Colloquia & Seminars
Fall 2012
Algorithmic requirements for extreme scale simulation
Speaker: David E. Keyes, Professor, Applied Mathematics and Computational Science, Director, Strategic Initiative in Extreme Computing, King Abdullah University of Science and Technology (KAUST)
Date: February 7, 2013 from 1:30 pm - 2:30 pm, Visualization Lab, 346 Lewis Science Library
Light refreshments will be served
Abstract
Diverging exponentials in computer hardware subsystem performance require rethinking of models and reimplementation of algorithms in scientific and engineering simulation. Much mathematics and software appears to be missing if emerging hardware is to be used near its potential, since our existing code base has been assembled with a premium on squeezing out flops and improving the execution rate of those that remain. Instead, for reasons of energy efficiency and system acquisition cost, we must now focus on squeezing out synchronizations, memory footprint, and memory transfers. High concurrency and power-efficient design of the individual cores put opposite pressures on algorithms: respectively, they require greater data locality and greater freedom to redistribute data and computation. After decades of programming model stability, new models and new hardware must be developed simultaneously, a process called co-design. We extrapolate current trends and describe directions for exascale algorithms.
Speaker Biography
David Keyes is the inaugural Dean of the Division of Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) at KAUST, an adjunct professor in Applied Physics and Applied Mathematics at Columbia University, and an affiliate of several laboratories of the U.S. Department of Energy. Keyes graduated in Aerospace and Mechanical Sciences from Princeton in 1978, earned a doctorate in Applied Mathematics from Harvard in 1984, and post-doc’ed in Computer Science at Yale. He works at the algorithmic interface between parallel computing and the numerical analysis of partial differential equations. For his algorithmic influence in scientific simulation, Keyes was recognized as a Fellow of SIAM and of the AMS, with the Sidney Fernbach Award of the IEEE Computer Society, and with ACM’s Gordon Bell Prize. Author or editor of more than a dozen federal agency reports and member of several federal advisory committees on computational science and engineering and high performance computing, in 2011, Keyes received the SIAM Prize for Distinguished Service to the Profession.
The Astronomical Multipurpose Software Environmentand the Ecology of Star Clusters
Speaker: Simon Portegies Zwart, Professor of Computational Astrophysics at the Sterrewacht Leiden of Leiden University
Date: February 13, 2012 from 12:30-1:30pm, Room Location TBD
Light Refreshments will be served at 11:45am in the PICSciE Reception area
Abstract
Star cluster ecology is the field of research where stellar evolution, gravitational dynamics, hydrodynamcs and the background potential dynamics of the parent galaxy interact to a complex non-linear evolution of self gravitating stellar systems. I will review the processes related to the ecology of stellar clusters, discuss the numerical hurdles and the physical principles. In addition, I will introduce the AMUSE framework with which we are performing simulations of the ecology of stellar clusters. AMUSE is a general purpose framework for interconnecting existing scientific software with a homogeneous and unified interface. The framework is based on the standard message passing interface any production ready code that is written in a language that supports its native bindings can be incorporated, in addition our framework is intrinsically parallel and it conveniently separates the all the numerical solvers in memory.
Speaker Biography
Simon Portegies Zwart was born in Amsterdam and studied astronomy at the University of Amsterdam. After his PhD with Frank Verbunt at Utrecht University he traveled over the world while working as a postdoctoral fellow at the University of Amsterdam, Tokyo University (Japan), MIT (USA) and back to Amsterdam. He currently is full professor of computational astrophysics at the Sterrewacht Leiden of Leiden University. His professional interests are high-performance computing and gravitational stellar dynamics, in particular the ecology of dense stellar systems. His personal interests include translating Egyptian hieroglyphs and brewing beer.
Perspectives on China’s Role in Global High Performance Computing
Speaker: William Tang, PPPL, Princeton University
Date: January 23, 2012 from 12:30-1:30pm, 121 Lewis Science Library
Light Refreshments will be served at 11:45 in the PICSciE Reception area.
Abstract
High performance computing is generally recognized to be an increasingly vital tool for accelerating progress in scientific research in the 21st Century. China’s rapid emergence in this area has been remarkable, and the current presentation will highlight associated impressions from a number of visits there by me and national colleagues over the past year. At the top of the most recent LINPACK list (November, 2011) are Japan’s Fujitsu K machine at No. 1, the Chinese supercomputers at Nos. 2 and 4, and the U.S. falling to No. 3. It is significant to note that the 2.57 petaflops performance level of the Chinese Tianhe-1A system at the National Supercomputer Center in Tianjin has passed the U.S.’s Cray XT5 system “Jaguar” at the Oak Ridge National Laboratory with 1.76 petaflops – previously the No. 1 machine in June 2010. The rapid rise of HPC hardware in China over the past decade is particularly notable since the Chinese systems, which were basically absent from the Top500 list prior to 2001, now occupy the Nos. 2 and 4 positions.
Speaker Biography
William M. Tang is the Director of the Fusion Simulation Program at the Princeton Plasma Physics Laboratory (PPPL) and serves on the Executive Committee for PICSciE which he helped establish during his 6-years as Associate Director. He is a Fellow of the American Physical Society, and in October, 2005, received the Chinese Institute of Engineers-USA (CIE-USA) Distinguished Achievement Award “for his outstanding leadership in fusion research and contributions to fundamentals of plasma science. He was the Chief Scientist at PPPL from 1997 until 2009 and also played a national leadership role in the formulation and development of the DoE’s multi-disciplinary program in advanced scientific computing applications, SciDAC (Scientific Discovery through Advanced Computing). He chaired the major DoE-SC meeting on “Scientific Grand Challenges in Fusion Energy Sciences and the Role of Computing at the Extreme Scale” (Spring, 2009).
Campus-Scale High Performance Cyberinfrastructure for Data-Intensive Research
Speaker: Larry Smarr, University of California – San Diego
Date: December 12, 2011 from 12:30-1:30 pm, Visualization Lab, Room 346 Lewis Library
Blue Waters Plus – A Super System to Solve Super Challenges
Speaker: William Kramer, Blue Waters Project, NCSA
Date: December 5, 2011 from 12:30-1:30pm, Visualization Lab, Room 346 Lewis Library
Lunch will be served at 11:45am in the PICSciE Reception area
Abstract:
Blue Waters is the NSF Track 1 system being deployed in the fall of 2012 for a diverse range of unique science and engineering challenges that require huge amounts of sustained performance. The Blue Waters project has used a number of principles, now frequently referred to as “co-design”, to improve the impact of the technology. Recently, the entire project was refocused to the new Cray XE/XK/Gemini/Sonexion technologies.
More than 25 teams, from a dozen distinct research fields, have already been selected to run projects on Blue Waters. These teams will achieve breakthroughs by using Blue Waters to model a broad range of phenomena, including: nanotechnology’s minute molecular assemblies, the evolution of the universe since the Big Bang, the damage caused by earthquakes and tornadoes, the mechanism by which viruses enter cells, and improved climate change predictions.
This talk will begin by explaining the goals and expectations of the Blue Waters Project and how the new Cray XE/XK/Gemini/Sonexion technologies will fulfill these expectations. To ensure the ongoing success of the Blue Waters science teams, the talk will cover how NCSA will verify the system will meet is requirements for a more than a sustained petaflop/s of computing for a diverse set of science application. The next part of the talk will discuss a significant ideas on creating new methods and algorithms to improve application codes to take full advantage of systems like Blue Waters, with particular attention for the areas of scalability, use of accelerators, simultaneous use of x86 and accelerated nodes within single codes and application resiliency. The final part of the talk will discuss some lessons learned from the co-design efforts.
Speaker Biography
William T.C. Kramer is deputy project director at the National Center for Supercomputing Applications; he is responsible for leading the Blue Waters project, a National Science Foundation-funded project, to deploy the first general purpose, open science, sustained-petaflop supercomputer as a powerful resource for the nation’s researchers. Blue Waters is an 8 year project with an overall funding of over $500M
Spring 2011
Understanding the Human Brain: The Ultimate Computational Challenge (in Theory and Practice)
Speaker: Professor Jonathan Cohen, Princeton Neuroscience Institute
April 11, 2011 from 12:30 pm - 1:30 pm, Visualization Lab, 346 Lewis Library
Abstract:
The human brain is the most complex device in the known universe. With an estimated 100 billion neurons, 100 trillion connections among them, and an inestimable number of potential circuits, the challenge to track these and understand their function is arguably the greatest challenge science has ever faced. It is a trivial assertion, therefore, that this challenge demands the most sophisticated approaches to mathematical analysis and numerical (computational) simulation we can garner. This is true both for theory development, as well as for data analysis. The former stems from the inherent complexity of the problem, and the latter from the size of the datasets required to make progress in addressing it. I will review the state-of-the along these dimensions, focusing in particular on the challenge posed by analyzing human brain imaging data — the most available measures we have of the functioning of the intact human brain.
Computational approaches to the study of collective behavior
Speaker: Prof. Iain Couzin, Department of Ecology & Evolutionary Biology, Princeton University
March 28, 2011 from 12:30 pm - 1:30 pm, Visualization Lab, 346 Lewis Library
Abstract:
A fundamental problem in a wide range of biological disciplines is understanding how functional complexity at a macroscopic scale (such as the functioning of a biological tissue) results from the actions and interactions among the individual components (such as the cells forming the tissue). Animal groups such as bird flocks, fish schools and insect swarms frequently exhibit complex and coordinated collective behaviors and present unrivaled opportunities to link the behavior of individuals with the functioning and efficiency of dynamic group-level properties.
Using an integrated experimental and theoretical approach involving both insects and vertebrates I will address both how, and why, animals coordinate behavior., and the computational tools that we have developed to facilitate their study. In some animal groups decision-making by individuals is so integrated that it has been associated with the concept of a “collective mind”. Since each organism has relatively local sensing ability, coordinated animal groups have evolved collective strategies that allow individuals to access higher-order computational abilities at the group level. I investigate the coupling between spatial and information dynamics in swarms, flocks, schools and herds and reveal the critical role uninformed individuals (those who have no information about the feature upon which a collective decision is being made) play in inhibiting extremism and promoting democratic consensus in groups.
Toward Exascale Computing in Gyrokinetic Particle-in-Cell Simulations of Fusion Plasmas
Speaker: Stephane Ethier, Computational Scientist, PPPL
March 24, 2011 from 12:30 pm - 1:30 pm, Visualization Lab, 346 Lewis Library
Abstract:
The last decade has witnessed a rapid emergence of larger and faster computing systems in the US supercomputing centers. Massively parallel machines have gone mainstream and are now the tool of choice for large scientific simulations. Scientific applications need to be modified, adapted, and optimized for each new system being introduced. With a few petascale systems now in production mode, the focus of the DOE Office of Advanced Scientific Computing Research has now shifted to the next level of "Exascale", which promises to be truly disruptive. With an estimated billion cores to deal with, scientific applications will need to manage extreme parallelism, limited bandwidth, frequent failures, and many more hardware and software challenges. In this talk, I will discuss the path to extreme scale computing from the point of view of the large-scale gyrokinetic particle-in-cell codes developed at Princeton University's Plasma Physics Laboratory to study microturbulent transport in fusion plasmas
3D Visualization and Physically-based Illumination
Speaker: David Banks, University of Tennessee and Oak Ridge National Laboratory
David Banks holds positions as tenured faculty in the EECS department at the University of Tennessee and as senior scientist in scientific computing at Oak Ridge National Laboratory. He is a member of the UT/ORNL Joint Institute for Computational Sciences, home to the top-ranked academic supercomputer in the world.
February 28, 2011 from 12:30 pm - 1:30 pm, Visualization Lab, 346 Lewis Library
Abstract:
"3D data visualization" applies computer graphics to datasets of various kinds. Graphics algorithms can be viewed as "solvers" for radiation transport. Our lab investigates the interplay among transport, rendering, visualization, and human perception. We have found that perception of 3D scenes can be improved by visualizing them using rendering algorithms that more accurately solve the transport equation. Surprisingly, such "physically-based” algorithms have not been widely adopted by scientific users.
New frontiers in quantum chemistry using supercomputers
Speaker: Jeffrey Hammond, University of Chicago / Argonne National Laboratory
Jeff Hammond is currently a Director's Postdoctoral Fellow at the Argonne Leadership Computing Facility. He received his PhD in chemistry from the University of Chicago as a DOE Computational Science Graduate Fellow.
February 21, 2011 from 12:30 pm - 1:30 pm, Visualization Lab, 346 Lewis Library
Abstract:
Recent advancements in high-performance computing present both challenges and new opportunities for quantum chemists. Accurate methods like coupled-cluster theory can now be applied to systems with
dozens of atoms, opening up new application areas related to biology and material science. I will present recent results obtained using the massively parallel quantum chemistry package NWChem, highlighting
the importance of accurate many-body simulations of electric-field response properties and electronic excited-states for a diverse set of chemical systems. The rigorous development of force-fields, including both inter- and intramolecular terms, will also be discussed. Finally, I will discuss recent developments in computer architecture - million-way parallelism and heterogeneous nodes - affect algorithms and software development in correlated electronic structure calculations.
Extracting Biological Insight from Complex Genome-Scale Data: Connecting Growth Control and Stress Response in Yeast
Speaker: David Botstein, Director, Lewis-Sigler Institute for Integrative Genomics
February 14, 2011 from 12:30 pm - 1:30 pm, Visualization Lab, 346 Lewis Library
Abstract:
The maintenance of cellular homeostasis in the face of rapidly changing environmental conditions has been the focus of our research for the past five years. Specifically, we have studied the relationship between the growth rate, which we can control directly by setting the dilution rate in chemostats, and the initiation of cell division cycle, response to environmental stress, and metabolism. We have exploited high-throughput methods, some of our own devising, to follow gene expression, metabolite levels, and relative fitness of mutants on a comprehensive scale in order to obtain a view of the integration of these functions at the system level.
The biggest challenge in this kind of research is not the acquisition, nor even the statistical analysis of the data. Instead, it is the visualization of the analysis of the results in a form that can be appreciated and communicated by scientists. Examples will be provided from our research that illustrate this challenge and some of the ways we have attempted to meet it.
