Rita V. Rodriguez CNS Division Of Computer and Network Systems
CSE Direct For Computer & Info Scie & Enginr
September 1, 2012
August 31, 2015 (Estimated)
Awarded Amount to Date:
Jill Gemmill firstname.lastname@example.org (Principal Investigator)
Amy Apon (Former Principal Investigator)
Walter Ligon (Co-Principal Investigator) Steven Stuart (Co-Principal Investigator) Melissa Smith (Co-Principal Investigator)
Jill Gemmill (Former Co-Principal Investigator)
300 BRACKETT HALL
SPECIAL PROJECTS - CISE,
MAJOR RESEARCH INSTRUMENTATION
Program Reference Code(s):
1189, 9150, 9251
Program Element Code(s):
1714, 7726, 1189
Proposal #: 12-28312
PI(s): Apon, Amy W.
Gemmill, Jill; Ligon, Walter B.; Smith, Melissa C.; Stuart, Steven J.
Institution: Clemson University
Title: MRI/Acq.: High Performance Computing Instrument for Collaborative Data-Enabled Science
This project, acquiring a high performance computing (HPC) for collaborative data-enabled science, aims to enable fundamental and applied research in areas of experimental HPC, including scalable file systems, accelerator technologies, middleware architectures, and cluster scheduling policies. The instrument will be used as a production resource to support several compelling science applications in materials and biomolecular modeling, bioinformatics (and others) and will contribute a significant new component of the institution?s well established and managed Palmetto cluster while providing critically needed file storage, and accelerator systems not currently available. Supported projects include:
- Scalable file system implementation,
- Exploiting and analyzing concurrency in heterogeneous computing environments,
- High performance cluster modeling, analysis, and characterization,
- File replication and consistency maintenance,
- Cloud architecture,
- Properties of advanced materials and biomolecular systems,
- Molecular dynamic simulation studies of poly-dots, new light-emitting nanoparticles,
- Biomolecular evolution,
- Optimizing catalysts for direct chemical remediation from water,
- Protein-surface interactions,
- Map/Reduce framework for next generation sequencing data assembly,
- Searching for identification of significantly conserved protein blocks,
- Digital manufacturing,
- Statistical inference in nonparametrics models of production,
- Analysis of the structures of hospital and banking industries,
- Multiple scatter rendering,
- Digital scholarship, and
- Applications of computing to the geosciences.
Regular planned input from the scientific team is expected to facilitate the development of policies for use of the instrument as a test bed for experimental high performance computing systems research as well as a shared production resource for scientific applications.
The instrument serves as a tool for the collaborative team that includes more than 20 faculty from 4 institutions, and more than 250 graduate and undergraduate students. The system will also be utilized by the already established ?Desktop to Teragrid? program that reaches more than a dozen universities across South Carolina, an EPSCoR state, and with regional partners. The proposal team includes 6 women senior personnel. The institution has outreach, education, and training activities, and has engaged SC?s only public HBCU, South Carolina State University, as well as other minority institutions within the region. Development of interdisciplinary curricula will support computational and data-enabled science and engineering.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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Chen Lu, Jason Schwier, Ryan Craven, Yu Lu, R. R. Brooks and Christopher Griffin, Brooks. "A Normalized Statistical Metric Space for Markov Models," IEEE Transactions on Cybernetics, v.43, 2013, p. 806.
Yu Lu, Jason Schwier, Ryan Craven, R. R. Brooks, and Christopher Griffin. "Inferring Statistically Significant Hidden Markov Models," IEEE Transactions on Knowledge and Data Engineering, v.25, 2013, p. 1548.
Abramyan, T., Collier, G., Kucukkal, T.G., Li, X., Snyder, J.A., Thyparambil, A.A., Vellore, N.A., Wei, Y., Yancey, J.A., Stuart, S.J., and Latour R.A.,. "Understanding Protein-Surface Interactions at the Atomistic Level Through the Synergistic Development of Experimental and Molecular Simulation Methods," American Chemical Society, v.Protein, 2012, p. 197.
J. A. Snyder, T. Abramyan, J. A. Yancey, A. A. Thyparambil, Y. Wei, S. J. Stuart, and R. A. Latou. "Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass," Biointerphases, v.7, 2012.
3. Stephen P. Ficklin and F. Alex Feltus. "A Systems-Genetics Approach and Data Mining Tool For the Discovery of Genes Underlying Complex Traits in Oryza Sativa," PloS ONE, v.8, 2013.
F. Alex Feltus, Stephen P. Ficklin, Scott M Gibson, and Melissa C. Smith. "Maximizing Capture of Gene Co-expression Relationships Through Pre-Clustering of Input Expression Samples: An Arabidopsis Case Study," BMC Systems Biology, v.7, 2013.
Jacob B Spangler and F. Alex Feltus.. "Conserved Noncoding Sequences are Associated with Rates of mRNA Decay in Arabidopsis.," Frontiers in Plant Science, 2013.
6. Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C. "The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color," Genome Biology, v.14, 2013.
Joshua P. Vandenbrink, Andrew H. Paterson, KC Das, Roger N. Hilten, and F. Alex Feltus. "Quantitative Models of Hydrolysis Conversion Efficiency and Biomass Crystallinity Index for Plant Breeding.," Plant Breeding, v.132, 2013, p. 252.
Scott M. Gibson, Stephen P. Ficklin, Sven Isaacson, Feng Luo, F. Alex Feltus, Melissa C. Smith. "Massive-Scale Gene Co-expression Network Construction and Robustness Testing using Random Matrix Theory," PLoS ONE, v.2, 2013.
F. Alex Feltus and Joshua P. Vandenbrink. "Bioenergy Grass Feedstock: Current options and prospects for improvement using emerging genetic, genomic, and systems biology toolkits.," Biotechnology for Biofuels, v.5, 2012.
Jacob B. Spangler, Stephen P. Ficklin, Feng Luo, Michael Freeling and F. Alex Feltus. "Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-expressed Gene Modules.," PLoS ONE 7, v.9, 2012.
Snyder J.A., Abramyan T., Yancey J.A., Stuart S.J., Latour R.A. "Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass," Biointerphases, v.7:1-4, 2012, p. 12.
Joshua P. Vandenbrink, Andrew H. Paterson, Lori Goff, Wenqian Kong, Huizhe Jin and F. Alex Feltus. "Identification of Bioconversion Quantitative Trait Loci in the Interspecific Bioenergy Grass Cross Sorghum bicolor x Sorghum propinquum," Theoretical and Applied Genetics, 2013.
V.K. Pallipuram, M.C. Smith, N. Raut, and X.Ren. "A Regression-Based Heterogeneous Performance Prediction Framework for GPGPU Clusters," Concurrency and Computation: Practice and Experience, v.26, 2014.
. Belenli, S. Kaya, L. Rebholz, and N. Wilson. "A subgrid stabilization finite element method for incompressible magnetohydrodynamics," International Journal of Computer Mathematics, v.90, 2013, p. 1506.
A. Bowers and L. Rebholz. "Numerical study of a regularization model for incompressible flow with deconvolution-based adaptive nonlinear filtering," Computer Methods in Applied Mechanics and Engineering,, v.258, 2013, p. 1.
A. Bowers, S. Le Borne, and L. Rebholz. "Error analysis and iterative solvers for Navier-Stokes projection methods with standard and sparse grad-div stabilization," Computer Methods in Applied Mechanics and Engineering,, v.275, 2014, p. 1.
A. Bowers, T.-Y. Kim, M. Neda, L. Rebholz, and E. Fried. "The Leray-$\alpha\beta$-deconvolution model: energy analysis and numerical algorithms," Applied Mathematical Modelling, v.37, 2013, p. 1225.
A. Linke and L. Rebholz. "On a reduced sparsity stabilization of grad-div type for incompressible flow problems," Computer Methods in Applied Mechanics and Engineering, v.261, 2013, p. 142.
A. W. Apon, L. B. Ngo, M. E. Payne, P. W. Wilson. "Assessing the Effect of High Performance Computing Capabilities on Academic Research Output.," Journal of Empirical Economics, v.48, 2014, p. 283.
B. Cousins, S. Le Borne, A. Linke, L. Rebholz, and Z. Wang. "Efficient linear solvers for incompressible flow simulations using Scott-Vogelius finite elements," Numerical Methods for Partial Differential Equations, v.29, 2013, p. 1217.
Cameron J. Bodenschatz, Sapan Sarupria, Rachel B. Getman. "Molecular-Level Details about Liquid H2O Interactions with CO and Sugar Alcohol Adsorbates on Pt (111) Calculated Using Density Functional Theory and Molecular Dynamics," Journal of Physical Chemistry, v.C, 2015, p. 13642.
Chengjian Li, Gang Li, Huijuan Zhao. "Hydrogenation Induced Deformation Mode and Thermal conductivity Variation in Graphene Sheets," CARBON, v.72, 2014, p. 185.
Chengjian Li, Gang Li, Huijuan Zhao. "Thermal Conductivity Variation of Graphene with Patterned Double-Side Hydrogenation," Journal of Applied Physics, v.118, 2015, p. 075102.
E. Jenkins, V. John, A. Linke and L. Rebholz. "On the parameter choice in grad-div stabilization for incompressible flow problems," Advances in Computational Mathematics, v.40, 2014, p. 491.
Haiying Shen, Guoxin Liu, Jill Gemmill, Lee Ward. "A P2P-based Infrastructure for Adaptive Trustworthy and Efficient Communication in Wide-Area Distributed Systems," IEEE Transactions on Parallel and Distributed Systems, v.25, 2014, p. 2222.
Haiying Shen, Guoxin Liu, Jill Gemmill, Lee Ward.. "A P2P-based Infrastructure for Adaptive Trustworthy and Efficient Communication in Wide-Area Distributed Systems," IEEE Transactions on Parallel and Distributed Systems, v.25, 2013, p. 2222.
Huijuan Zhao. "Strain and Chirality Effects on the Mechanical and Electronic Properties of Silicene and Silicane under Uniaxial Tension," Physics Letters A, v.376, 2012, p. 3545.
Ilker Ozcelik, Richard R. Brooks. "Deceiving entropy based DoS detection," Computers & Security, v.48, 2015.
Jaewoong Hur and Steven J. Stuart. "Modified reactive empirical bond-order potential for heterogeneous bonding environments," The Journal of Chemical Physics, 2012, p. 054102.
Joshua P. Vandenbrink, Andrew H. Paterson, KC Das, Roger N. Hilten, and F. Alex Feltus. "Tissue specific analysis of hydrolysis related traits and pretreatment efficacy in the bioenergy grass Sorghum bicolor," Industrial Crops & Products, v.50, 2013, p. 118.
K. Galvin, L. Rebholz, and C. Trenchea. "Efficient, unconditionally stable, and optimally accurate FE algorithms for approximate deconvolution models," SIAM Journal on Numerical Analysis, v.52, 2014, p. 678.
S. Dey A. Gupte. "Analysis of MILP techniques for the Pooling problem," Operations Research, v.43, 2015, p. 412.
T. Heister, M. Olshanskii, L. Rebholz, and K. Galvin. "Natural vorticity boundary conditions on solid walls," Computer Methods in Applied Mechanics and Engineering, v.297, 2015, p. 18.
Yingbo Li and Robert Lund. "Multiple Changepoint Detection Using Metadata," Journal of Climate, v.28, 2015, p. 4199.
Yingye Gan, Huijuan Zhao. "Chirality Effect of Mechanical and Electronic Properties of Monolayer MoS2 with Vacancies," Physics Letters A, v.378, 2014, p. 2910.