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UMBC High Performance Computing Facility
Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available in Spring 2014. Currently, the cluster tara is still available. Please see the 2013 Resources Pages under the Resources tab.
HPCF Publications
This page lists publications from use of HPCF as well as technical reports of papers on all aspects of scientific computing and their applications, with links to preprints/reprints whenever possible. Please send your submissions in PDF form to the chair of the user committee, Matthias K. Gobbert. In particular, all publications involving use of machines in HPCF are required to be submitted for inclusion here and will be flagged accordingly.
2014
[1] Joseph P. Cornish, Neus Sanchez-Alberola, Patrick K. ONeill, Ronald O'Keefe, Jameel Gheba, and Ivan Erill. Characterization of the SOS meta-regulon in the human gut microbiome. Bioinformatics, 2014. (HPCF machines used: tara.). [ bib | http ]
[2] David Stonko, Michelle Starz-Gaiano, and Bradford E. Peercy. Implementing a numerical package to model collective cell migration. Technical Report HPCF-2014-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.). [ bib | .pdf ]
[3] Andrew M. Raim. Computational Methods in Finite Mixtures using Approximate Information and Regression Linked to the Mixture Mean. Ph.D. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2014. (HPCF machines used: tara.). [ bib ]
2013
[1] Sai K. Popuri, Andrew M. Raim, Nagaraj K. Neerchal, and Matthias K. Gobbert. An implementation of binomial method of option pricing using parallel computing. Technical Report HPCF-2013-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[2] Andrew M. Raim. Introduction to distributed computing with pbdR at the UMBC High Performance Computing Facility. Technical Report HPCF-2013-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
Files for download with this report: pbdRtara2013.tar.gz
[3] B. C. Davis and I. F. Thorpe. Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase. Proteins: Structure, Function and Bioinformatics, 81:40-52, 2013. (HPCF machines used: tara.). [ bib | http ]
[4] I. E. Weidlich, I. V. Filippov, J. Brown, N. Kaushik-Basu, R. Krishnan, M. C. Nicklaus, and I. F. Thorpe. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorganic and Medicinal Chemistry, 21:3127-3137, 2013. (HPCF machines used: tara.). [ bib | http ]
[5] M. Fioravante, A. Shook, I. F. Thorpe, and P. Rheingans. Visualizing motional correlations in molecular dynamics using geometric deformations. Computer Graphics Forum, 32(3pt3):311-320, 2013. (HPCF machines used: tara.). [ bib | http ]
[6] B. C. Davis and I. F. Thorpe. Molecular simulations illuminate the role of regulatory components of the RNA polymerase from hepatitis C virus in influencing protein structure and dynamics. Biochemistry, 52(26):4541-4552, 2013. (HPCF machines used: tara.). [ bib | http ]
[7] Jonas Schäfer, Xuan Huang, Stefan Kopecz, Philipp Birken, Matthias K. Gobbert, and Andreas Meister. A memory-efficient finite volume method for advection-diffusion-reaction systems with non-smooth sources, submitted, 2013. (HPCF machines used: tara.). [ bib ]
[8] Samuel Khuvis. Efficiency improvements in numerical methods for studying connectivity in a model of a pancreatic islet of heterogeneous beta cells. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib ]
[9] Jonas Schäfer. Investigation of performance of Krylov subspace methods for stationary and time-dependent reaction-advection-diffusion equations discretized by the finite volume method. Diploma thesis, University of Kassel, Germany, 2013. (HPCF machines used: tara.). [ bib ]
[10] Nil Mistry, Jordan Ramsey, Benjamin Wiley, Jackie Yanchuck, Xuan Huang, Andrew Raim, Matthias K. Gobbert, Nagaraj K. Neerchal, and Philip J. Farabaugh. Clustering of multidimensional data sets with applications to spatial distributions of ribosomal proteins. Technical Report HPCF-2013-10, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[11] Matthew G. Bachmann, Ashley D. Dyas, Shelby C. Kilmer, Julian Sass, Andrew Raim, Nagaraj K. Neerchal, Kofi P. Adragani, George Ostrouchov, and Ian F. Thorpe. Block cyclic distribution of data in pbdR and its effects on computational efficiency. Technical Report HPCF-2013-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[12] William J. Bailey, Claire A. Chambless, Brandynne M. Cho, Jesse D. Smith, Andrew M. Raim, Kofi P. Adragani, and Ian F. Thorpe. Identifying nonlinear correlations in high dimensional data with application to protein molecular dynamics simulations. Technical Report HPCF-2013-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[13] Nil Mistry, Jordan Ramsey, Benjamin Wiley, Jackie Yanchuck, Xuan Huang, Matthias K. Gobbert, Christopher Mineo, and David Mountain. Contention of communications in switched networks with applications to parallel sorting. Technical Report HPCF-2013-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[14] Gemma Gearhart, Shuai Jiang, Thomas J. May, Jane Pan, Samuel Khuvis, Matthias K. Gobbert, Bradford E. Peercy, and Arthur Sherman. Investigating oscillation loss in computational islets. Technical Report HPCF-2013-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[15] J. P. Cornish, N. Sanchez-Alberola, P. K. O'Neill, R. O'Keefe, J. Gheba, and I. Erill. The SOS response of the human gut microbiome, submitted to Biology Direct, 2013. (HPCF machines used: tara.). [ bib ]
[16] P. K. O'Neill, R. Forder, and I. Erill. Informational requirements for transcriptional regulation, submitted to Journal of Computational Biology, 2013. (HPCF machines used: tara.). [ bib ]
[17] X. Huang, S. Khuvis, S. Askarian, M. K. Gobbert, and B. E. Peercy. Coupled PDEs with initial solution from data in COMSOL 4. In Jinlan Huang, editor, Proceedings of the COMSOL Conference 2013, Boston, MA, 2013. (HPCF machines used: tara.). [ bib | .pdf ]
[18] Zana A. Coulibaly, Bradford E. Peercy, and Matthias K. Gobbert. Insight into spontaneous recurrent calcium waves in a 3-D cardiac cell based on analysis of a 1-D deterministic model. Submitted. [ bib ]
[19] Andrew M. Raim and Nagaraj K. Neerchal. Modeling overdispersion in binomial data with regression linked to a finite mixture probability of success. In JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association, 2013. (Submitted). [ bib | preprint | http ]
[20] Andrew M. Raim, Minglei Liu, Nagaraj K. Neerchal, and Jorge G. Morel. On the method of approximate Fisher scoring for finite mixtures of multinomials. Statistical Methodology, 18:115-130, 2014. (HPCF machines used: tara.). [ bib | preprint | http ]
[21] Hui Guo, Xiang Li, and Douglas D. Frey. Development of chromatofocusing techniques employing mixed-mode column packings for protein separations. Journal of Chromatography A, 1323:57-65, 2014. (HPCF machines used: tara.). [ bib | http ]
2012
[1] Yu Wang, Marc Olano, Matthias K. Gobbert, and Wesley Griffin. A GPU memory system comparison for an elliptic test problem. Technical Report HPCF-2012-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[2] D. Wicks Kollonige, L. C. Sparling, P. Sawamura, B. Baker, and S. G. Trahan. A case study of complex stratospheric influence on U.S. surface air quality in February 2010, 2012. Submitted. (HPCF machines used: tara.). [ bib ]
[3] V. K. Gupta K. B. Neeves and C. D. Eggleton. Single-molecule dynamic force spectroscopy on live cells, 2012. Submitted. (HPCF machines used: tara.). [ bib ]
[4] V. K. Gupta and C. D. Eggleton. A theoretical method to determine unstressed o-rate from multiple bond rupture force spectroscopy, 2012. Submitted. (HPCF machines used: tara.). [ bib ]
[5] Matthew W. Brewster. Study of free alternative numerical computation packages. SIAM Undergraduate Research Online (SIURO), 5, 2012. (HPCF machines used: tara.). [ bib | preprint | .pdf ]
[6] Jonas Schäfer. Performance studies for the two-dimensional Poisson problem discretized by finite differences. Technical Report HPCF-2012-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[7] Sai K. Popuri, Andrew M. Raim, Matthew W. Brewster, and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, Scilab, and R on tara. Technical Report HPCF-2012-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[8] Randal McKissack. Cluster computing using Intel Concurrent Collections. Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[9] Robert Forder. Simulating the evolution of transcriptional regulatory motifs. Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[10] Ecaterina Coman. IDL: A possible alternative to Matlab? Senior Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[11] Jordan B. Angel, Amy M. Flores, Justine S. Heritage, Nathan C. Wardrip, Andrew M. Raim, Matthias K. Gobbert, Richard C. Murphy, and David J. Mountain. Graph 500 performance on a distributed-memory cluster. Technical Report HPCF-2012-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .html | .pdf ]
[12] Rosemary K. Le, Christopher V. Rackauckas, Anne S. Ross, Nehemias Ulloa, Sai K. Popuri, Nagaraj K. Neerchal, and Brian R. Smith. Water quality monitoring of Maryland's tidal waterways. Technical Report HPCF-2012-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. In Progress. (HPCF machines used: tara.). [ bib | .html | .pdf ]
[13] Annie Castner, Jenny Louthan, Edwardo Rivera, Christian Weigandt, Jonathan S. McHenry, Nagaraj K. Neerchal, Matthias K. Gobbert, and Michael Dillon. Simulation of a university as a dynamical system. Technical Report HPCF-2012-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. In Progress. (HPCF machines used: tara.). [ bib | .html | .pdf ]
[14] Andrew M. Raim, Minglei Liu, Nagaraj K. Neerchal, and Jorge G. Morel. An Approximate Fisher Scoring Algorithm for finite mixtures of multinomials. Technical Report HPCF-2012-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
[15] Ecaterina Coman, Matthew W. Brewster, Sai K. Popuri, Andrew M. Raim, and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, Scilab, R, and IDL on tara. Technical Report HPCF-2012-15, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib | .pdf ]
Files for download with this report: ComanHPCF2012/
[16] Yu Wang, Marc Olano, Matthias K. Gobbert, and Wesley Griffin. Parallel computing for long-time simulations of calcium waves in a heart cell. PAMM Proc. Appl. Math. Mech., 12(1):637-638, 2012. (HPCF machines used: tara.). [ bib | reprint | http ]
[17] Aaron Churchill, Guan Wang, Matthias K. Gobbert, and Thomas I. Seidman. Efficient simulation of a reaction-diffusion system with a fast reaction in the asymptotic limit. (HPCF machines used: tara.), submitted, 2012. [ bib | .pdf ]
[18] Rosemary K. Le, Christopher V. Rackauckas, Anne S. Ross, and Nehemias Ulloa. Assessment of statistical methods for water quality monitoring in Maryland's tidal waterways. SIAM Undergraduate Research Online (SIURO), 6, 2013. (HPCF machines used: tara.). [ bib | preprint | .pdf ]
[19] Matthew Brewster. Alternatives to the mathematical software package MATLAB in research and education. UMBC Review: Journal of Undergraduate Research, 14:50-65, 2013. (HPCF machines used: tara.). [ bib ]
[20] Jordan B. Angel, Amy M. Flores, Justine S. Heritage, Nathan C. Wardrip, Andrew M. Raim, Matthias K. Gobbert, Richard C. Murphy, and David J. Mountain. The Graph 500 benchmark on a medium-size distributed-memory cluster with high-performance interconnect. 2012. Submitted. (HPCF machines used: tara.). [ bib | .pdf ]
[21] Alex C. Szatmary. Deformation and motion of cells and biological capsules in fluid flow, investigated with numerical methods. Ph.D. Thesis, Department of Mechanical Engineering, University of Maryland, Baltimore County, 2012. (HPCF machines used: tara.). [ bib ]
2011
[1] Robert Forder. A parallel simulation of the evolution of transcription factor binding sites. Technical Report HPCF-2011-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .pdf ]
[2] Amanda Peterson. Parameter estimation for the Dirichlet-multinomial distribution. Technical Report HPCF-2011-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .pdf ]
[3] Alex C. Szatmary and Charles D. Eggleton. Elastic capsule deformation in general irrotational linear flows. Fluid Dynamics Research, 44(5), 2012. (HPCF machines used: tara.). [ bib | http ]
[4] F. Jacobsen and K.E. Omland. Species tree inference in a recent radiation of orioles (genus icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group. Molecular Phylogenetics and Evolution, 61:460-469, 2011. [ bib | http ]
[5] T. Tesfa, D. G. Tarboton, D. W. Watson, K. A.Schreuders, M. E. Baker, and R. M. Wallace. Extraction of hydrological proximity measures from dems using parallel processing. Environmental Modeling and Software, 26(12):1696-1709, 2011. [ bib | http ]
[6] D. E. Weller, M. E. Baker, and T. E. Jordan. Empirical tests for effects of riparian buffers on watershed nitrate discharges. Ecological Applications, 21(5):1679-1695, 2011. [ bib ]
[7] Hafez Tari, H.-J. Su, and J.D. Hauenstein. Classification and complete solution of the kinetostatics of a compliant Stewart-Gough platform. Mechanism and Machine Theory, 49:177-186, 2012. (HPCF machines used: tara.). [ bib | http ]
[8] R. S. King, M. E. Baker, P. F. Kazyak, and D. E. Weller. How novel is too novel? stream community thresholds at exceptionally low levels of catchment urbanization. Ecological Applications, 21(5):1659-1678, 2011. [ bib | DOI ]
[9] Joseph Cornish, Robert Forder, Ivan Erill, and Matthias K. Gobbert. Simulation of the evolution of information content in transcription factor binding sites using a parallelized genetic algorithm. Technical Report HPCF-2011-9, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .pdf ]
[10] Matthew Brewster and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, and Scilab on tara. Technical Report HPCF-2011-10, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .pdf ]
Files for download with this report: BrewsterGobbertTR2011/
[11] Samantha Allen, Dorothy Kirlew, Neil Obetz, Derek Wade, April Albertine, Nagaraj K. Neerchal, and Martin Klein. Assessment of simple and alternative bayesian ranking methods utilizing parallel computing. Technical Report HPCF-2011-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .html | .pdf ]
[12] Jeremy Bejarano, Koushiki Bose, Tyler Brannan, Anita Thomas, Kofi Adragni, Nagaraj K. Neerchal, and George Ostrouchov. Sampling within k-means algorithm to cluster large datasets. Technical Report HPCF-2011-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .html | .pdf ]
[13] Andrew Coates, Alexey Ilchenko, Matthias K. Gobbert, Nagaraj K. Neerchal, Patrick O'Neill, and Ivan Erill. Optimization of computations used in information theory applied to base pair analysis. Technical Report HPCF-2011-13, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .html | .pdf ]
Files for download with this report: EHn.py, EHn.m, EHn.c, EHn.h, Makefile,
[14] Richard Adjogah, Randal Mckissack, Ekene Sibeudu, Andrew M. Raim, Matthias K. Gobbert, and Loring Craymer. Intel Concurrent Collections as a method for parallel programming. Technical Report HPCF-2011-14, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .html | .pdf ]
Files for download with this report: REU2011Team4_code.tgz
[15] Samuel Trahan. Multi-Scale Analysis of Observations of Tropical Cyclones with Applications to High-Resolution Hurricane Modeling. Ph.D. Thesis, Department of Physics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib ]
[16] Samuel Trahan and Lynn Sparling. An analysis of NCEP tropical cyclone vitals and potential effects on forecasting models. Weather and Forecasting, 27:744-756, 2012. (HPCF machines used: tara.). [ bib | http ]
[17] Mattie K. B. Whitmore. Modeling and simulation of groundwater flow and contaminant transport in a cross-section of the delmarva peninsula. M.S. Thesis, Department of Mathematics and Statistics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib ]
[18] David W. Trott and Matthias K. Gobbert. Finite element convergence for time-dependent PDEs with a point source in COMSOL 4.2. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2011, Boston, MA, 2011. (HPCF machines used: tara.). [ bib | http | .pdf ]
[19] Mattie K. B. Whitmore, David W. Trott, Bradford E. Peercy, Matthew E. Baker, and Matthias K. Gobbert. COMSOL modeling of groundwater flow and contaminant transport in two-dimensional geometries with heterogeneities. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2011, Boston, MA, 2011. (HPCF machines used: tara.). [ bib | .pdf ]
[20] N. Petra, J. Zweck, S. E. Minkoff, A. A. Kosterev, and J. H. Doty III. Modeling and design optimization of a resonant optothermoacoustic trace gas sensor. SIAM J. Applied Mathematics, 71:309-332, 2011. (HPCF machines used: tara.). [ bib | http ]
[21] N. Petra, J. Zweck, S. E. Minkoff, A. A. Kosterev, and J. H. Doty III. Validation of a model of a resonant optothermoacoustic trace gas sensor. In Conference on Lasers and Electro-Optics, Baltimore, MD, 2011. (HPCF machines used: tara.). [ bib ]
[22] J. Zweck and C. R. Menyuk. A chromatic dispersion estimation method for arbitrary modulation formats. In Conference on Lasers and Electro-Optics, Baltimore, MD, 2011. (HPCF machines used: tara.). [ bib ]
[23] Andrei Draganescu. Multigrid preconditioning of linear systems for semismooth Newton methods applied to optimization problems constrained by smoothing operators. Optimization Methods and Software, 2011. Submitted. (HPCF machines used: tara). [ bib ]
[24] V. K. Gupta and C. D. Eggleton. A theoretical method to determine unstressed off-rate from multiple bond rupture force spectroscopy. J. Chemical Physics, 2011. Submitted. (HPCF machines used: tara). [ bib ]
[25] M. A. Talukder and C. R. Menyuk. Temperature-dependent coherent carrier transport in quantum cascade lasers. New J. Phys., 13:083027, 2011. (HPCF machines used: tara.). [ bib | http | .pdf ]
[26] Michael Curtis. A collaborative filtering model: Statistical properties of alternating least squares. UMBC Review: Journal of Undergraduate Research and Creative Works, 13:10-21, 2012. (HPCF machines used: tara.). [ bib | preprint ]
[27] Thomas I. Seidman, Matthias K. Gobbert, David W. Trott, and Martin Kružík. Finite element approximation for time-dependent diffusion with measure-valued source. Numer. Math., 122(4):709-723, 2012. (HPCF machines used: tara.). [ bib | preprint | http ]
[28] R. Chris Wilson. Multivariate Retrieval of Carbon Monoxide. Ph.D. Thesis, Department of Physics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib | .pdf ]
[29] J. H.Lowry, M. E. Baker, and R. D. Ramsey. Determinants of urban tree canopy in residential neighborhoods: household characteristics, urban form, and the geophysical landscape. Urban Ecosystems, pages 1-20, 2011. [ bib | DOI ]
[30] R. S. King and M. E. Baker. An alternative view of ecological community thresholds and appropriate analyses for their detection: comment. Ecological Applications, pages 2833-2839, 2011. [ bib | DOI ]
[31] P. Budy, M. Baker, and S. K. Dahle. Predicting fish growth potential and identifying water quality constraints: a spatially-explicit bioenergetics approach. Environmental Management, 48(4):691-709, 2011. [ bib | DOI ]
[32] F. Hilton, R. Armante, T. August, C. Barnet, A. Bouchard, C. Camy-Peyret, V. Capelle, L. Clarisse, C Clerbaux, P. Coheue, A. Collard, C. Crevoisier, G. Dufour, D. Edwards, F. Faijan, N. Fourrie, A. Gambacorta, M. Goldberg, V. Guidard, D. Hurtmans, S. Illingworth, N. Jacquinet-Husson, T. Kerzenmacher, D. Klaes, L. Lavanant, G. Masiello, M. Matricardi, A. McNally, S. Newman, E. Pavelin, S. Payan, E. Pequignot, S. Peyridieu, T. Phulpin, J. Remedios, P. Schlussel, C. Serio, L. Strow, C. Stubenrauch, J. Taylor, D. Tobin, W. Wolf, and D. Zhou. Hyperspectral earth observation from IASI: five years of accomplishments. Bull. Amer. Met. Soc., 93:347-370, 2012. (HPCF machines used: tara.). [ bib | http ]
[33] L. N. Yurganov, V. Rakitin, A. Dzhola, T. August, E. Fokeeva, M. George, G. Gorchakov, E. Grechko, S. Hannon, A. Karpov, L. Ott, E. Semutnikova, R. Shumsky, and L. Strow. Satellite- and ground-based CO total column observations over 2010 russian fires: accuracy of top-down estimates based on thermal IR satellite data. Atmospheric Chemistry & Physics, 11:7925-7942, 2011. (HPCF machines used: tara.). [ bib | http ]
[34] D. K. Zhou, A. M. Larar, X. Liu, W. L. Smith, L. L. Strow, P. Yang, P. Schlussel, and X. Calbet. Global land surface emissivity retrieved from satellite ultraspectral IR measurements. IEEE Transactions on Geoscience and Remote Sensing, 49:1277-1290, 2011. (HPCF machines used: tara.). [ bib ]
[35] Zhibo Zhang, Steven Platnick, Andrew Ackerman, Graham Feingold, Toshi Matsui, Laurent C-Labonnote, Cornet, and Jerome Riedi. Simulating the radiative and polarization characteristics of drizzling warm clouds using LES and 3-D radiative transfer models. In AGU Annual Fall Meeting, San Francisco, 2011. (HPCF machines used: tara.). [ bib ]
[36] D. Wicks Kollonige. The Impact of Upper Tropospheric Dynamics on Surface Air Quality of the United States. Ph.D. Thesis, Department of Physics, University of Maryland, Baltimore County, 2011. (HPCF machines used: tara.). [ bib ]
[37] V. K. Gupta and C. D. Eggleton. Effect of cell and microvillus mechanics on the transmission of applied loads to single bonds in dynamic force spectroscopy. Phys. Rev. E., 84(1), 2011. [ bib ]
2010
[1] Hafez Tari, Hai-Jun Su, and Tien-Yien Li. A constrained homotopy technique for excluding unwanted solutions from polynomial equations arising in kinematics problems. Mechanism and Machine Theory, 45(6):898-910, 2010. UMBC High Performance Computing Facility HPCF-2010-1 (HPCF machines used: hpc.). [ bib ]
[2] Andrew M. Raim and Matthias K. Gobbert. Parallel performance studies for an elliptic test problem on the cluster tara. Technical Report HPCF-2010-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[3] Hafez Tari and Hai-Jun Su. Complete solution to the eight-point path generation of slider-crank four-bar linkages. Journal of Mechanical Design, 132(8):081003, 2010. UMBC High Performance Computing Facility HPCF-2010-3 (HPCF machines used: hpc.). [ bib | http ]
[4] Michael Muscedere, Andrew M. Raim, and Matthias K. Gobbert. Parallel performance studies for a parabolic test problem on the cluster tara. Technical Report HPCF-2010-4, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[5] Neeraj Sharma. A comparative study of several numerical computational packages. M.S. Thesis, Applied Mathematics, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib ]
[6] Hafez Tari and Matthias K. Gobbert. A comparative study of the parallel performance of the blocking and non-blocking MPI communication commands on an elliptic test problem on the cluster tara. Technical Report HPCF-2010-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[7] Neeraj Sharma and Matthias K. Gobbert. A comparative evaluation of Matlab, Octave, FreeMat, and Scilab for research and teaching. Technical Report HPCF-2010-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[8] David W. Trott and Matthias K. Gobbert. Finite element convergence studies using COMSOL 4.0a and LiveLink for MATLAB. Technical Report HPCF-2010-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
Files for download with this report: 2dpoisson.mph, driver_getmodel.m, getmodel.m, getmodel_unaltered.m
[9] Andrew M. Raim, Matthias K. Gobbert, Nagaraj K. Neerchal, and Jorge G. Morel. Maximum-likelihood estimation of the random-clumped multinomial model as a prototype problem for large-scale statistical computing. Journal of Statistical Computation and Simulation, 83(12):2178-2194, 2013. (HPCF machines used: tara.). [ bib | preprint | http ]
[10] David W. Trott and Matthias K. Gobbert. Conducting finite element convergence studies using COMSOL 4.0. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2010, Boston, MA, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[11] David W. Trott and Matthias K. Gobbert. Parallel performance studies for a three-species application problem on the cluster tara. Technical Report HPCF-2010-11, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[12] H. H. Aumann and L. L. Strow. Analysis of AIRS and IASI system performance under clear and cloudy conditions. In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7807, 2010. (HPCF machines used: tara.). [ bib ]
[13] A. A. Bradley and S. S. Schwartz. Summary verification measures and their interpretation for ensemble forecasts. Monthly Weather Review, 2010. [ bib ]
[14] V. K. Gupta, I. A. Sraj, K. Konstantopoulos, and C. D. Eggleton. Multi-scale simulation of L-selectin VPSGL-1-dependent homotypic leukocyte binding and rupture. Biomechanics and Modeling in Mechanobiology, 9(5):613-627, 2010. (HPCF machines used: tara.). [ bib ]
[15] M. Habib, A. A. Bradley, S. S. Schwartz, and A. Kruger. Verification of NWS ensemble river forecasts for the Des Moines river. Journal of Hydrometeorology, 2010. In preparation. [ bib ]
[16] A. Seck, C. Welty, and R. M. Maxwell. Considerations in regional integrated hydrologic modeling: Grid resolution, topography, and overland flow processes. In American Geophysical Union, Fall Meeting 2010, 2010. (HPCF machines used: tara.). [ bib ]
[17] I. Sraj, J. Chichester, E. Hoover, R. Jimenez, J. Squier, C. D. Eggleton, and D. W. M. Marr. Cell deformation cytometry using diode-bar optical stretchers. Journal of Biomedical Optics, 15(4):047010, 2010. (HPCF machines used: tara.). [ bib ]
[18] I. Sraj, D. W. M. Marr, and C. D. Eggleton. Linear diode laser bar optical stretchers for cell deformation. Biomedical Optics Express, 1(2):482-488, 2010. (HPCF machines used: tara.). [ bib ]
[19] I. Sraj, A. C. Szatmary, D. W. M. Marr, and C. D. Eggleton. Dynamic ray tracing for modeling optical cell manipulation. Optics Express, 18(16):16702-16714, 2010. (HPCF machines used: tara.). [ bib ]
[20] Hafez Tari and Hai-Jun Su. Complex solution framework for the kinetostatic synthesis of a compliant four-bar mechanism. Mechanism and Machine Theory, 2010. Submitted. (HPCF machines used: tara.). [ bib ]
[21] Sidafa Conde, Teresa Lebair, Christopher Raastad, Virginia Smith, Kyle Stern, David Trott, Matthias K. Gobbert, Bradford E. Peercy, and Arthur Sherman. Enabling physiologically representative simulations of pancreatic beta cells. Technical Report HPCF-2010-21, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[22] Julia Baum, Cynthia Cook, Michael Curtis, Joshua Edgerton, Scott Rabidoux, Andrew Raim, Nagaraj Neerchal, and Robert Bell. Parallelization of matrix factorization for recommender systems. Technical Report HPCF-2010-22, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2010. (HPCF machines used: tara.). [ bib | .pdf ]
[23] N. Petra, A. A. Kosterev, J. Zweck, S. E. Minkoff, and J. H. Doty III. Numerical and experimental investigation of a resonant optothermoacoustic sensor. In Proceedings of the Lasers and Electro-Optics (CLEO) Conference 2010, San Jose, California, 2010. (HPCF machines used: tara.). [ bib ]
[24] F. Jacobsen, N.R. Friedman, and K.E. Omland. Congruence between nuclear and mitochondrial DNA: combination of multiple nuclear introns resolves a well-supported phylogeny of new world orioles (icterus). Molecular Phylogenetics and Evolution, 56:419-427, 2010. [ bib ]
[25] J. X. Warner, Z. Wei, L. L. Strow, C. D. Barnet, L. C. Sparling, G. Diskin, and G. Sachse. Improved agreement of AIRS tropospheric carbon monoxide products with other EOS sensors using optimal estimation retrievals. Atmospheric Chemistry & Physics, 10:9521-9533, 2010. (HPCF machines used: tara.). [ bib ]
2009
[1] Neeraj Sharma and Matthias K. Gobbert. Performance studies for multithreading in Matlab with usage instructions on hpc. Technical Report HPCF-2009-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[2] Amanda K. Gassman and Matthias K. Gobbert. Solving a two-dimensional elliptic model problem with the conjugate gradient method using matrix-free SSOR preconditioning in Matlab. Technical Report HPCF-2009-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[3] Guan Wang, Aaron Churchill, Matthias K. Gobbert, and Thomas I. Seidman. Efficient computation for a reaction-diffusion system with a fast reaction with continuous and discontinuous initial data using COMSOL Multiphysics. Technical Report HPCF-2009-3, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[4] Noemi Petra and Matthias K. Gobbert. Performance studies with COMSOL Multiphysics via scripting and batch processing. Technical Report HPCF-2009-4, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
Files for download with this report: poisson2d.m, poisson2d_graphics.m, poisson2d_matlab.m, poisson2d_infile.mph, qsub-COMSOL_with_MATLAB, qsub-COMSOL
[5] Guan Wang and Matthias K. Gobbert. Performance comparison between blocking and non-blocking communications for a three-dimensional Poisson problem. Technical Report HPCF-2009-5, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[6] Zana Coulibaly, Michael Muscedere, Matthias K. Gobbert, and Bradford E. Peercy. Long-time simulation of calcium waves in a heart cell to study the effects of calcium release flux density and of coefficients in the pump and leak mechanisms on self-organizing wave behavior. Technical Report HPCF-2009-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[7] Aaron Churchill, Matthias K. Gobbert, and Thomas I. Seidman. Efficient computation for a reaction-diffusion system with a fast reaction in two spatial dimensions using COMSOL Multiphysics. Technical Report HPCF-2009-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[8] Andrew M. Raim and Matthias K. Gobbert. Parallel performance studies for a maximum likelihood estimation problem using TAO. Technical Report HPCF-2009-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[9] A. Szatmary and C. D. Eggleton. Modeling fluid-structure interactions in non-periodic viscous flow with the immersed boundary method and Chorin's projection method in Fourier space. Technical Report HPCF-2009-9, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib ]
[10] S. G. DeSouza-Machado, L. L. Strow, B. Imbiriba, K. McCann, R. M. Hoff, S. E. Hannon, J. V. Martins, D. Tanré, J. L. Deuzé, F. Ducos, and O. Torres. Infrared retrievals of dust using AIRS: Comparisons of optical depths and heights derived for a North African dust storm to other collocated EOS A-Train and surface observations. Journal of Geophysical Research (Atmospheres), 115, 2010. (HPCF machines used: hpc.). [ bib ]
[11] Michael J. Reid. Parallel performance studies for a numerical simulator of atomic layer deposition. UMBC Review: Journal of Undergraduate Research, 11:30-41, 2010. (HPCF machines used: hpc.) Pre-print PDF is given here. [ bib | .pdf ]
[12] Yushu Yang. Parallel studies for chemically reacting systems. Technical Report HPCF-2009-12, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[13] Noemi Petra and Matthias K. Gobbert. Parallel performance studies for COMSOL Multiphysics using scripting and batch processing. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2009, Boston, MA, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[14] Matthias K. Gobbert, Aaron Churchill, Guan Wang, and Thomas I. Seidman. COMSOL Multiphysics for efficient solution of a transient reaction-diffusion system with fast reaction. In Yeswanth Rao, editor, Proceedings of the COMSOL Conference 2009, Boston, MA, 2009. (HPCF machines used: hpc.). [ bib | .pdf ]
[15] A. Bhaskar, C. Welty, and R. Maxwell. Urban watershed modeling across landscape scales. In American Geophysical Union, Fall Meeting, 2009. (HPCF machines used: hpc.). [ bib ]
[16] D. A. Elliott, H. H. Aumann, L. L. Strow, and S. E. Hannon. Two-year comparison of radiances from the atmospheric infrared sounder (AIRS) and the infrared atmospheric sounding interferometer (IASI). In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7456, 2009. (HPCF machines used: hpc.). [ bib ]
[17] E. M. Manning, H. H. Aumann, R. G. Deen, Y. Jiang, L. L. Strow, and S. E. Hannon. Spectral calibration in hyperspectral sounders. In Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, volume 7452, 2009. (HPCF machines used: hpc.). [ bib ]
[18] H. Shen and D. D. Frey. Serial displacement chromatofocusing and its applications in 2D-PAGE and 2D-HPLC. part 1: Theory and general considerations. J. Chromatogr. A, 1216:977-986, 2009. [ bib ]
2008
[1] Matthias K. Gobbert. Parallel performance studies for an elliptic test problem. Technical Report HPCF-2008-1, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | .pdf ]
[2] Michael Muscedere and Matthias K. Gobbert. Parallel performance studies for a parabolic test problem. Technical Report HPCF-2008-2, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | .pdf ]
[3] Michael J. Reid and Matthias K. Gobbert. Parallel performance studies for a hyperbolic test problem. Technical Report HPCF-2008-3, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | .pdf ]
[4] Shiming Yang and Matthias K. Gobbert. Convergence order studies for elliptic test problems with COMSOL Multiphysics. Technical Report HPCF-2008-4, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: kali.). [ bib | .pdf ]
[5] Robin Blasberg and Matthias K. Gobbert. Parallel performance studies for a clustering algorithm. Technical Report HPCF-2008-5, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | .pdf ]
[6] Samuel Trahan. MPI performance on the hpc.rs.umbc.edu cluster. Technical Report HPCF-2008-6, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | www: ]
[7] Robin Blasberg and Matthias K. Gobbert. MVAPICH2 vs. OpenMPI for a clustering algorithm. Technical Report HPCF-2008-7, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | .pdf ]
[8] Robin Blasberg and Matthias K. Gobbert. Clustering large data sets with parallel affinity propagation. Technical Report HPCF-2008-8, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib ]
[9] Michael J. Reid. Comparison of parallel performance between MVAPICH2 and OpenMPI applied to a hyperbolic test problem, Senior Thesis, Department of Mathematics and Statistics. Technical Report HPCF-2008-9, UMBC High Performance Computing Facility, University of Maryland, Baltimore County, 2008. (HPCF machines used: hpc.). [ bib | .pdf ]
[10] Matthias K. Gobbert and Shiming Yang. Numerical demonstration of finite element convergence for Lagrange elements in COMSOL Multiphysics. In Vineet Dravid, editor, Proceedings of the COMSOL Conference 2008, Boston, MA, 2008. (HPCF machines used: kali.). [ bib | .pdf ]
[11] A. Gambacorta, C. Barnet, B. Soden, and L. Strow. An assessment of the tropical humidity-temperature covariance using AIRS. Geophys. Res. Lett., 35, 2008. (HPCF machines used: hpc.). [ bib ]
[12] Matthias K. Gobbert. Long-time simulations on high resolution meshes to model calcium waves in a heart cell. SIAM Journal on Scientific Computing, 30(6):2922-2947, 2008. (HPCF machines used: kali.). [ bib ]
[13] P. Graff, M. Georganopoulos, E. Perlman, and D. Kazanas. A multizone model for simulating the high-energy variability of TeV. The Astrophysical Journal, 689(1):68, 2008. [ bib ]
[14] L. L. Strow and S. E. Hannon. A 4-year zonal climatology of lower tropospheric CO2 derived from ocean-only atmospheric infrared sounder observations. Journal of Geophysical Research (Atmospheres), 113, 2008. (HPCF machines used: hpc.). [ bib ]
[15] D. G. Tarboton and M. E. Baker. Toward an algebra for terrain-based flow analysis. In N. Mount, G. Harvey, G. Priesthall, and P. Apin, editors, Representing, Modelling, and Visualizing the Natural Environment. CRC Press-Taylor & Francis, London, 2008. [ bib ]

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