Steven Gordon

Ohio Supercomputer Center

Environmental Biology

Massively Parallel Graph Analytics

(jrn)
Jul 2014 - Aug 2016

2017

Andrew C. Kirby, Michael Brazell, Zhi Yang, Rajib Roy, Behzad Reza Ahrabi, Dimitri Mavriplis, Jay Sitaraman, and Michael K. Stoellinger (2017): Wind Farm Simulations Using an Overset Hp-Adaptive Approach with Blade-Resolved Turbine Models, American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A.
Michael J. Brazell, Andrew C. Kirby, and Dimitri Mavriplis (2017): A High-Order Discontinuous-Galerkin Octree-Based AMR Solver for Overset Simulations, American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A.
Hime, Paul Michael (2017): Genomic Perspectives on Amphibian Evolution across Multiple Phylogenetic Scales, Theses and Dissertations--Biology, University of Kentucky Libraries, Num 45
Jon Calhoun, Marc Snir, Luke N. Olson, and William D. Gropp (2017): Towards a More Complete Understanding of SDC Propagation, ACM Press, Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing (HPDC '17), pp131, Washington, D.C., U.S.A.
S. R. Totorica, T. Abel, and F. Fiuza (2017): Particle Acceleration in Laser-Driven Magnetic Reconnection, Physics of Plasmas, AIP Publishing, Vol 24, Num 4, pp041408
Shu-Ching Ou, Justin A. Drake, and B. Montgomery Pettitt (2017): Nonpolar Solvation Free Energy from Proximal Distribution Functions, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp3555--3564
Katharine J. Cahill, Scott Lathrop, and Steven Gordon (2017): Building a Community of Practice to Prepare the HPC Workforce, Procedia Computer Science (17th annual International Conference on Computational Science, ICCS 2017), Elsevier BV, Vol 108, pp2131--2140, Zürich, Switzerland
Larissa J. Reames (2017): Diurnal Variations in Severe Weather Forecast Parameters of Rapid Update Cycle-2 Tornado Proximity Environments, Weather and Forecasting, American Meteorological Society, Vol 32, Num 2, pp743--761
George M. Slota, Kamesh Madduri, and Sivasankaran Rajamanickam (2017): Distributed Graph Layout for Scalable Small-world Network Analysis, (submitted)

2016

N. V. Pogorelov and M. C. Bedford and I. A. Kryukov and G. P. Zank (2016): Pickup Ion Effect of the Solar Wind Interaction with the Local Interstellar Medium, Journal of Physics: Conference Series, IOP Publishing Ltd, Vol 767, Num 1, pp012020
Justin A. Drake, Robert C. Harris, and B. Montgomery Pettitt (2016): Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility, Biophysical Journal, Elsevier BV, Vol 111, Num 4, pp756--767
Joshua S. Méndez Harper, and Josef Dufek (2016): The Effects of Granular Dynamics on the Triboelectric Charging of Volcanic ash: Experiments and Numerical Simulations, presented at the 2016 Electrostatics Joint Conference, West Lafayette, Indiana, U.S.A.
Jon Calhoun, Franck Cappello, Luke Olson, and Marc Snir (2016): Lossy Checkpointing PDE Simulations: Mathematical Guidance for Compression Error Setting, (submitted)
Samuel R. Totorica, Tom Abel, and Frederico Fiuza (2016): Nonthermal Electron Energization from Magnetic Reconnection in Laser-Driven Plasmas, Phys. Rev. Lett., American Physical Society (APS), Vol 116, Num 9, pp095003
A. L. Jones (2016): Development of an Accurate 3D Monte Carlo Broadband Atmospheric Radiative Transfer Model, Ph.D. Dissertation, University of Illinois
Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper (2016): LES of an Aero-Optical Turret Flow at High Reynolds Number, American Institute of Aeronautics and Astronautics (AIAA), 54th AIAA Aerospace Sciences Meeting, San Diego, California, U.S.A.
Ariana Minot, Yue M. Lu, and Na Li (2016): A Distributed Gauss-Newton Method for Power System State Estimation, IEEE Transactions on Power Systems, Institute of Electrical & Electronics Engineers (IEEE), Vol 31, Num 5, pp3804-3815
Ariana Minot, Yue M. Lu, and Na Li (2016): A Parallel Primal-Dual Interior-Point Method for DC Optimal Power Flow, IEEE, 2016 Power Systems Computation Conference (PSCC), pp1-7, Genoa, Italy

2015

Jon Calhoun, Marc Snir, Luke Olson, and Maria Garzaran (2015): Understanding the Propagation of Error Due to a Silent Data Corruption in a Sparse Matrix Vector Multiply, IEEE, 2015 IEEE International Conference on Cluster Computing, pp541-542, Chicago, Illinois, U.S.A.
J. Calhoun, L. Olson, M. Snir, and W.D. Gropp (2015): Towards a More Fault Resilient Multigrid Solver, Society for Computer Simulation International, Proceedings of the High Performance Computing Symposium (HPC '15), pp1-8, Alexandria, Virginia, U.S.A.
Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper (2015): Numerical Investigation of Aero-Optical Distortions Over a Hemisphere-on-Cylinder Turret with Gaps, American Institute of Aeronautics and Astronautics (AIAA), 46th AIAA Plasmadynamics and Lasers Conference, Dallas, Texas, U.S.A.
Sara I. L. Kokkila Schumacher, Edward G. Hohenstein, Robert M. Parrish, Lee-Ping Wang, and Todd J. Martínez (2015): Tensor Hypercontraction Second-Order Møller–Plesset Perturbation Theory: Grid Optimization and Reaction Energies, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 7, pp3042--3052
Ariana Minot, and Na Li (2015): A Fully Distributed State Estimation Using Matrix Splitting Methods, Institute of Electrical & Electronics Engineers (IEEE), 2015 American Control Conference (ACC), pp2488-2493, Chicago, Illinois, U.S.A.
Varvara E. Zemskova, Brian L. White, and Alberto Scotti (2015): Available Potential Energy and the General Circulation: Partitioning Wind, Buoyancy Forcing, and Diapycnal Mixing, J. Phys. Oceanogr., American Meteorological Society, Vol 45, Num 6, pp1510--1531
George M. Slota, and Kamesh Madduri (2015): Parallel Color-Coding, Parallel Computing, Elsevier BV, Vol 47, pp51--69
George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri (2015): High-Performance Graph Analytics on Manycore Processors, Institute of Electrical & Electronics Engineers (IEEE), 2015 IEEE International Parallel and Distributed Processing Symposium, pp17-27, Hyderabad, India
George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri (2015): Supercomputing for Web Graph Analytics, (submitted)

2014

Jon Calhoun, Luke Olson, and Marc Snir (2014): FlipIt: An LLVM Based Fault Injector for HPC, Springer Science + Business Media, Lecture Notes in Computer Science, pp547--558
Kris Beckwith, Seth Veitzer, Stephen F. McCormick, John W. Ruge, Luke N. Olson, and Jon C. Calhoun (2014): Fully-Implicit Ultrascale Physics Solvers and Application to Ion Source Modelling, Institute of Electrical & Electronics Engineers (IEEE), 2014 IEEE 41st International Conference on Plasma Sciences (ICOPS) held with 2014 IEEE International Conference on High-Power Particle Beams (BEAMS), pp1-8, Washington, D.C., U.S.A.

2012

N. V. Pogorelov, S. N. Borovikov, M. C. Bedford, J. Heerikhuisen, T. K. Kim, I. A. Kryukov, and G. P. Zank (2012): Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite, Astronomical Society of the Pacific, 7th Annual International Conference on Numerical Modeling of Space Plasma Flows (ASTRONUM2012), Vol 474, pp165, Big Island, Hawai'i, U.S.A.

Matthew Clayton Bedford: A Multi-ion Model of the Heliosphere with Secondary Charge Exchange


American Geophysical Union, Fall Meeting 2014; San Francisco, California, U.S.A., Dec 15, 2014

Edwin Mathews: High-Fidelity Computation of Aero Optics


Blue Waters Symposium 2015, May 11, 2015
Jon Calhoun: Effect and Propagation of Silent Data Corruption in HPC Applications
Blue Waters Symposium 2015, May 12, 2015

George M. Slota: Massively Parallel Graph Analytics


Blue Waters Symposium 2015, May 12, 2015

George Slota: Parallel Graph Algorithms on Modern Systems


29th IEEE International Parallel and Distributed Processing Symposium (IPDPS15); Hyderabad, India, May 26, 2015

Edwin Mathews, K. Wang, M. Wang, and E. J. Jumper: LES Prediction and Analysis of the Aero-optical Environment Around a 3-D Turret


68th Annual Meeting of the American Physical Society (APS) Division of Fluid Dynamics; Boston, Massachusetts, U.S.A., Nov 22, 2015

Maureen T. Brooks: Linking Satellite Observations with Coupled Bio-physical Models of Sargassum


2016 Ocean Sciences Meeting; New Orleans, Louisiana, U.S.A., Feb 23, 2016

Justin Drake and B.M. Pettitt: The Protein Backbone: How Structural and Thermodynamic Properties Scale with The Length of a Model, Disordered Polypeptide


251st American Chemical Society National Meeting and Exposition; San Diego, California, U.S.A., Mar 15, 2016

Justin Drake and B.M. Pettitt: The Protein Backbone: How Structural and Thermodynamic Properties Scale With Chain Length


21st Annual Structural Biology Symposium; Galveston, Texas, U.S.A., Apr 23, 2016

George Slota: Extreme-scale Graph Analysis on Blue Waters


Blue Waters Symposium 2016, Jun 14, 2016
Barbara Zemskova: Ocean Energetics and Convection
Blue Waters Symposium 2017, May 18, 2017

UIUC’s Supercomputer Has a Projected $1B Impact On Illinois’ Economy

Nestled on the outskirts of the University of Illinois at Urbana-Champaign campus — at the corner of Oak Street and St. Mary’s Road — is Blue Waters, a supercomputer that was first instituted as a result of a 2007 National Science Foundation grant and an initial $60 million investment from the State of Illinois.A report released this past week on the economic impact of this supercomputer — on the UIUC campus, its five surrounding counties, as well as nationwide spillover effects — puts a whole new meaning to the term “return on investment.”.

Blue Waters Graduate Fellow: Ronald Stenz

For my research, I am trying to determine the impacts that precipitation centrifuging has on tornado dynamics. I have always been fascinated with severe weather and tornadoes, which inspired me to study atmospheric sciences. I am studying this particular topic because in numerical simulations of tornadoes, an unrealistic rain blob appears in the core of simulated tornadoes. My goal is to make these simulations more realistic with a centrifuging algorithm, and to determine the resulting effect on tornado dynamics. Since gathering accurate and dense observations around a tornado is incredibly difficult and dangerous, numerical modeling is a major tool used to understand tornadoes. For my research I use a model called CM1 to numerically simulate tornadoes so we can study how they form, what environments they form in, and what factors lead to intensification or weakening of tornadoes..

Blue Waters Graduate Fellow: Erin Teich

Very generally, what we study in our labs is a process called self-assembly. And this is relevant for a lot of different processes, but it turns out that material on a variety of scales basically self-organizes. This allows for the creation of materials by basically harnessing the urge that things have on certain temperature and energy scales in order to self-organize. They do that because they want to minimize their free energy.For the Blue Waters Fellowship, I'll be looking at disordered materials via simulation. There are materials called glasses, which is just like everyday glass, and amazingly enough, they are still not well understood. Physicists have been studying glass for decades and decades, and really centuries if you think about it, and physical properties of glasses still aren't well understood; like how glasses form, and whether or not that's a phase transition. So with the Blue Waters Fellowship, I'll be simulating glass formation in colloidal systems on the microscale, and trying to uncover, if possible, some of the reasons why glass formation happens in those types of systems..

Blue Waters Graduate Fellow: Andrew Kirby

I am studying Mechanical Engineering at the University of Wyoming. I research numerical methods for computational fluid dynamics (CFD). My research is in the field of CFD. Specifically, I develop numerical solvers for the Navier-Stokes equations which govern fluid dynamics. I apply these methods that I develop to applications in wind energy and aerospace. We hope to simulate entire wind farm systems to determine properties such as power and thrust of the wind turbines and how their interactions interplay with each other. CFD also allows you to visualize your results. It gives a nice feedback loop on seeing you results (that are usually really cool to look at too). Lately, I have been really interested in the high performance computing aspect as well. I really enjoy trying to write really fast and efficient code that runs on the largest supercomputers in the world..

Blue Waters Graduate Fellow: Paul Hime

advances in genome sequencing technologies have opened up exciting new avenues for phylogeneticists to survey broad swaths of the genome and to untangle some of the difficult branches in the Tree of Life. This new flood of genetic data itself is necessary, but not sufficient, to answer some of the most thorny evolutionary questions. As the amount of data available to evolutionary biologists has expanded, so too have the computational challenges to appropriately modeling DNA evolution between organisms.My doctoral research in the Weisrock Lab at University of Kentucky uses new computational and statistical approaches to reconstruct evolutionary relationships. I utilize amphibians (frogs, salamanders, and caecilians) as a model system in which to explore these exciting questions. Access to extremely powerful supercomputing resources is vital to this research, and the Blue Waters Fellowship through the NCSA provides unprecedented opportunities to advance this work. ... the NSF-funded Blue Waters supercomputer will allow me to probe aspects of phylogenetics which have previously been inaccessible due to computational constraints..

Ten PhD students from across the country selected as Blue Waters Graduate Fellows

Ten outstanding computational science PhD students from across the country have been selected to receive Blue Waters Graduate Fellowships for 2016-2017. The fellowship program, now in its third year, provides substantial support and the opportunity to leverage the petascale power of National Center for Supercomputing Applications (NCSA) at the University of Illinois’s Blue Waters supercomputer to advance their research. The awards are made to outstanding PhD graduate students who have decided to incorporate high performance computing and data analysis into their research..

Blue Waters Graduate Fellow: Sean Seyler

Proteins, such as membrane transporters or enzymes, are much like nanomachines that undergo structural changes—conformational transitions—between multiple states in order to perform chemical or mechanical work. These transitions are rare events that, due to the equilibrium sampling problem, are difficult to reproduce in equilibrium molecular dynamics (MD) simulation. The paradigm for studying these processes is the so-called structure-function connection; in principle, one should be able to infer a protein's function (its dynamical structural changes) given information about its structure (its 3D "shape" and amino acid sequence). Given the enormous computational difficulty of simulating highly complex, heterogeneous biomacromolecules on sufficiently long time scale, the majority of my research is focused on the development of computational methods and software tools that can help to more effectively sample and quantify protein conformational motions and transitions..

Blue Waters Graduate Fellow: Elizabeth Agee

My research is focused on the interactions between forest ecosystems and hydrology. Over 50% of global evapotranspiration comes from forested ecosystems, so this represents a significant pathway for understanding global water and energy cycling. The question that drives my research is how these pathways will respond to climate change. Using Blue Waters, I will explore how tree species in the Amazon rainforest use water in different ways and how those differences influence community resilience to drought events. It is my hope that this work will improve the representation of tropical forests in the current suite of land surface models and provide mechanistic insights into forest community dynamics..

Blue Waters Graduate Fellow: Sherwood Richers

My primary interest in neutrino transport has a couple of objectives. Let's look at core-collapse supernovae first. The big problem in this field is that observers watch stars explode on a daily basis, but when we put the most complete set of physics possible in the largest simulations running on supercomputers (like Blue Waters), they don't consistently explode. Something is missing, and that something might be a proper treatment of neutrino transport. The equations describing neutrino transport are notoriously difficult to simulate, so they have to be heavily approximated, but I am trying to remove as much of the approximation as I can..

Blue Waters Graduate Fellow: Iryna Butsky

I really enjoyed my research on galactic magnetic fields, and I wanted to pursue it further. I'm very interested in studying the contribution of cosmic rays to the turbulent dynamo which amplifies galactic magnetic fields. Cosmic rays are tricky to model in galaxy simulations and have thus oftentimes been ignored. However, they could be key to the explanation of the strength of observed field strengths..

Blue Waters Graduate Fellow: Michael Howard

The goals of my research are two-fold: (1) to develop massively parallel software for doing simulations of multiphase/complex fluids, and (2) to use this software to study enhanced oil recovery. I first plan to implement a developed algorithm for doing these types of simulations (multiparticle collision dynamics—MPCD) on GPUs. GPU acceleration will allow us to study problems at realistic length and time scales. To date, there has only been limited public availability of these types of codes, and so I plan to release the software open-source. I will then apply my software to study the initial stages of enhanced oil recovery—the process by which additional oil is extracted from geological formations..

Four additional students named Blue Waters Graduate Fellows

Four additional computational science PhD students have been selected to receive Blue Waters Graduate Fellowships, which provide graduate students in diverse fields with substantial support and the opportunity to leverage the petascale power of NCSA’s Blue Waters supercomputer to advance their research. Six graduate fellows were named earlier this spring. Because of the large number of qualified applicants, NCSA sought and was awarded additional fellowship funding from the National Science Foundation, enabling the Blue Waters project to support a total of 10 graduate fellows..

Six PhD students from across the country selected as Blue Waters Graduate Fellows

Six outstanding computational science PhD students from across the country have been selected to receive Blue Waters Graduate Fellowships for 2015-2016. The fellowship program, now in its second year, provides graduate students in diverse fields with substantial support and the opportunity to leverage the petascale power of NCSA’s Blue Waters supercomputer to advance their research..

How layout of urban areas affect supercell thunderstorms

Many things go into consideration when planning a city layout, roads, transportation needs, location relative to natural features. However, one thing has not previously been considered is the shape of the city and how that shape affects the severity of natural disasters, such as extreme thunderstorms or tornadoes.With the help of Blue Waters at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign, Larissa Reames, a Ph.D student at the University of Oklahoma and a 2015-2016 NCSA Blue Waters Graduate Fellow, is undertaking exciting meteorology research on the effects of supercell thunderstorms and how the specific layout of a city can affect a storm’s impact..

Blue Waters pushes magnetic reconnection research

Magnetic reconnection is the scientific process in which oppositely aligned magnetic field lines in a plasma break and form new connections. The newly connected magnetic fields are bent and have a tension that can accelerate the plasma like a slingshot.This process is still not well-understood, but base knowledge is the energy released from the magnetic field accelerates the particles in the plasma during reconnection. Plasma jets, and more generally, plasma, is an important subject in high-energy-density laboratory astrophysics. "Plasma is the most abundant form of ordinary (non-dark) matter in the universe, so understanding plasmas is necessary for understanding systems in astrophysics," said Sam Totorica, NCSA Blue Waters Graduate Fellow from Stanford University..

Extreme-scale Graph Analysis on Blue Waters

In this video from the 2016 Blue Waters Symposium, George Slota from Pennsylvania State University presents: Extreme-scale Graph Analysis on Blue Waters..

Six PhD students from across the country selected as Blue Waters Graduate Fellows

Six outstanding computational science PhD students from across the country have been selected to receive the first Blue Waters Graduate Fellowships, which provide graduate students in diverse fields with substantial support and the opportunity to leverage the petascale power of NCSA’s Blue Waters supercomputer to advance their research. Over three years this fellowship program will award more than $1 million and nearly 30 million integer-core hours to support graduate research..