Colloquia & Seminars
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
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.
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
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.
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
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.
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.
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
Blue Waters Plus – A Super System to Solve Super Challenges
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
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
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
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
"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
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
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.