was witnessed. Both two and three dimensional simulations were performed. 3. Symposium "Challenges and Opportunities for High Performance Computing in Agriculture". A symposium together
with workshops was organized. The agenda is given below and the slides of the presentations are at www.hpc.usu.edu. Monday, March 26, 2007 09:30-11:30 Workshop: Scientific Computing using Python 09:30-11:30 Roundtable: Utah HPC Infrastructure 11:45-12:45 Welcome Lunch 01:00-01:45 Keynote Address Dr. Colien Hefferan, administrator of CSREES 01:45-03:15 Presentations: HPC in Agriculture 03:15-03:45 Refreshment Break 03:45-05:00 Panel discussion: Application of HPC in Agricultural Research 06:00-08:00 Dinner Tuesday, March 27, 2007 08:00-08:30 Continental Breakfast 08:30-11:00 Technical & Industry Presentations 11:00-12:30 Panel discussion: Bringing HPC to New Research Communities 12:30-01:30 Closing Remarks and Luncheon 02:00-03:00 Workshop: Visualization 03:00-04:00 Workshop: Parallel Computing 101.
Impacts
This project has started to introduce HPC to the Agricultural community. The workshops educate students and faculty about the possibilities of HPC in agricultural research.
Publications
- No publications reported this period
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