BEGIN:VCALENDAR
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X-WR-CALNAME:MCS Events
BEGIN:VEVENT
DTSTART:20090128T150000
DTEND:20090128T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:Carbon emission programs are designed to reduce greenhouse gas emissions by implementing either a carbon tax or a cap-and-trade program.  In this talk, we discuss the extent to which a foreign oil producer, such as OPEC, can manipulate cap-and-trade programs by cutting production, resulting in a collapse of some carbon emission markets.  This possible manipulation needs to be understood in an international setting with trade among developing countries that have no regulation and other countries that each have their own independent carbon emission program.  We analyze a leader-follower computable general equilibrium model to understand this issue that results in mathematical programs with equilibrium constraints that need to be solved. Numerical results providing insights into the possible manipulation of carbon emission programs by foreign oil  producers are provided.\n\n
SUMMARY:The Manipulation of Carbon Emission Programs by Foreign Oil Producers
UID:508
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090205T160000
DTEND:20090205T170000
DTSTAMP:20091122T063007Z
LOCATION:GCIS W301, University of Chicago
DESCRIPTION:The activities of my research group and collaborations focus on the development of bioinformatics systems essential for functional genomics, genetics and phenotypic research. The sequencing of mouse, human and other genomes and the rapid accumulation of very large data sets has resulted in an overwhelming amount of information from multiple sources containing a variety of content and formats. The challenge is to bring all the data together and make it easily accessible to researchers directly and/or for additional computer analysis. Our current research centers on combining bio-ontologies (defined, controlled, structured vocabularies) and database systems to identify molecular elements that contribute to the processes of particular diseases, such as lung cancer. This work is undertaken as part of the Gene Ontology Consortium, a group of 19 model organism databases and genome annotation centers. My group, as part of the Mouse Geneome Informatics Consortiun at The Jackson Laboratory, is responsible for the functional and comparative annotation of mouse genes.
SUMMARY:Evidence and Inference: Comparative Biology in the Age of Genomics
UID:528
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090402T150000
DTEND:20090402T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:Learn how to prepare an award winning LDRD proposal from the pros!
SUMMARY:Hot Tips for preparing DCG LDRD proposals
UID:533
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090225T150000
DTEND:20090225T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:In this informal talk we discuss several aspects related to\nthe importance and use of uncertainty in modeling and simulation. Uncertainty has become pervasive in real computations. In this context, the deterministic solution represents just one possible outcome. We briefly discuss the need for uncertainty in simulations and present several computational efficient models for uncertainty representation in reactive flow simulations. Ties between uncertainty quantification and data assimilation - the process of integrating measurements in simulations - will also be addressed.\n
SUMMARY:The certain importance of uncertainty in modeling and simulation
UID:534
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090129T103000
DTEND:20090129T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 360, Conference Room L119, Argonne National Laboratory
DESCRIPTION:Scientific codes are used on a wide range of hardware architectures and operating systems.  The developers and users of these codes need to be sure that the code performs correctly on all of the systems where it is used.  The scale of this task can be quite large, especially when you consider that various revisions of the same operating system are best treated separately.  To assist in the testing effort, the National Science Foundation (NSF) funds a build and test pool consisting of the hardware and software used by the NSF community.  This saves each development group from having to maintain their own build and test systems.  In addition, the NSF funds the development of Metronome, a continuous-integration build and test system.  Automating the use of the build systems lowers the cost of development by discovering bugs when they are committed.\n\nThis talk will cover the design principles of Metronome, as well as practical experience from using it on a large distributed computing application.  It will also compare and contrast the use of Metronome with BuildBot, a popular open-source build tool.
SUMMARY:Build and Test for Distributed Computing Applications
UID:540
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090130T130000
DTEND:20090130T140000
DTSTAMP:20091122T063007Z
LOCATION:RI 405 (Research Institutes), University of Chicago
DESCRIPTION:High performance computing has become an increasingly important fixture in science, from aiding in the processing of data collected in experiments, to acting as a virtual laboratory in which experiments are done. Thus, high performance computing is creating a third branch of scientific effort. This trend has driven research and development in a variety of different areas from fundamental hardware design to the software that makes the resources useful. With each iteration of this development cycle computational science has become more and more\ncomplex. This effort addresses this complexity in two key interrelated areas: visualization and collaboration.\n\nVisual representation is the key method to simplify the explanation of a complex environment. Consequently, a large research and development community effort has grown to support scientific visualization. It has also spawned research in advanced displays to provide infrastructure\nfor exploring data products. These include immersive displays like the CAVE Automatic Virtual Environment or high resolution displays constructed of multiple individual units like the ActiveMural. This work includes influential contributions in all of these areas.\n\nAt the same time, complex tasks are often simplified by effort sharing. We see that the teams of individuals working together to do this new form of science have become larger and more distributed. Research efforts in collaboration technology have grown to address this problem. Here we describe the Access Grid and tools built for sharing information as part of this effort. As will be seen in this thesis, collaboration technology both relies on visualization technology and supports it in enabling interactions at a distance.\n\nThroughout this work we have taken a user driven iterative approach using real applications from a variety of scientific domains. This end-to-end testbed approach guarantees realistic experimental circumstances with real world stresses and constraints.\n\nThe main contributions of this dissertation are: a) discovery of requirements for the connecting of collaboration and visualization technology to high performance computing; b) development of infrastructure and demonstrations for enabling coupled advanced displays and high performance resources, including the first remote\nconnection of two spatially immersive virtual environments (CAVE to CAVE); and c) development of infrastructure for efficient pixel transport using commodity video codecs to support collaborative scientific visualization.
SUMMARY:Visualization and Collaboration Technologies to Support High-Performance Computing Research
UID:539
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090202T103000
DTEND:20090202T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:The representational accuracy of the isosurface meshes produced by marching isosurfacing methods is usually defined by the closeness of the produced mesh to the isosurface given by trilinear interpolation. In this seminar, a new metric that evaluates the accuracy of marching isosurfacing methods is introduced. The new metric is an accurate estimate of spatial discrepancy between a produced mesh and the trilinear interpolation isosurface. Computation of the new metric is also described. Experimental results of the accuracy examination of several well-known isosurfacing methods using the new metric are presented. An analysis of the accuracy and rendering cost of the mesh produced by each considered method is also given. In addition, possible future extensions of this research work are discussed.
SUMMARY:Evaluation of Accuracy of Marching Isosurfacing Methods
UID:548
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090203T103000
DTEND:20090203T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Very large, software-intensive systems are normally built from a combination of established legacy components and new components contributing new functionality. The cost of building such systems and maintaining them through-life can be reduced by adopting the principles and architectures of Open Systems. These principles and architectures will be discussed. The case for the benefits to be obtained from Open Systems will be argued. \n	\nExamples of Open Systems will be drawn from defense applications, from open source applications and from web services, in support of this thesis. It is hoped that the presentation will engender a lively debate, which will allow the speaker to tailor the content to the types of application of interest to the audience.
SUMMARY:Systems and Open Architecture – the benefits case
UID:550
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090311T150000
DTEND:20090311T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:With the advance in performance and capabilities of modern computers, the drive towards large-scale integrated simulations of complex flow systems is growing. The different flow physics in different components of these systems often calls for integration of different solvers. In this talk, we present a computational methodology that we developed for coupling compressible and low Mach number codes, motivated by the necessity to model systems where flow conditions vary substantially - from supersonic to almost stagnating.\n\nWe describe the details of implementation on structured overlapping meshes, formulate unsteady interface conditions, validate our choice of interface conditions by comparing numerical errors for different formulations, and show the results of numerical experiments performed on a wide range of steady and unsteady laminar and turbulent problems.\n
SUMMARY:Code Integration for Large-Scale Systems Simulations: Compressible - Low Mach Number Coupling
UID:556
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090216T143000
DTEND:20090216T153000
DTSTAMP:20091122T063007Z
LOCATION:Ryerson 251, University of Chicago
DESCRIPTION:There is a sea change happening in academic research -- a transformation caused by a data deluge that is affecting all disciplines.  Modern science increasingly relies on integrated information technologies and computation to collect, process, and analyze complex data.  Data-centric science is the \"Fourth Paradigm.\"  Tools, technologies, and platforms must seamlessly integrate into standard scientific methodologies and processes.  Microsoft External Research is committed to open access, open tools, and interoperability in the heterogeneous world of academic research.  This talk will illustrate the far-reaching changes that this new paradigm will have on scientific discovery.
SUMMARY:eScience and the Fourth Paradigm
UID:557
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090304T150000
DTEND:20090304T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:In machine learning and data mining, data are often represented in numerical form, as a matrix or a tensor. In many cases, the data are onnegative. For example, in text mining, a collection of documents is converted to a term-document matrix whose (i,j) entry is the frequency of term i in document j. In face recognition, a face image in grayscale is represented as a nonnegative matrix, and a set of face images forms a 3-dimensional data tensor.\n\nLow-rank approximation by principal component analysis (for a matrix) or tensor decomposition (for a tensor) is frequently used to filter out noise or capture important features. However, certain properties may be lost due to the introduction of negative values. It has been proven by numerical evidence that adding the nonnegative constraints helps detect the essential features of the data. The resulting technique is called nonnegative matrix factorization (NMF) for matrices or nonnegative tensor factorization (NTF) for tensors.\n\nThe NMF and NTF computation can be formulated as a simple-bound nonconvex optimization problem, to minimize the matrix distance or divergence subject to the nonnegativity constraints. Various alternating algorithms have been proposed to solve it. We show that virtually all alternating algorithms for NMF can be adapted to compute NTF, and draw the relations between the algorithms in the literature. The initialization schemes and sparseness constraints for NMF and NTF will also be discussed.\n
SUMMARY:From Nonnegative Matrix Factorization to Nonnegative Tensor Factorization
UID:558
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090218T150000
DTEND:20090218T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:CyberSecurity is a growing concern especially in open grids, where attack propagation is easy due to existing collaborations. We consider how to respond optimally to an attack in grid environments.\n\nWe present an optimization model that takes the existing collaborations   as input and minimizes the disruption to the grid whilst reducing   threat-levels at unaffected sites. Our optimization model outputs which   collaborations must be suspended or monitored to reduce threat-levels at   unaffected sites.\n\n
SUMMARY:Optimal Response to Attacks on The Open Science Grid
UID:559
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090216T103000
DTEND:20090216T113000
DTSTAMP:20091122T063007Z
LOCATION:Bldg: 221, Conference Room A216, Argonne National Laboratory
DESCRIPTION:As the types of problems we solve in high-performance computing and other areas become more complex, the amount of data generated and used is growing at a rapid rate.  Today many terabytes of data are common; tomorrow petabytes of data will be the norm. One of the challenges in high-performance computing is to provide users with reliable data access in a distributed, heterogeneous environment. In this talk, we will review the existing I/O paradigms in high-performance computing environments and explore better alternatives across both local and wide-area networks.  We propose three different techniques to accommodate the I/O requirements of scientific applications.  We present a new design for a high-performance, scalable parallel file system that obviates the need for dedicated I/O and metadata servers by utilizing Object-based Storage Devices. We also propose a new remote I/O paradigm that takes advantage of the increasing popularity of high-speed wide-area networks and centralized data repositories to perform I/O over wide-area networks. Lastly, we present a scalable I/O forwarding solution that attempts to bridge the increasing performance gap between the processing power and the I/O subsystems of massively-parallel leadership-class machines such as the IBM Blue Gene/P.
SUMMARY:Rethinking I/O in High-Performance Computing Environments
UID:560
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090415T150000
DTEND:20090415T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:In this work we improve the existing tools for the recovery and prediction of human decisions based on multiple factors. We use essentially a latent factor method, and obtain the decision-influencing factors from the observed correlations in the available statistical information by singular value decomposition-based principal factor identification. We generalize on widely-used linear representations of decision-making functions by using adaptive high-order polynomial interpolation and applying an iterative and adaptive post-processing to arrive at an estimated probability of every possible outcome of a decision. The novelty of the method consists in the use of flexible, nonlinear predictive functions, and in the suggested post-processing procedure. Our experiments show that the introduced approach is at least competitive in the class of SVD-based prediction methods, and that the precision grows with the increase in the order of the polynomial basis. We suggest that the method may be successfully applied instead of a widely used linear SVD-based methods.\n\n
SUMMARY:Polynomial Interpolation for Predicting Decisions and Recovering Missing Data
UID:561
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090223T103000
DTEND:20090223T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Conference Rm. A216, Argonne National Laboratory
DESCRIPTION:Funded by the Japanese government, the University of Tokyo, University of Tsukuba, and Kyoto University are developing a seamless and highly productive parallel programming \nenvironment for high performance computing.  Started in 2008, this four-year research and  development initiative aims to provide a new portable, efficient, and convenient parallel programming environment for a variety of machines, such as small-scale to large-scale PC clusters and next-generation petascale supercomputers.  Researchers are developing a new parallel programming language, numerical libraries, and runtime systems.  After presenting an overview of the project, researchers will discuss the portable, single runtime environment \ndeveloped at the University of Tokyo, which consists of a portable user-level file system and an implementation-independent MPI runtime system.  Using this runtime environment, the binary code developed in the PC cluster may run in a supercomputer center, although the supercomputer runtime environment is different.  The presentation will conclude with a preview of future research efforts.
SUMMARY:Towards Seamless and High-Productive Parallel Programming Environment
UID:562
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090319T150000
DTEND:20090319T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Room A216, Argonne National Laboratory
DESCRIPTION:Optimizing large-scale scientific applications for a variety of modern high-performance computing systems is a non-trivial process given the state-of-the-art in performance tuning software. Current performance systems do not facilitate large-scale performance experiments that require multiple application runs nor do they present performance data in a form that would enable the application scientists to efficiently optimize their codes. We will present a component environment that automates performance data collection, storage, analysis, and visualization for parallel scientific applications. This system aims to enable application scientists to efficiently collect meaningful performance data that will facilitate their efforts in code optimizations.\n
SUMMARY:Automatic Generation of Performance/Memory Models for Parallel Scientific Applications
UID:563
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090224T100000
DTEND:20090224T110000
DTSTAMP:20091122T063007Z
LOCATION:Bldg: 360, Conference Room L119, Argonne National Laboratory
DESCRIPTION:This talk will have two parts.  In the first part, we will survey the current situation with regard to programming models for scalable parallel computers, identifying some important research needed in this area.  In the second, we will present the Asynchronous Dynamic Load Balancing library (ADLB), a package that is being used to present a much simpler programming model than message passing while allowing applications to scale to (at least) tens of thousands of processors. It is being used on Intrepid for Argonne\'s GFMC nuclear physics code, an INCITE award winner, but is likely to be useful for other applications as well.
SUMMARY:Programming Models, Languages, and Libraries, and a Simple API for Specifying Very Large Computation
UID:565
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090325T150000
DTEND:20090325T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Room A216, Argonne National Laboratory
DESCRIPTION:With the increasing scaling of manufacturing technology, process variation is a phenomenon that has become more prevalent. As a result, in the context of Chip Multiprocessors (CMPs) for example, it is possible that identically-designed processor cores on the chip have non-identical peak frequencies and power consumptions. To cope with such a design, each processor can be assumed to run at the frequency of the slowest processor, resulting in wasted computational capability. This talk considers an alternate approach and proposes an algorithm that intelligently maps (and remaps) computations onto available processors so that each processor runs at its peak frequency.\n\n
SUMMARY:Process Variation Aware Thread Mapping for Chip Multiprocessors
UID:566
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090302T160000
DTEND:20090302T170000
DTSTAMP:20091122T063007Z
LOCATION:Charles M. Harper Center, 5708 S. Woodlawn Room 10, University of Chicago
DESCRIPTION:To be announced.
SUMMARY:Energy Challenges in the 21st Century
UID:568
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090408T150000
DTEND:20090408T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Room A216, Argonne National Laboratory
DESCRIPTION:The Boltzmann Transport Equation (BTE) is a powerful and general conservation equation which is capable of describing in detail the transport of electrons and phonons in metals, semiconductors, and a variety of solid-state devices. It is often called semi-classical because it describes particles as classical point particles, but includes scattering through quantum-mechanical perturbation theory. Therefore the BTE is capable of describing electrical and thermal transport down to the nanoscale. New structures, such as Carbon Nanotubes (CNTs), provide new challenges to the transport modeling community. In this talk we will discuss the BTE and its application to modeling electrical transport in single-walled CNTs. We will present a simple approach to discretizing the BTE using the upwind method, and cover electron-phonon scattering and the Linear Analytic method for computing scattering rates for use in transport simulation. Finally we will reflect on some possible extensions to enable coupled electro-thermal transport and parallel implementations.
SUMMARY:Boltzmann Equations for Nanoscience Applications
UID:570
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090316T103000
DTEND:20090316T000008
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:In this talk, I will describe my work on optimizing matrix-vector multiplication with combinatorial techniques.  My research has focused on two different combinatorial scientific computing topics related to matrix-vector multiplication.\n\nFor the first topic, I address the optimization of serial matrix-vector multiplication for relatively small, dense matrices, which can be used in finite element assembly. Previous work showed that combinatorial optimization of matrix-vector multiplication can lead to faster evaluation of finite element stiffness matrices by removing redundant operations. Based on a graph model characterizing row relationships, a more efficient set of operations can be generated to perform matrix-vector multiplication. I improved this graph model by extending the set of binary row relationships and using hypergraphs to model more complicated row relationships, yielding significantly improved results over previous models.\n\nFor the second topic, I address parallel matrix-vector multiplication for large sparse matrices.  Parallel sparse matrix-vector multiplication is a particularly important numerical kernel in computational science. We have focused on optimizing the parallel performance of this operation by reducing the communication volume through smarter two-dimensional matrix partitioning. We have developed and implemented a recursive algorithm based on nested dissection to partition structurally symmetric matrices. In general, this method has proven to be the best available for partitioning structurally symmetric matrices (when considering both volume and partitioning time) and has shown great promise for information retrieval matrices.
SUMMARY:Optimizing Matrix-Vector Multiplication with Combinatorial Techniques
UID:571
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090302T130000
DTEND:20090302T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Confernece Room A216, Argonne National Laboratory
DESCRIPTION:Chelsio Communications is leading the convergence of networking, storage and clustering interconnects with its robust, high-performance and proven unified wire technology.  Featuring a highly scalable and programmable architecture, Chelsio offers 10-Gigabit Ethernet and multi-port Gigabit Ethernet adapter cards, delivering the low latency and superior throughput required for high-performance computing applications.\n\nThe topics that will be covered by Chelsio’s CEO and President will be:\n\n- An introduction to Chelsio Communications\n- Discussion of Chelsio’s product offerings  \n- The directions and features that the 10GE market is talking and how Chelsio is addressing it\n- A brief discussion of Chelsio’s future roadmap\n- Discussion of Argonne\'s needs and future directions in Networking, Clustering and Storage\n- How may Chelsio best support Argonne?\n
SUMMARY:A Unified Wire Approach to the HPC Data Center
UID:572
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090402T130000
DTEND:20090402T140000
DTSTAMP:20091122T063007Z
LOCATION:Ryerson room 251, University of Chicago
DESCRIPTION:Advanced techniques in biomedical computing, imaging,and visualization are already changing the face of biology and medicine in both research and clinical practice.  These techniques have the potential to provide comprehensive models and views of the human body in unprecedented depth and detail.  As a result, biomedical computing and visualization will help produce exciting new biomedical scientific discoveries and clinical treatments.  In this talk, I will discuss the state of the art in biomedical computing, medical imaging, and visualization research and present examples of their vital roles in cardiology, neuroscience, neurosurgery, and radiology.
SUMMARY:Computing the Future of Biomedicine
UID:573
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090309T103000
DTEND:20090309T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Visualization has proven its value in scientific advances by helping scientists gain insight from their data and verify and correct scientific computations. As the amount of scientific data collected from sensors or simulations grows up to the order of petabytes, visualization of this large-scale data often requires high-performance distributed computing. However, it is typically challenging to develop or use visualization tools on a scalable distributed environment since they require a deep understanding of visualization algorithms, parallel processing, complex configurations and data handling. I envision the virtualization of a distributed visualization environment, which enables users to create their visualization as easily as they do on their desktop computers, while fully making use of underlying distributed visualization resource.\n\nThe individual components of a data visualization pipeline can be abstracted as: data retrieval, filtering/mining, rendering and display. My PhD work, the Scalable Adaptive Graphics Environment (SAGE) and Visualcasting, virtualizes the last component in the pipeline. With SAGE and Visualcasting, displays are totally virtualized from visualization applications. They just pass image buffers to SAGE. SAGE then scales the images to arbitrarily sized display walls ranging from a single desktop panel to a scalable array of LCD panels that are stitched together. Visualcasting extends this display virtualization by broadcasting SAGE image streams to multiple heterogeneous display clients. An analytical model of SAGE and Visualcasting was built and verified. This model will be extended to address major research questions in virtualizing the entire data visualization pipeline and then be used to investigate candidate approaches for the virtualization.\n\nThis research will improve the performance and usability of the visualization and analysis tools on ALCF\'s new visualization cluster EUREKA and motivate INCITE project investigators to leverage advanced visualization capabilities in their applications. Potentially this will change the paradigm of large-scale data visualization and expedite adoption of distributed visualization techniques to the broader DOE computational science community.
SUMMARY:Virtualization of a Distributed Visualization Environment
UID:574
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090317T103000
DTEND:20090317T113000
DTSTAMP:20091122T063007Z
LOCATION:Bldg: 221, Conference Room A216, Argonne National Laboratory
DESCRIPTION:The Parallel Multi-block Adaptive Grid generation (PMAG) algorithm has been designed to handle a general multi-block topology. The algorithm is designed to adapt a multi-block grid concurrently with each block solved in an individual process. These processes can be run on a single parallel machine or distribution over a network of workstations. MPI is used as the message passing interface. Grid adaption in PMAG is based on the weight functions. These weight functions have demonstrated the capacity to detect shocks of differing strengths, primary and secondary vortices, and shear layers adequately. A simple tri-diagonal solver is used for generating the elliptic grids. PMAG is designed to allow boundary point movement by defining the boundaries as NURBS surfaces. This guarantees that the geometric definition is preserved accurately. PMAG is effectively demonstrated in application to realistic cases involving chemically reacting species and flow involving hypersonic flows and viscous boundary layers. 
SUMMARY:Parallel Multi-block Adaptive Grid Generation For Flow Calculations
UID:576
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090326T103000
DTEND:20090326T000008
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Room A216, Argonne National Laboratory
DESCRIPTION:The talk will cover our experiences on performance analysis, tuning and implementation of (1) Parallel I/O* and (2) FFT algorithm optimizations** carried out for Blue Gene/L Supercomputer. \n\nIn order to provide sustainable Parallel I/O performance, we designed and implemented highly scalable parallel file I/O architecture for the Blue Gene/L system.  Our architecture leveraged the benefit of the hierarchical and functional partitioning design of the system software with separate computational and I/O cores. Exploiting the scalability aspect of GPFS (General Parallel File System) at the backend and using MPI I/O as an application interface, the architecture was able to deliver at least one order of magnitude higher I/O bandwidth for a real application; i.e., for HOMME application we achieved an aggregate bandwidth of 1.8 GB/Sec and 2.3 GB/Sec for write and read accesses, respectively). The implementation also included the support of high-level parallel I/O data interfaces such as parallel HDF5 and parallel NetCDF scaling up to thousands of processors.\n\nTo enhance the 2D/3D FFT algorithm (as a part of HPC Challenge Benchmark Suite), we have exploited (1) single-node FFT performance, (2) all-to-all collective performance, and (3) overlap of computation and communication. Through effective exploitation of Blue Gene/L\'s double-FPU intrinsics, careful placement of all-to-all operations and synchronizations to maximize the interleave of communications and computations, substantial performance enhancement was achieved; i.e., a highly scalable FFT implementation with 20% performance improvement over the FFTW baseline on the LLNL Blue Gene/L system.\n\n__________________\n  *Joint work with ANL (R. B. Ross, R. Thakur, R. Latham, W. D. Gropp) and H. Yu, C. Hawson, J. Moreira, T Engelsiepen from IBM Research.\n**Joint work with J. Gunnels, Y. Shabharwal, R. Garg from IBM Research.
SUMMARY:Experiences on Performance Enhancement of Parallel I/O and FFT on Blue Gene/L Supercomputer
UID:577
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090331T103000
DTEND:20090331T000008
DTSTAMP:20091122T063007Z
LOCATION:Building 360, Conference Room L119, Argonne National Laboratory
DESCRIPTION:Review of several applications of large-scale parallel computing, with focus on parallelism in the calculations and how it was exploited. From computational science, topics include: Particle-in-cell simulation of tokamak plasma microturbulence, groundwater flow contaminant transport, and multimaterial hydrodynamics. From computational finance, the topic is valuation of mortgage-backed securities.
SUMMARY:Plasmas, Fluids, and Toxic Assets: Examples of Large-Scale Parallel Computing
UID:583
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090407T103000
DTEND:20090407T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 360 / Conference Room L119, Argonne National Laboratory
DESCRIPTION:Seminar
SUMMARY:Architecting FLASH - A Complex Multiphysics Application Code that Scales from Laptops to Largest Supercomputers
UID:586
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090407T103000
DTEND:20090407T113000
DTSTAMP:20091122T063007Z
LOCATION:Bldg: 221, Conference Room A216, Argonne National Laboratory
DESCRIPTION:Urgent and emergency computing systems provide scientists with tools and capabilities to quickly allocate high-performance computing resources for time-critical applications. The usage and availability of storage and network resources in urgent computing environments can negatively impact the execution of data intensive emergency computing applications. In this talk, we present our work on supporting time-critical applications dependent on storage and network resources. We analyze the usage of current urgent computing systems and evaluate the data requirements for a potential emergency computing application. We present several data management policies and robust resource allocation techniques for urgent computing environments. Using the previously analyzed application and environment data, we evaluate these policies and techniques.
SUMMARY:Data Management for Urgent and Emergency Computing Environments
UID:587
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090409T103000
DTEND:20090409T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:The impact of commodity multi-core processors on the general computing community has been extensive. One can no longer assume that an application will run faster on successive generations of processors unless the application has been parallelized to take advantage of the increasing core count. The parallel computing community has also been adversely impacted by multi-core processors. While the increase in computation power and density from multi-core processors is encouraging, the majority of scientific parallel computing applications depend as much on memory subsystem performance as on compute performance. To make the problem worse, the MPI model, upon which nearly all scalable parallel applications are based, exacerbates the limited memory bandwidth available to a processor.\nWe have developed an operating system page table mapping strategy called SMARTMAP that allows processes on a multi-core processor to directly access each other\'s memory through simple virtual address bit manipulation. The SMARTMAP capability allows the cooperating parallel processes on a compute node to run independently as separate address spaces, but also provides the ability for the processes to act as threads running in a single address space. When used to implement MPI, SMARTMAP eliminates all extraneous memory-to-memory copies imposed by UNIX-based shared memory strategies, significantly reducing pressure on the memory subsystem for intra-node data transfers. In addition, SMARTMAP can easily support operations that UNIX-based shared memory cannot, such as direct, in-place, threaded MPI reduction operations and one-sided get/put operations.\nThis talk will describe the implementation of SMARTMAP in the Catamount lightweight kernel that runs on the Cray XT-based Red Storm platform at Sandia National Labs.  We will show performance results comparing a SMARTMAP-enabled MPI to traditional UNIX-based shared memory approaches for MPI.  We will also briefly describe several related ongoing research projects, including our next-generation open-source lightweight kernel and proposed extensions to MPI for multi-core processors being pursued by Sandia and Oak Ridge National Lab under the auspices of the DOE Institute for Advanced Architectures and Algorithms.\nBio:\nRon Brightwell received his BS in mathematics in 1991 and his MS in computer science in 1994 from Mississippi State University. He joined Sandia National Laboratories in 1995 and is currently a Principal Member of Technical Staff. While at Sandia, he has designed and developed software for lightweight compute node operating systems and high-performance networks on several large-scale massively parallel systems, including the Intel Paragon and TeraFLOPS, and the Cray T3 and XT series of machines.  His research interests include high-performance, scalable communication interfaces and protocols for system area networks, operating systems for massively parallel processing machines, and parallel program performance analysis libraries and tools.\n
SUMMARY:Enhanced Operating System Support for MPI on Multi-Core Processors
UID:589
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090414T110000
DTEND:20090414T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, room A-261, Argonne National Laboratory
DESCRIPTION:Many vital structures in complex biological systems are formed through the self-organization of initially disordered, discrete elements into coherent bodies. During cell division, for example, microtubules undergo microscopic interactions with molecular motors to form macroscopic structures including the cytoskeleton of daughter cells and the mitotic spindle which properly segregates chromosomes.  Understanding how to predict, control and orchestrate self-assembly processes on a precise biomolecular level is essential to the development of new classes of biosensors and bio-mimetic devices.\n\nWe model the motor-mediated self-organization of microtubules using a mean-field theory that captures the inherent stochastic nature of motor-filament interactions.  Our model reveals that for a sufficiently large motor density, the filament network experiences an ordering transition toward a polar state.  In our work we explicitly take into account the specifics of motor dynamics such as force-velocity relations and force-dependent detachment rates.  We show that the transition to the oriented state is both continuous and discontinuous when force-dependent motor detachment becomes important.  This result predicts an ordering hysteresis for experiments on alignment dynamics in semi-dilute and dense solutions of biological filaments.\n\n
SUMMARY:Motor-Mediated Self-Organization of Microtubules in Active Filament Solutions
UID:590
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090416T150000
DTEND:20090416T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:A chemical supply chain is an integrated network of facilities and transportation options for the procurement of raw materials, transformation of raw materials into intermediate and final products, and distribution of the final products to customers. Due to the increasing pressure to remain competitive in the global marketplace, it has become one of the major goals for most chemical companies to ensure optimal design and operation of not only the chemical production processes but also the entire chemical supply chains. This involves optimizing the network and process design, capacity and production planning, distribution and allocation planning, detailed scheduling and inventory control of a chemical supply chain to reduce the overall cost, and to maximize the profits, responsiveness and customer satisfaction. Furthermore, the supply, manufacturing, and distribution activities of a chemical supply chain have to deal with many uncertainties, such as demands, process yields, prices, breakdowns and natural disasters. Explicitly considering these uncertainties in the design and operation will add more complexity to the optimization models and consequently lead to greater algorithmic challenges. We are interested in the development of mathematical and computational tools that address the following areas: 1) Modeling of the design, planning and scheduling problems for chemical supply chains; 2) Multi-scale optimization to coordinate decision-making across geographically distributed locations and across time horizons spanning from days to years; 3) Optimization under uncertainty to account for stochastic variations and to manage the risks; 4) Algorithms and decomposition methods to support the three previous points. \n\nIn this talk, we will focus on three examples about chemical supply chain optimization under uncertainty. The first example is about the design, planning and scheduling of chemical supply chains under responsive criterion and economic criterion with the presence of demand uncertainty. A bi-criterion mixed-integer nonlinear programming (MINLP) model is developed to take into account multiple tradeoffs and to simultaneously predict the optimal locations of manufacturing sites and distribution centers, process technology, production profiles, detailed schedules, and inventory levels under different specifications of supply chain responsiveness. The second one addresses the design of chemical supply chains with multi-echelon inventory under uncertainty while taking into account risk-pooling effect. The steady-state network design and transportation decisions are integrated well with the stochastic inventory decisions by using an MINLP model, of which the large-scale instances are solved effectively by a tailored global optimization algorithm. The last example is a general computational framework for global chemical supply chain planning under uncertainty. The model formulation, computational strategies and simulation method will be discussed. Real-world industrial applications with up to 12,000 uncertain parameters are investigated to illustrate the economic benefits of considering uncertainties. A few other related projects will also be discussed along with these three examples. We will conclude this talk with some future extensions of these works to address the problems in energy & sustainability areas.
SUMMARY:Optimization Models and Algorithms for Chemical Supply Chain Design and Operation under Uncertainty
UID:591
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090415T103000
DTEND:20090415T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Threading Building Blocks (TBB) is an open source (GPL) C++ template library which provides portable support for shared memory task parallelism. It works on Linux, Windows, and Solaris as well as more exotic systems (e.g. Xbox). Its aim is to support scalable parallelism by letting you focus on the tasks which make up your problem rather than the threads which happen to execute it. This presentation will provide a short introduction to TBB and give a flavor of how it can be used.
SUMMARY:An Introduction to Threading Building Blocks
UID:594
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090427T164500
DTEND:20090427T174500
DTSTAMP:20091122T063007Z
LOCATION:Charles M. Harper Center, 5807 S. Woodlawn, Room 1, University of Chicago
DESCRIPTION:Please join us for University of Chicago\'s Chicago colloquium series: Energy in the 21st Century. Sponsored by the James Franck Institute, the U. Chicago Energy Initiative, and the Computation Institute
SUMMARY:Issues and Priorities for Energy
UID:600
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090424T103000
DTEND:20090424T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 / Conference Room A216, Argonne National Laboratory
DESCRIPTION:Seminar
SUMMARY:Scheduling and Synchroniztion for Multiprocessors
UID:598
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090423T103000
DTEND:20090423T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Behemoth petaflop computing systems will propel atmospheric simulation science to unprecedented scales; yet individual node speed remains key for time-critical applications such as real-time forecasting or climate prediction. Even very large simulations able to exploit weak scaling will be limited by cost-performance in terms of energy and dollars consumed. For these reasons, new generations of multi- and many-core processors being mass produced for commercial IT and \"graphical computing\" (video games) are being scrutinized for their ability to exploit fine-grain parallelism abundant in atmospheric models. This presentation will describe work to identify and characterize expensive computational kernels from WRF, and community weather model, in terms of computational intensity, data parallelism, bandwidth requirements and memory footprint with the aim of accelerating weather and climate model using these new processors.
SUMMARY:GPU Acceleration for Weather and Climate
UID:599
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090520T150000
DTEND:20090520T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, room A-261, Argonne National Laboratory
DESCRIPTION:We discuss some graphs coloring problems that are related to the efficient evaluation of sparse derivative matrices.  In particular, we consider the problems of finding optimal acyclic and star colorings, which model two different methods for the evaluation of Hessians. Both of these problems are known to be intractable even in severely restricted cases.  We present a formula that describes the acyclic and star chromatic numbers of graphs that are decomposable with respect to the join operation, which builds a new graph from a collection of two or more disjoint graphs by adding all possible edges between them.  We also show that our results lead to linear time algorithms for finding optimal acyclic and star colorings of cographs, which have the unique property that they are recursively decomposable with respect to the join and disjoint union operations.\n
SUMMARY:Acyclic and Star Colorings of Joins of Graphs and an Algorithm for Cographs
UID:601
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090504T130000
DTEND:20090504T140000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Confernece Room A261, Argonne National Laboratory
DESCRIPTION:Bio: James is pursuing a PhD in Computer Science at The Ohio State University\nunder the advisement of Prof. Sadayappan.  His work focuses on programming\nmodels and runtime systems for large-scale parallel computing.\n\nAbstract:  Unified Parallel C (UPC) is a language extension to the popular C programming language that adds support for parallel programming with distributed, shared data.  UPC targets both shared and distributed memory systems and presents the programmer with a logical partitioned global address space that is physically distributed across the processors and is potentially distributed across compute nodes in distributed memory systems or different memory banks in systems with nonuniform memory hierarchies.  Under UPC, every data element has affinity to a distinct processor and UPC exposes this data locality information to the programmer so that it can be leveraged to enhance\nperformance.  UPC facilitates access to the global address space through built-in language support as well as through explicit one-sided communication operations that allow processors to access any data in the global address space\nregardless of where it is stored.\n\nIn this tutorial we will cover introductory through advanced topics in the UPC programming language as well as runtime and performance considerations when targeting UPC\napplications at large-scale systems.
SUMMARY:An Introduction to the Unified Parallel C Parallel Programming Language
UID:602
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090527T150000
DTEND:20090527T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, room A-261, Argonne National Laboratory
DESCRIPTION:Empirical performance tuning has been emerging as an attractive means of tuning performance for increasingly complex computer architectures and application programs. We have been developing technologies to automate empirical tuning process of leadership class scientific applications. In this talk, I will describe our recent experience of tuning a scientific application called Nek5000 based on empirical performance tuning.\n\n
SUMMARY:Empirical Performance Tuning
UID:604
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090515T133000
DTEND:20090515T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Stochastic mixed integer program (SMIP) is considered as one of the most important and challenging problems in operations research and computer science. Such models require strategic discrete decisions to be made without full knowledge of the future, followed by tactical actions after information regarding the future is revealed. This is a natural setting for decision-making under uncertainty with applications arising from telecommunication network design, finance, homeland security, energy systems and many more.\n\nIn this research, we establish and enhance the scalability of stochastic mixed integer programming by first discussing several enhanced cut-generation methods to accelerate the computational performance of the decomposition-based branch-and-cut (D2-BAC) algorithm to tackle very large-scale SMIPs. We also explore the advantages of parallelism over serial processing in solving SMIPs by constructing portable parallel implementations. Moreover, we develop a coupled branch-and-bound algorithm to accommodate a broader class of SMIPs with continuous first-stage variables, and prove its finite convergence. Finally, in collaboration with AT&T, we propose a stochastic programming model to deliver a robust network design for the next-generation IP-over-Optical networks, as part of the DARPA CORONET project. Customized L-Shaped methods are developed for solving some large-scale practical network instances.
SUMMARY:Decomposition Methods for Two-Stage Stochastic Mixed-Integer Programming: Algorithms, Applications, and Computations
UID:605
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090520T133000
DTEND:20090520T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:In many stochastic optimization applications, there is some uncertainty about the probability distribution P of random parameters. In this talk, we study the minimax decision model for two-stage stochastic linear optimization problems\nwith the assumption that P belongs to a class of probability distributions specified by the first and second moments. We also incorporate risk considerations into the model with piecewise linear disutility functions. We show that the model is tractable for problems with random objective and some special instances of problems with random right-hand side, which are in general NP-hard. We are able to provide explicit constructions of the worst-case\nextremal distributions for the minimax problems in these cases. We then demonstrate and compare the performance of minimax solutions with that of data-driven solutions under contaminated distributions using numerical examples. Applications include a production-transportation problem and a single facility minimax distance problem. \n\nComputational results show that the minimax solutions clearly hedge against the worst-case distributions and provide lower variability in objective value than data-driven solutions under most of the contaminated distributions. Finally, we present an additional application of the proposed minimax model in providing moment bounds for an option pricing problem.
SUMMARY:Models for Minimax Stochastic Linear Optimization Problems with Risk Aversion
UID:606
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090521T140000
DTEND:20090521T150000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Room A216, Argonne National Laboratory
DESCRIPTION:A multiscale theoretical and computational methodology will be presented for studying biomolecular systems across multiple length and time scales. The approach provides a systematic connection between all-atom molecular dynamics, coarse-grained modeling, and mesoscopic phenomena. At the heart of the approach is the multiscale coarse-graining method for rigorously deriving coarse-grained models from the underlying molecular-scale interactions. Applications of the multiscale approach will be given for membranes and proteins, although the overall methodology is applicable to many other complex condensed matter systems. Recent applications to large protein complexes will also be described. The computational challenges and opportunities for this area of molecular modeling will be especially emphasized.
SUMMARY:Systematic Multiscale Modeling of Biomolecular System
UID:607
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090610T150000
DTEND:20090610T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, room A-261, Argonne National Laboratory
DESCRIPTION:This seminar is to discuss wind power forecasting and its use in power system operations. The presentation is structured into two parts. The first part concentrates on surveying existing wind power forecasting methodologies and identifying strengths and limitations of different approaches. The second part of the presentation addresses how power system operators can incorporate advanced wind forecasting technologies into their operations. Improved unit commitment and dispatch algorithms to address variability and uncertainty of wind power will be discussed. A numerical example will be shown to illustrate one feasible unit commitment and dispatch solution to integrate variable wind energy into power system operations.\n\n \n
SUMMARY:Wind forecasting and integration into power system operations
UID:608
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090528T103000
DTEND:20090528T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 / Conference Room A216, Argonne National Laboratory
DESCRIPTION:Vehicles reentering the atmosphere travel at very high velocities, causing extremely high temperature gas flows. The protection of the vehicle from this extreme high-energy environment is critical. A commonly used thermal protection system is an ablative heat shield, as used (for example) in the Apollo program and as planned for NASA\'s new Orion vehicle. The physical phenomena involved include strong shocks, aerothermochemistry, thermal non-equilibrium, thermal radiation, turbulence and the response of complex materials. Reliable computational models of this system would be of great value in design and operation of reentry vehicles. However, the models of some of these phenomena are known to be unreliable (e.g. turbulence) and others are difficult to parametrize (e.g. aerochemistry). The complexity of the phenomena, the nature of the models and the difficulty of experiments in this high-energy system make verification and validation of computational models challenging.\n\nThe Center for Predictive Engineering and Computational Sciences (PECOS) at the University Texas is taking on the challenge of verification and validation in the context of reentry vehicle simulations. In this talk, these challenges are discussed, along with some of our strategies being pursued to address them.\n
SUMMARY:Validation and Verification Challenges in the Modeling of Atmospheric Reentry Vehicles
UID:609
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090601T140000
DTEND:20090601T150000
DTSTAMP:20091122T063007Z
LOCATION:Room A134, Bdg. 221, Argonne National Laboratory, RI405, 5640 S. Ellis Ave., University of Chicago
DESCRIPTION:Abstract: Many computer models, including climate prediction models such as C-goldstein and economic models such as E3MG, take many hours, or even weeks, to execute. This type of model can have tens to hundreds of free (adjustable) parameters, each of which is only approximately known. Under the Bayesian view, the true value of the code output is a random variable, drawn from a distribution that is conditioned by our prior knowledge, and in this case by the previous code runs; the computer code is thus viewed as a random function.\n\nIn this informal talk, I introduce the BACCO suite of software and show how it can be used to generate statistical inferences about such random functions. The software may be used to furnish computationally cheap—yet statistically rigorous—estimates of the computer code output.\n\nThe talk concludes with some examples of a cutting-edge type of analysis (the \'calibrator\') that can be used to assimilate field data into computer models. In particular, the posterior PDF for the model\'s parameter space can be calculated using very flexible and realistic statistical assumptions.\n\n
SUMMARY:Bayesian Analysis of Computer Code Output: Something for Nothing
UID:614
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090701T150000
DTEND:20090701T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Energy systems modeling:  Guenter Conzelmann and Tom Veselka will provide an overview of the different energy systems modeling activities at Argonne\'s Decision and Information Sciences (DIS) division. The presentation will particularly highlight new modeling opportunities and challenges for DOE in the areas of renewables and commercial buildings\nsimulation.\n
SUMMARY:Hydopower and Energy Market Modeling
UID:615
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090715T150000
DTEND:20090715T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:We establish results for the problem of tracking a time-moving manifold arising in on-line nonlinear programming by casting this as a generalized equation. We demonstrate that if points along a solution manifold are consistently strongly regular, it is possible to track the manifold approximately by solving a linear complementarity problem (LCP) at each time step. We derive sufficient conditions that guarantee that the tracking error remains bounded to second order with the size of the time step, even if the LCP is solved only to first order accuracy. We make use of these results to derive a fast augmented Lagrangean tracking algorithm and demonstrate the developments through a numerical case study.
SUMMARY:Generalized Equation Concepts for On-Line Nonlinear Programming
UID:616
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090602T093000
DTEND:20090602T000008
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Andrew will introduce the new Argonne Leadership Computing Facility (ALCF), its mission, its current systems and the systems expected to arrive at Argonne this fall.  The ALCF ( <a href=\'http://www.alcf.anl.gov/\'>http://www.alcf.anl.gov/</a>) is a national leadership computing facility designed to provide resources that make computationally intensive projects of the largest scales possible.   \n\nCurrently the ALCF supports 9 INCITE computational science projects covering disciplines as diverse as protein folding to modeling jet engines.
SUMMARY:Overview of the Argonne Leadership Computing Facility
UID:617
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090602T103000
DTEND:20090602T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Scanned volumetric scalar datasets (as from structural MR or CT) have been the focus of much work in visualization and image analysis. Research in volume visualization has successfully blurred the distinction between methods that merely present pictures of volume data (pure \"visualization\"), versus methods that generate spatial information about material regions and boundaries (\"classification\" or \"segmentation\").  The same underlying information about local differential structure, as captured by the image gradient and Hessian, as well as quantities derived from these, play a role in setting the opacity functions that determine visibility in traditional volume rendering, as well as in image analysis methods for extracting geometric models of mathematically defined image features.  I will describe work I\'ve done in this topic, ranging from semi-automatic generation of transfer functions, to recent work on using particle systems to sample image features.  The recent particle system work may be especially useful for applications of microCT imaging.
SUMMARY:Visualizing and Analyzing Local Differential Structure in Volume Data
UID:618
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20080511T080000
DTEND:20080511T090000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, test
DESCRIPTION:test
SUMMARY:test
UID:619
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090611T133000
DTEND:20090611T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 / Conference Room A216, Argonne National Labortory
DESCRIPTION:The advent of the Petascale era, provides a great opportunity as well as a great challenge for computational science and engineering. Large scale scientific applications need to scale to unprecedented numbers of processing cores and adapt to multi-core architectures with complex memory and network hierarchies in order to fully leverage the computational resources available. In addition to possible human errors, the limit for code writing and the ever-growing complexity of many scientific codes make the development of parallel scientific applications an intimidating task. In addressing these issues, we are developing a generic collaborative problem-solving environment from mathematical abstractions for automating the development of highly scalable and efficient codes that can solve a wide range of scientific problems. In such an environment, application developers, either software engineers or domain experts, can contribute to a code with their expertise at their maximum scale, thus enhance the overall programming productivity and speed up scientific discoveries.
SUMMARY:Automating the Development of Parallel Multidisciplinary Scientific Applications
UID:620
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090708T150000
DTEND:20090708T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:Mixed Integer Nonlinear Programming (MINLP) is a broad class optimization problems that are encountered in many different applications. The presence of both nonconvex functions and variables that are constrained to be integers makes the problem difficult at many levels. In this talk, we describe MINOTAUR, a framework that is under development for solving such problems.
SUMMARY:Solving MINLPs using MINOTAUR: Description, Goals and the story so
UID:622
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090730T150000
DTEND:20090730T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, room A-261, Argonne National Laboratory
DESCRIPTION:Many recent phenomena of high interest in condensed matter physics are linked to the existence of short-ranged correlations.  The most prominent examples are provided by transition metal oxides, where complex disorder results in a balance of the spin, orbital, charge and strain degrees of freedom and give rise to competing ground states with incompatible order and exotic phenomena such as colossal magnetoresistance, negative thermal expansion, quantum spin liquids, and high temperature superconductivity.  Traditional crystallography provides well developed and sophisticated tools for obtaining the long-range order of crystalline solids, but only indirect and insufficient evidence of disorder.  While there are several techniques that are very sensitive to the existence of local disorder, none provide detailed information on the correlations between defects or the length scales of short-range ordering processes.  Single crystal diffuse scattering probes both the local distortions around point defects as well as the defect to defect correlations on length scales of 1 to 10nm and provides the most powerful tool for studying complex short range correlations, such as the formation of stripes, checkerboards, ladders, or phase separation.  However, there remain formidable difficulties in obtaining and analyzing large enough volumes of data with sufficient momentum and energy resolution required for accurate modeling.  I will discuss several systems that we are currently studying at MSD as well as some new techniques being developed to collect and analyze diffuse scattering.
SUMMARY:Challenges of using Diffuse Scattering to Measure Short Range Correlations in Crystalline Materials
UID:623
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090618T133000
DTEND:20090618T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:HMesher leverages the strengths of its parent, the p-mesher from PolyFEM: relatively coarse mesh while preserving geometric integrity, conforming meshes in complex CAD assemblies, mesh-geometry associativity, and generation of a hex-dominant mesh from the tetrahedral mesh. The HMesher (Hybrid Mesher) offers a meshing solution for an h-type FE, and it is integrated currently in CATIA V5, as part of LMS VirtualLab Meshing
SUMMARY:HMesher: Mesh Generation for CAD Assemblies
UID:624
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090916T150000
DTEND:20090916T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 203 Auditorium, Argonne National Laboratory
DESCRIPTION:Trajectories generated by classical molecular dynamics (MD) are best\ninterpreted in a statistical sense due to the weak definition of\ninitial conditions and chaotic nature of the underlying equations of\nmotion. For this reason, accuracy and efficiency of a time integration\nscheme should be measured with respect to statistical averages, rather\nthan deviations from an ``exact trajectory\'\'. A practical MD time\nintegrator must be both stable and statistically accurate, allowing for\nits use over long time intervals with large stepsizes. In this talk, I\nwill survey some results from backward error analysis for geometric\nintegrators and show how (under certain assumptions) these results can\nbe applied to understanding the statistical properties of integrators\nfor MD.
SUMMARY:Geometric Integrators for Classical Molecular Dynamics: Theory and Application
UID:625
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090930T080000
DTEND:20090930T170000
DTSTAMP:20091122T063007Z
LOCATION:JW Marriott Starr Pass Resort, Tucson, Arizona
DESCRIPTION:Participation is encouraged in the Grace Hopper Celebration of Women in Computing Conference.   The CELS directorate, along with the CIS and HR divisions, is a Bronze Sponsor at this event.   The conference is designed to bring the research and career interests of women in computing to the forefront. It is the largest technical conference for women in computing and results in collaborative proposals, networking and mentoring for junior women and increased visibility for the contributions of women in computing.  Conference presenters are leaders in their respective fields, representing industry, academia and government. Top researchers present their work while special sessions focus on the role of women in today’s technology fields.
SUMMARY:Grace Hopper Celebration of Women in Computing
UID:626
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090623T150000
DTEND:20090623T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 / Conference Room A261, Argonne National Labortory
DESCRIPTION:The runtime environment and parallel execution of the ab initio electronic structure package GAMESS is handled by the distributed data interface (DDI). In addition, DDI provides application developers with a virtual shared memory environment built around the model of a parallel global address space that is portable to all major hardware classes. DDI has proved to be a robust implementation and currently supports more than twelve different types of distributed data quantum chemistry application in GAMESS. A decade on and we are planning for the forthcoming era of petascale computing resources that pose new challenges for DDI. In this seminar, I will describe the implementation and use of DDI in GAMESS and work underway to enable DDI to support petascale quantum chemistry applications. This work is support by NSF grant \"Enabling Petascale Applications in the Chemical Sciences\" (Award 0749156).
SUMMARY:Enabling Petascale Quantum Chemistry Using the Distributed Data Interface in GAMESS
UID:627
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090602T100000
DTEND:20090602T170000
DTSTAMP:20091122T063007Z
LOCATION:Building 360, rm. L119 or online, Argonne National Laboratory
DESCRIPTION:Over one billion processing hours are available through DOE’s INCITE program for 2010, which is jointly managed by the Argonne and Oak Ridge Leadership Computing Facilities. Our Proposal Writing webinar can help you stake your claim. Sign up today – proposals are due July 1, 2009!\n\nJoin Katherine Riley, ALCF scientific applications engineer, and Bronson Messer of Oak Ridge’s Scientific Computing group, as they provide tips and suggestions to improve the quality of your INCITE proposal submission.
SUMMARY:INCITE Proposal Writing Webinar
UID:628
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090527T080000
DTEND:20090527T120000
DTSTAMP:20091122T063007Z
LOCATION:Argonne Guest House, Argonne National Laboratory
DESCRIPTION:Ready to run your project on 40 racks of the Blue Gene/P? Then come Leap to Petascale at the Argonne Leadership Computing Facility (ALCF). We\'ll tell you more about the ALCF and the petascale resources here. Then, ALCF performance engineers will help you scale and tune your applications on 40 racks of Blue Gene/P. This is an especially great opportunity for anyone considering applying for a 2010 INCITE award (Proposals for INCITE are due July 1, 2009).
SUMMARY:Leap to Petascale Workshop
UID:629
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090722T140000
DTEND:20090722T164500
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:<strong>Wes Kendall</strong>\nTitle: Terascale Analysis of Variable Interactions in MODIS\nAbstract:\nThe temporal and spatial dynamics of climatic variables are highly dependent on each other, and it is important to be able to identify multivariate interactions when assessing problems such as drought and fire damage. As climatic datasets grow beyond the terascale, previous serial methods for performing these types of analyses are infeasible to application scientists. To enhance scientific discovery at this magnitude, we developed a parallel framework that closely integrates parallel I/O techniques with an intuitive interface for issuing Boolean range queries on scientific data. Our techniques allowed us to visualize various interactions between two variables in over a terabyte of satellite data from NASA\'s Moderate Resolution Imaging Spectroradiometer (MODIS) project. We applied our methods on the entire dataset with scalability up to 16,000 cores and end-to-end execution times consistently around one minute.\n\n<strong>Alexe Mihai</strong>\nTitle: Automatic differentiation of the nuclear reactor simulation code MATWS\nAbstract: \nA tangent linear model is built for the FORTRAN 77 nuclear reactor simulation code MATWS using the automatic differentiation tool ADIFOR. The sensitivities of a few variables of interest are computed, and then validated against finite differences. The resulting derivative information will be used for uncertainty quantification and sensitivity analysis. We also describe the a priori code modifications required by ADIFOR, and the post-processing of the differentiated code.\n\n<strong>Luis de la Torre</strong>\nTitle: Carbon Emissions Trading with a Computable General Equilibrium Model\nAbstract: \nEmissions trading markets seek to reduce pollution levels by setting a cap on total emissions and allowing producers to trade pollution permits. The American Clean Energy and Security Act, passed in the House on June 26, 2009, proposes emissions trading markets for greenhouse gases including carbon dioxide.  We use a complementarity problem to model a multi-factor, multi-region economy in which a foreign producer has market power to affect prices, in order to compare policy alternatives between carbon emissions trading markets and production and use taxes. We also discuss a safety valve system, a combination of tax and emissions trading in which emissions permit prices are bounded.\n\n\n<strong>Julio Goez</strong>\nTitle: Algorithm for the estimation of Computational Noise \nAbstract: \nEstimating the computational noise present in the evaluation of a function f could play an important role in the development of convergence criteria for optimization algorithms. There are  different reasons for the presence of  noise in the evaluation of a function, for example the use of iterative methods in the computation, or single precision operations. In this presentation we will describe an algorithm for estimating stochastic computational noise. Based on our tests, this algorithm can determine the noise level of a nonlinear function with fewer than 10 evaluations (independent of the dimension), with more evaluations providing more precise estimates. \n\n<strong>Kathy King</strong>\nTitle: Optimizing Public Health Emergency Logistics with Dynamic Programming\nAbstract: \nIn the event of a public health emergency like pandemic flu or a large-scale bioterrorist attack, it is important that vaccines, antibiotics, or other medical countermeasures be distributed quickly to minimize mortality and morbidity. Federal, state, and local authorities plan to work together to rapidly distribute the necessary supplies from stockpiles to the affected population. We use a stochastic dynamic programming model of the state and local level supply chain to determine an optimal strategy for allocating limited staff, resources, and medical supplies. We also present an approximate algorithm for solving the dynamic program with realistically large data sets.\n\n<strong>Chungen Shen</strong>\nTitle: A Non-monotone Filter Method for Nonlinear Optimization\nAbstract: \nWe propose a non-monotone filter sequential quadratical programming (SQP) algorithm in which the l and g-filters are introduced. The g-filter being a traditional monotone filter guarantees the global convergence. The l-filter is a non-monotone filter that allows more flexibility for accepting a trial point. Under standard conditions,we prove the super-linear local convergence without second order correction (SOC) steps.\n\n<strong>Andy Terrel</strong>\nTitle: FEM automation of Oldroyd-B &#64258;uids\nAbstract:\nOver the past several years the FEniCS projects have developed many advances in the automation of &#64257;nite element codes. These techniques allow the researcher to study numerous models and numerical discretizations quite rapidly. With this technology, we study the numerous viscoelastic models and discretizations presented by Baaijens. This allows us to systematically address many stability questions with quick comparisons between numerous test problems. We present both the abstractions for the FEM automation as well as the comparisons for the different Oldroyd-B type models.\n\n<strong>Krystal Richards and Seneca Gibson</strong>\nTitle: Experiences On Empirical Performance Tuning of Scientific Applications - S3D and MADNESS\nAbstract:\nEmpirical performance tuning has been emerging as a popular and attractive means of dealing with very complex computer architectures and application programs.  Two important scientific application packages, S3D (numerical simulations of turbulent combustion) and MADNESS (simulation framework for solving quantum chemical problems) are installed and tested on target platform (AMD Quad-Core Phenom) for empirical performance tuning.  Tasks involving preparation, processing, and methods will be discussed.  Some experimental results in profiling, identifying kernels, and tuning the codes will be presented. \n
SUMMARY:SASSy : Student Argonne Summer Symposium
UID:630
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090527T080000
DTEND:20090527T120000
DTSTAMP:20091122T063007Z
LOCATION:Argonne Guest House, Argonne National Laboratory
DESCRIPTION:Ready to run your project on 40 racks of the Blue Gene/P? Then come Leap to Petascale at the Argonne Leadership Computing Facility (ALCF). We\'ll tell you more about the ALCF and the petascale resources here. Then, ALCF performance engineers will help you scale and tune your applications on 40 racks of Blue Gene/P. This is an especially great opportunity for anyone considering applying for a 2010 INCITE award (Proposals for INCITE are due July 1, 2009).
SUMMARY:Leap to Petascale Workshop
UID:631
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090701T103000
DTEND:20090701T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:MPI is the industry standard for distributed memory parallel programming and Unified Parallel C (UPC) is a relative newcomer that promises high productivity with comparable performance.  In comparison with MPI\'s\ntwo-sided messaging model, UPC provides a partitioned global address space programming model that allows for one-sided access to distributed, shared data.\n\nHybrid programming models that mix MPI with shared memory parallelism through threads or OpenMP have been successful at improving performance through data locality and reducing data replication.  In this presentation we will explore a new hybrid programming model that mixes MPI with UPC, drawing on the strengths of each model.  We will discuss\nruntime system issues such as ensuring mutual progress on communication and MPMD-style launching of hybrid jobs as well as algorithmic and performance implications of the hybrid model.\n\nBio:\nJames is pursuing a PhD in Computer Science at The Ohio State University under the advisement of Prof. Sadayappan.  His work at OSU focuses on dynamic load balancing and scalable runtime systems to support task parallelism.  His research interests include parallel programming models, fault tolerance, high performance computing applications, and runtime systems.\n
SUMMARY:Hybrid Parallel Programming with MPI and UPC
UID:632
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090812T150000
DTEND:20090812T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:Given a graph, a simple strategy for measuring the closeness of vertices is as follows. We initially associate to each vertex a random number, then update the value of each vertex by the average of the values of its neighbors, and perform this update a few times. The closeness between a pair of vertices is indicated by the difference of the two associated values. This closeness is inspired by the concepts used in Bootstrap Algebraic Multigrid in which it allows a better interpolation of low-residual errors.\nIn this talk, I will unravel the mystery of this simple process, explain the intuition behind it, and analyze its convergence properties. This measurement has been successfully used for solving (or improving the existing algorithms for) a number of combinatorial problems, including graph partitioning, maximum matching, minimum p-sum, etc. I will present the results in these scenarios, which show the superior usefulness of this closeness concept. \n\n
SUMMARY:Measuring the Connection Strengths between Graph Vertices
UID:633
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090707T103000
DTEND:20090707T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221, Room A216, Argonne National Laboratory
DESCRIPTION:In this talk, I will describe our recent work towards building a lightweight Software Persistent Memory (SoftPM) infrastructure and the new capabilities that it enables. Fundamentally, SoftPM eliminates the duality of data management in applications, whereby memory-resident data is readily accessible but volatile, and storage-resident data is persistent, yet not directly accessible to the process. SoftPM allows applications to allocate persistent memory in much the same way volatile memory is allocated, and easily restore, browse, and interact with past versions of persistent memory state. This simplifies the implementation of three broad capabilities required in a variety of applications -- recoverability (e.g., checkpoint-restart), record-replay (e.g., scientific data visualization), and execution branching (e.g., simulation model-space exploration). I will discuss research challenges, our approach, and some promising preliminary results.\n\nIn the latter part of the talk, I will give a brief overview of other ongoing systems work in our lab.
SUMMARY:Software Persistent Memory and Its Applications
UID:634
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090701T150000
DTEND:20090701T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 360 / Conference Room L119, Argonne National Labortory
DESCRIPTION:We have developed a program package GPAW [1] for density functional calculations (DFT) using real-space grids together with the projector augmented wave method. In addition to the basic ground state properties, excited state properties such as optical absorption spectra can be calculated with the time-dependent density functional theory (TD-DFT) where we have implemented both linear response and real-time propagation formulations of the theory.\n\nGPAW is well suited for massively parallel calculations, and we will present current parallelization strategies as well as examples about the parallel scalability. We will present also some examples about the applicability of GPAW \nboth in DFT and TD-DFT calculations.\n\n[1] wiki.fysik.dtu.dk/gpaw\n\n
SUMMARY:GPAW: Efficient Tool for Real-Space, Real-Time Electronic Structure Calculations
UID:635
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090630T133000
DTEND:20090630T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:The work on an arithmetic analogue (i.e., in mixed characteristic) of a certain geometric object, called an affine Grassmannian, that are common over equal-characteristic local fields.  A finite-dimensional Grassmannian variety is the parameter space of subspaces of a given vector space; the points of this space (corresponding to subspaces) form a continuous family. Affine Grassmannian is a generalization of this when the given vector space is defined over a local field (think of the field of quotients of formal power series), and that the subspaces are replaced by certain lattices, that is, maximal-rank submodules over the ring of integers of the local filed.\n\nWhen the local field is in mixed characteristic, such parameter space was constructed and studied by W. Haboush. It is a union of finite dimensional projective varieties over the residue field, each of which has singularities. The results that are obtained is that this singular variety is still normal (i.e. singularities are \"not bad\") and locally complete intersection, making it the next best thing to have, after a nonsingular variety.\n\nTerminologies appearing above, in terms of examples will be mentioned. Some ideas will be going into constructing this parameter space, and if time permits, relevance to other branches of mathematics such as number theory, representation theory or physics will be mentioned.
SUMMARY:Results on the Parameter Space of Certain Lattices in Mixed Characteristic
UID:636
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090629T103000
DTEND:20090629T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:In fluid mechanics two ways can be used to describe the behavior of a flow field.  One is the Lagrangian method which describes the time rate of change in the flow properties along the traces of identifiable flow parcels.  The other is the Eulerian method which observes the properties of flow at a fixed position over time. \n\nIn this talk, I will discuss the analogies of Lagrangian and Eulerian methods in visualization of time-varying scalar data. I will briefly overview some traditional visualization methods for time-varying data, which I will argue are mostly Lagrangian. Then I will describe our recent research in analyzing time-varying scientific data with Eulerian approaches. The new approaches allow us to obtain more accurate spatio-temporal information about the features in time-varying data sets. I will discuss the essential components of our analysis environment including multiscale data representations, distance metrics and classification schemes, and a method for multivariate data visualization. Our goal is to complement the existing visualization techniques, and provide the scientists with better quantitative data analysis tools.
SUMMARY:Visualizing Time-Varying Data using Lagrangian and Eulerian Approaches
UID:637
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090702T140000
DTEND:20090702T150000
DTSTAMP:20091122T063007Z
LOCATION:Building 202, Conference Room B169, Argonne National Laboratory
DESCRIPTION:For the last five years a network of research institutions in Europe and the US (including Argonne) have collaborated on the assembly of a minimal protocell - a self-replication system with tightly coupled catalytic cooperation among \"genes\", metabolism, and container.  In this talk I will report scientific progress and challenges for this work as well as discuss a vision for a \"living technology\" in part based on our ability to assemble artificial \"living\" materials.  Experimentally, we have recently demonstrated this coupling by having an informational molecule (8-oxoguanine) catalytically control the light driven metabolic (Ru-bpy based) production of container materials (fatty acids).  This is a significant milestone towards assembling a minimal self-replicating molecular machine.  Work in progress for our container associated gene-replication system will also be presented.  \n\nCoupling is needed between the gene-metabolism-container system and the container associated gene-replication system to form a functional protocell. I present a variety of physics based simulation (molecular dynamics, dissipative particle dynamics and reaction kinetics) of the coupled protocell components and its life-cycle, and they expose a number of anticipated systemic challenges associated with the remaining experimental implementation of the protocell.  Finally I will outline how simple self-replicating materials could be useful as part of \"living technology\", a central component of the nano-bio-info-cogno (NBIC) knowledge convergence, and sketch how the protocell work might provide new clues to the origin of life.\n\n
SUMMARY:Assembly of a Minimal Protocell
UID:638
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090701T133000
DTEND:20090701T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:The first component of this work is a parallel algorithm for constructing non-uniform octree meshes for finite element computations. Prior to octree meshing, the linear octree data structure must be constructed and a constraint known as 2:1 balancing\" must be enforced; parallel algo-\nrithms for these two subproblems will also be presented. \n\nThe second component of this work is a parallel matrix-free geometric multigrid algorithm for solving elliptic partial dierential equations (PDEs) using these octree meshes. The last component of this work is a parallel multiscale Gauss\nNewton optimization algorithm for solving the elastic image registration problem. The registration problem is discretized using nite elements on octree meshes and the parallel geometric multigrid algorithm is used as a preconditioner in the Conjugate Gradient (CG) algorithm to solve the linear system of equations formed in each Gauss Newton iteration.\n\nThe parallel octree meshing and multigrid algorithms have several physical and computer science applications such as in solid/fluid mechanics, heat/mass transfer, electromagnetism, image processing and unstructured mesh generation. Potential applications for the image registration algorithm include automatic identication of abnormalities in medical images, motion reconstruction from temporal sequences of images and planning of surgeries.\nSeveral ideas were used to reduce the overhead for constructing the octree meshes. These include (a) a way to lower communication costs by reducing the number of synchronizations and reducing the communication message size, (b) a way to reduce the number of searches required to\nbuild element-to-vertex mappings, and (c) a compression scheme to reduce the memory footprint of the entire data structure. To our knowledge, the multigrid algorithm presented in this work is the only matrix-free multiplicative geometric multigrid implementation for solving nite element equations on octree meshes using thousands of processors. The proposed registration algorithm is also unique; it is a combination of many different ideas: adaptivity, parallelism, fast optimization\nalgorithms, and fast linear solvers.\n\nAll the algorithms were implemented in C++ using the Message Passing Interface (MPI) standard and were built on top of the PETSc library from Argonne National Laboratory. The multigrid implementation has been released as an open source software: Dendro. Dendro has been tested on several NSF TeraGrid platforms. Our largest run was a highly nonuniform, 8- billion-unknown, elasticity calculation on 32,000 processors.
SUMMARY:Parallel Octrees, Multigrid and Elastic Image Registration
UID:639
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090713T103000
DTEND:20090713T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:Major progress in magnetic fusion research has led to ITER - a multi-billion dollar burning plasma experiment supported by seven governments (EU, Japan, US, China, Korea, Russia, and India) representing over half of the world\'s population. Currently under construction in Cadarache, France, it is designed to produce 500 million Watts of heat from fusion reactions for over 400 seconds with gain exceeding 10 - thereby demonstrating the scientific and technical feasibility of magnetic fusion energy. Strong research and development programs are needed to harvest the scientific information from ITER to help design a future demonstration power plant with a gain of 25. Advanced computations at the petascale and beyond in tandem with experiment and theory are essential for acquiring the scientific understanding needed to develop whole device integrated predictive models with high physics fidelity. This is the primary motivation for the Fusion Simulation Program (FSP) - a new DOE-SC initiative supported by the Offices of Fusion Energy Science and Advanced Scientific Computing Research -- that is entering the project definition phase. Since ITER and leadership class computing are prominent missions of the DOE today, producing such a world-leading predictive capability for fusion represents a key exascale-relevant strategic project for the future.
SUMMARY:Fusion Simulation Program (FSP):  Simulations at the Petascale and Beyond for Fusion Energy Sciences
UID:641
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090805T150000
DTEND:20090805T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:Performance experiments can involve multiple execution runs where parameters such as execution platform, measurement tools, methods of measurement, application parameters, and analysis techniques can vary. In order to manage the layers of complexity involved in experimental setup, execution, and post-analysis, a degree of abstraction and automation is necessary at each stage. A layer of abstraction is needed to hide the intricacies involved in experimental set-up and runs for varying sets of experimental parameters. We present an integrated component-based environment that automates the process of running multiple performance experiments and parameter selection of parallel scientific applications. Our toolkit will enable application scientists to easily modify the experimental parameters over multiple execution runs and to selectively retrieve the data for analysis and generation of performance models.
SUMMARY:An Automated Component-Based Performance Experimentation Environment
UID:642
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090721T110000
DTEND:20090721T000008
DTSTAMP:20091122T063007Z
LOCATION:Research Institute, Room 480, University of Chicago
DESCRIPTION:The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher.   Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain.  However, effective design and implementation of computational tools that genuinely facilitate the generation of novel and significant scientific insights remains poorly understood.  In this talk, I will describe a set of efforts that combines natural language processing for information extraction, graphical network models for semantic data integration, and some novel user interface approaches into a system that has recently played a pivotal role in making a significant biomedical discovery.
SUMMARY:3R Systems for Biomedical Discovery Acceleration
UID:643
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091028T150000
DTEND:20091028T160000
DTSTAMP:20091122T063007Z
LOCATION:1416, Conference Center, Bldg 240, Argonne National Laboratory
DESCRIPTION:This talk is set at a basic level. Differentiation and Integration are \noften the earliest and possibly the best understood topics in elementary calculus. So it may come as a surprise to some that serious problems may be encountered in programming Numerical Quadrature and Numerical Differentiation.\n\nAmong the topics treated are the performance profile of the automatic\nquadrature routine; a software interface problem; round-off error amplification in numerical differentiation; and, at the very end, possibilities for using complex variable analysis.\n\nThese lead to generally conceptual problems. The questions which arise can be understood with minimal mathematical sophistication.  But a particular answer, if one exists, might be complicated. In this talk we concentrate on the questions.
SUMMARY:The Area and the Slope; many questions; fewer answers.
UID:644
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090930T150000
DTEND:20090930T160000
DTSTAMP:20091122T063007Z
LOCATION:TCS Building, Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:Asynchronous Dynamic Load Balancing
UID:647
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090923T150000
DTEND:20090923T160000
DTSTAMP:20091122T063007Z
LOCATION:TBA, Argonne National Laboratory
DESCRIPTION:Ion channels are irresistible objects for biological study because they are the [nano] ‘valves of life’ controlling an enormous range of biological function, much as transistors control computers. Ion channels are much easier to simulate than many proteins because conformation changes are not involved in channel function, once the channel is open. Open channels are interesting objects for chemical study because they effectively select among chemically similar ions, under unfavorable circumstances. Channels are interesting objects for physical study because they contain an enormous density of charge, fixed, mobile, and induced. Direct simulation of channel behavior in atomic detail is difficult if not impossible. Macroscopic electric fields and concentration gradients produce substantial flows which are the natural biological function of the channel, making equilibrium analysis unhelpful. Multiscale issues are nontrivial: simulations must deal with concentrations of 10^(&#8722;7) to 55 M of different chemical species. Ion transit takes ~ 10^(&#8722;8) sec compared to a calculation time step of 10^(&#8722;16) sec and a biological time scale of 10^(&#8722;4) — 1 sec.\n\nComputations in full three dimensions are not yet feasible. In reduced dimensionality, however, a simple physical model does surprisingly well. One model with the same two parameters accounts for qualitatively different selectivity of both calcium and sodium channels in a wide range conditions. The model does not involve any traditional chemical binding energies at all. The binding free energy is an output of the calculation, produced by the crowding of charged spheres in a very small space.\nHow can such a simple model give such specific results when crystallographic wisdom and chemical intuition says that selectivity depends on the precise structural relation of ions and side chains? The answer is that structure is the computed consequence of the forces in this model and is very important indeed, but as an output of the model, not as an input. The relationship of ions and side chains vary with ionic solution and are different in different channels and solutions. Selectivity is a consequence of the ‘induced fit’ of side chains to ions and vice versa.\n\nThe simplified model (probably) works because the structures in both the model and the real channel are self-organized and at their free energy minimum, forming different structures in different conditions. A variational approach is immediately suggested by these results and one is well under way, applying the methods of Chun Liu (Associate Director, IMA Minnesota) and colleagues, perfected in electro-rheology.\n\nPractical exploitation to design selective biomimetic membranes for desalination and detoxification depends on computation. Trial and error methods are not likely to be efficient enough to allow practical design. Computational success depends on the accurate (± 3%) estimation of both energy and entropy of the self-organized structure in three dimensions of space and one of time.\n\nComputational design of these biomimetric systems is an unmet challenge that can soon be met because of the memory bandwidth and size of next generation computers.\n\n\n
SUMMARY:Self-organized selectivity in Calcium and Sodium Channels: Biomimetic Designs now ready for Serious Computation
UID:648
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090909T150000
DTEND:20090909T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION:We study the refractive index sensitive transmission of a 3D\nplasmonic crystal, which can exhibit strong optical responses near certain wavelengths and are used in chemical sensing applications. Our goal is to design a a square array of subwavelength cylindrical nanowells in a polymer conformally coated with a gold film that maximizes the optical response.\n\nEvery choice of design parameters requires the solution of a 3D finite-difference time-domain simulations that runs for 12 hours of wall-clock time on a 125-nopde linux cluster. We reveal \"How the Optimization Was Won\" using low-tech tools such as email, matlab, and AMPL.\n\nGovernment health warning: \n-------------------------\nThis talk is content-free! It does not contain any enlightening or educational material. Attending this talk may seriously harm your ability to carry out world-class research!\n\nJoint work with Stephen Gray (CNM), Joanna Maria (UIUC), and\nBoyana Norris (MCS). 
SUMMARY:Optimization By Email of 3D Plasmonic Crystal Structures
UID:650
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090819T150000
DTEND:20090819T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A261, Argonne National Laboratory
DESCRIPTION: 
SUMMARY:The XM Travel System and How it Applies to LANS
UID:651
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090826T103000
DTEND:20090826T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 360 / Conference Room L119, Argonne National Labortory
DESCRIPTION:Programmers and application developers using HPC systems require simple-to-use tools to determine how efficiently their codes are executing on a target machine, and for analysis and eventual improvement of their application’s performance.  \n\nMany factors contribute to an application’s performance on HPC systems. Extracting meaningful runtime performance data, managing very large performance data volumes, extracting useful information from them, interpreting that runtime information to identify and locate those factors, which most affect performance, are all tasks difficult for a programmer to manage.  Tools to extract and record system events indicative of execution performance have been available for some time.  What has been lacking is a means to manage, reduce complexity, and extract hidden execution performance problems. \n\nA performance tool set, from a recent system vendor, based on existing performance packages like PAPI cross-platform hardware performance counter interface, developed at the University of Tennessee, TAU (Tuning Analysis and Utilities) performance tool suite, developed at the University of Oregon, and others, is used to illustrate runtime performance inefficiencies in example codes.\n
SUMMARY:HPC Tools for Performance Profiling and Analysis on Some Code Examples
UID:654
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091007T150000
DTEND:20091007T160000
DTSTAMP:20091122T063007Z
LOCATION:TCS Building, Argonne National Laboratory
DESCRIPTION:Parallel File Systems today are comprised of multiple software components combined to provide concurrent and efficient access across hundreds or possibly thousands of storage devices.  Using traditional programming models to develop these systems leads to large code bases, full of code that is difficult to follow, debug, and build on.  In this presentation, I will describe a programming model based on concurrent state machines that has been useful in the implementation of the Parallel Virtual File System (PVFS), enabling concise specification of logical control flow.  I will also describe a new approach that attempts to address a number of the lessons learned in PVFS.
SUMMARY:Event Driven Programming Models for Parallel Storage Systems
UID:655
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091020T080000
DTEND:20091020T050000
DTSTAMP:20091122T063007Z
LOCATION:UIC Forum, Chicago
DESCRIPTION: Dramatic growth in data and equally rapid decline in the cost of highly integrated clusters has spurred the emergence of the data center as the platform of choice for a growing class of data-intensive applications. To encourage conversations between those developing applications, algorithms, software, and hardware for such \"cloud\" platforms, we are convening the second workshop on Cloud Computing and Its Applications (CCA\'09).\n\nThis workshop will provide two days of invited talks on cloud computing, data intensive scalable computing, and related topics.\n\nTopics of interest include:\n<ul>\n    <li> compute and storage cloud architectures and implementations</li>\n    <li> map-reduce and its generalizations</li>\n    <li> programming models and tools</li>\n    <li> novel data-intensive computing applications</li>\n    <li> data intensive scalable computing</li>\n    <li> distributed data intensive computing</li>\n    <li> content distribution systems for large data</li>\n    <li> data management within and across data centers</li>\n    <li> models, frameworks and systems for cloud security</li>\n</ul>\n\n<strong>Organizing Committee</strong>\n\nIan Foster\nArgonne National Laboratory\nUniversity of Chicago\n\nRobert Grossman\nUniversity of Illinois at Chicago\nOpen Data Group\n\nDouglas Thain\nUniversity of Notre Dame\n\nPhilip Yu\nUniversity of Illinois at Chicago\n\nKate Keahey\nArgonne National Laboratory\nUniversity of Chicago\n\nYunhong Gu\nUniversity of Illinois at Chicago
SUMMARY:CCA09: Cloud Computing and Its Applications
UID:656
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090903T150000
DTEND:20090903T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 221 Conference Room A216, Argonne National Laboratory
DESCRIPTION:In our work, we consider a class of complex interaction-transport systems of atmospheric chemistry in the context of SVD-based model reduction. Many tasks of simulation, optimization and control can be performed more efficiently, if the intermediate complexity of the chemical model is reduced. We use an SVD-based approach (\"method of snapshots\") to extract information from a set of full model observations and project the model equations onto a reduced order space so that the full dynamics are preserved with only a moderate error. \n\nWe examine and improve many features of the method. In particular, we show how to measure sensitivities of the model reduction process, and use the results to select the placement and weighting of observations to best reproduce specific events in the full model behavior. We develop techniques for reduced space basis selection that allow us to take into account multiple events. We show how to construct reduced models to replace the full model in iterative parameter optimization procedures so that fewer steps and lower computational cost is needed for the search to converge. \n\nThe overall result of our study is a more complete understanding of how to perform factor analysis, simulation and optimization of nonlinear models using model reduction tools.
SUMMARY:Model Reduction for Simulation and Optimization in Chemical Kinetics
UID:657
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090910T120000
DTEND:20090910T130000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:The effective use of data is key to advances in almost all \ndisciplines. Data-intensive research is emerging as a new paradigm. Researchers in many disciplines have opportunities for significant advances as a result of the pervasive growth in digital data, communication and devices. There are many challenges in enabling researchers to become adept in this new and fast-changing context.\n\nThe talk will report progress towards understanding how to economically enable a large community of researchers to become fluent in whatever uses of data will benefit their research.  We recognize that there are many different data-related activities and that there are many variations in the nature, maturity, structure and scale of the data.  We propose a characterisation of clusters of similar requirements in the search for commonalities that may help provision and engagement.  The talk will be illustrated with examples from a range of disciplines and is part of \na fact-finding tour of US research centers.\n\n[<a href=\'http://www.ci.uchicago.edu/events/2009/CI_data-intensiveSeminar.pdf\'>pdf</a>]
SUMMARY:Exploiting and Providing Research  Data: Finding Strategies to Help  Researchers
UID:658
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090922T110000
DTEND:20090922T120000
DTSTAMP:20091122T063007Z
LOCATION:Research Institue, Room 480, University of Chicago
DESCRIPTION:The CI\'s \"Disciplinary Deep Dive\" (3-D) program aims to identify opportunities for collaborative research across the University and Argonne.\n\nA 3-D features an appropriate mix of workshops, lectures, and informal discussions. We welcome ideas for topics and volunteers to organize the meetings. 
SUMMARY:Explanatory Combinatorial Dictionary in Natural Language Processing
UID:661
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091202T150000
DTEND:20091202T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 (TCS), Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:TBA
UID:666
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091125T150000
DTEND:20091125T160000
DTSTAMP:20091122T063007Z
LOCATION:1404&1405, Conference Center, Bldg 240, Argonne National Laboratory
DESCRIPTION:Quantum chemistry is the field of computational science\nwhich attempts to elucidate molecular processes by solving the\nmany-body electronic Schroedinger equation.  The computational\nchallenges associated with this task are quite different from\nmainstream supercomputing.  Codes like NWChem make very little use of\nMPI and are not frequently used on BlueGene platforms.  I will explain\nwhy this is presently true by describing the subset of quantum\nchemistry algorithms resulting from coupled-cluster theory.  Unique\nscientific opportunities in quantum chemistry which follow from MPI-3\nand BlueGene/Q conclude this talk.
SUMMARY:Quantum chemistry for computer scientists
UID:667
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091104T150000
DTEND:20091104T160000
DTSTAMP:20091122T063007Z
LOCATION:TCS Building, 1404&1405, Conference Center, Bldg 240
DESCRIPTION:Scientists and engineers must understand results from experiment and simulation generated data to gain insights and perform knowledge discovery. However, the potential of large-scale systems for analytic capabilities may be difficult to achieve because of limited I/O, file system performance, and a lack of appropriate interfaces for data analysis. In this talk, I will present an active storage for scalable data analysis that enables end-to-end optimizations needed for performance and productivity gains when utilizing petascale systems. Specifically, I will present our design of an active storage node that will allow data analysis, mining, and statistical operations to be executed from within the parallel I/O runtime systems. I will then present the design of a parallel I/O runtime interface that will utilize customized active storage nodes to perform I/O operations. Lastly, I will present our experimental results using a set of data analysis kernels running on our active storage prototype. 
SUMMARY:Scalable Data Analysis and Active Storage
UID:668
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091014T150000
DTEND:20091014T160000
DTSTAMP:20091122T063007Z
LOCATION:TBA, Argonne National Laboratory
DESCRIPTION:PerfSuite is an open source package for application software performance\nanalysis on Linux-based systems developed at the National Center for\nSupercomputing Applications (NCSA).  Since its initial public release in 2003,\nPerfSuite has gained a worldwide user base due to its emphasis on usability and flexibility.  In addition to routine use for application measurement, tuning, and benchmarking in production environments, PerfSuite has been extended and deployed in novel ways both at NCSA and through collaborations with other research groups.  Through the ongoing NSF SDCI (Software Development for Cyberinfrastructure) program, PerfSuite is currently involved in the POINT (Productivity from Open, Integrated, Tools) project that brings together the PerfSuite, TAU, PAPI, and Scalasca software packages with the overall goal of improving the integration and interoperability of these components.\n\nThis talk will provide an overview of PerfSuite, beginning with the motivation\nfor and history of its development.  Past and current collaborative activities\nin which PerfSuite has been involved will be discussed, and finally an overview\nof current directions and development plans for PerfSuite will be outlined,\nincluding recently-released support for the Java programming language.
SUMMARY:The PerfSuite Toolset for Application Performance Analysis: Evolution, Status, and Future Directions
UID:674
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090914T143000
DTEND:20090914T153000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Conference Room 2.C.1, Argonne National Laboratory
DESCRIPTION:Researchers have long relied on shared resources and distributed computing,while industry and home users typically have utilized dedicated hardware and single-threaded programs. Recently though, advanced in networking, virtualization and middleware have have enabled many businesses and individual users to move much of their environment to network-based resources.  Google, Amazon and others have made vast computing, storage and network available and lowered the cost of entry a few cents.  We will examine the evolution of computing toward \"the cloud\" and explore some of the critical technologies.  The cloud presents both opportunities and challenges for users of high performance computing (HPC) infrastructure. Rather needing to develop for a highly specialized supercomputing or grid environment, the cloud promises users a highly flexible environment with any resource dynamically available.  However, the performance requirements of HPC software puts unique demands on the infrastructure that current cloud implementations cannot satisfy.  We will talk about cloud infrastructures and how they might be customized for HPC, with special emphasis on networking.  This seminar is intended to provide an opportunity for open discussion.
SUMMARY:Clouds for HPC: Opportunities and Challenges in Compute, Storage and Networking
UID:663
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090921T103000
DTEND:20090921T113000
DTSTAMP:20091122T063007Z
LOCATION:Auditorium in building 203, Argonne National Laboratory
DESCRIPTION:In the first part of this talk, we will discuss challenges in dealing\nwith large graphs in general, including the task of visualizing all of\nthe sparse matrices in the University Florida Sparse Matrix\nCollection. While traditional graph visualization methods can be\ninvaluable in getting an overall sense out of large data sets, they\nare not as helpful in conveying the underlying structural information,\nclusters, and neighborhoods. In the second part of this talk, we\ndescribe an algorithm, GMap, for visualizing graphs as maps. GMap\novercomes some of the shortcomings with the help of the geographic map\nmetaphor. The effectiveness this algorithm is illustrated with\nvisualization examples from several domains, namely Netflix movies, TV\nshows, Amazon books, and last.fm music. Some results of this talk can\nbe found at http://www.research.att.com/~yifanhu/gallery.html 
SUMMARY:Visualization of large relational data sets and clusters as graphs and maps
UID:664
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090915T130000
DTEND:20090915T170000
DTSTAMP:20091122T063007Z
LOCATION:Building 401, Room A1100, Argonne National Laboratory
DESCRIPTION:One of the foundational issues in high-performance computing is the ability to move large (multi-gigabyte, and even terabyte) data sets between sites. Simple file transfer mechanisms such as FTP and SCP are not sufficient either from the reliability or the performance perspective. Globus implementation of GridFTP is the most widely used open source production quality data mover available today.\n\nIn the first half of this tutorial, the presenters will cover GridFTP server administration. They will walk through the steps required for setting up and configuring GridFTP server on Linux/Unix machines. In the second half, they will explain the steps required for installing the commonly used GridFTP client \'globus-url- copy.\' They will demonstrate the use of globus-url-copy and describe a set of best practices for obtaining maximal file transfer performance with GridFTP.\n\nParticipants are urged to bring a laptop with access to Linux machines to get hands-on experience.
SUMMARY:Tutorial on GridFTP
UID:665
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091114T080000
DTEND:20091114T170000
DTSTAMP:20091122T063007Z
LOCATION:Portland Convention Center, Portland, Oregon
DESCRIPTION:SC09 will be the 22nd consecutive year of the SC Conference series – once again featuring an exceptional Technical Program, industry and research exhibits, Education Program and many other activities. For 2009, three new Technology Thrust areas have been added: Bio-Computing, Sustainability, and the 3D Internet.\n\nEstablished 21 years ago, the conference has built a diverse community of participants including researchers, scientists, computing center staff members, IT and data center management, application developers, computer manufacturing personnel, program managers, journalists and congressional staffers. This diversity is one of the conference\'s main strengths, making it a yearly \"must attend\" forum for stakeholders throughout the technical computing community.
SUMMARY:SC09: Bio-Computing, Sustainability,  3D Internet
UID:672
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090928T143000
DTEND:20090928T153000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Conference Room 3C1, Argonne National Laboratory
DESCRIPTION:Complex Networks are pervasive in our society.  Realistic biological, information, social and technical networks share a number of unique features that distinguish them from physical networks.  Examples of such features include: irregularity, time-varying structure, heterogeneity among individual components and selfish/cooperative game-like behavior by individual components.  Furthermore, the network structure, the dynamical process on the network and the behavior of constituent agents co-evolve over time.  The size and heterogeneity of these networks, their co-evolving nature and the technical difficulties in applying dimension reduction techniques commonly used to analyze physical systems makes reasoning, prediction and controlling of these networks even more challenging.  Recent quantitative changes in high performance and wireless computing capability have created new opportunities for collecting, integrating, analyzing and accessing information related to such large complex networks.  The advances in network and information science that build on this new capability provide entirely new ways for reasoning and controlling these networks. Together, they enhance our ability to formulate, analyze and realize novel public policies pertaining to these complex networks.  Over the last 15 years, our group has established a theory based program for modeling, simulation and associated decision support tools for understanding such large socio-technical systems. Complementing this modeling environment is a scalable service delivery framework that provides policy analysts and scientists seamless access to the modeling environment. After a brief overview, I will describe our approach within the context of a specific application: development of modeling and decision support environments to study epidemics in co-evolving social and wireless networks.
SUMMARY:Building Virtual Cities:  Policy Informatics for Large Co-evolving Socio-Technical Networks
UID:670
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091109T103000
DTEND:20091109T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, TCS (1404, 1405, 1406), Argonne National Laboratory
DESCRIPTION:Remy Evard, former Deputy Division Director of MCS and CIO of Argonne, has been working for Novartis Pharmaceuticals since early 2007. Remy is the CIO of the Novartis Institutes for BioMedical Research (NIBR), the global research organization of Novartis.  NIBR\'s mission is to discover new therapies for patients in need, which it accomplishes by carrying out biomedical scientific research. Remy will compare and contrast the working environments, culture, and use of computing of Argonne and Novartis, considering different aspects such as for-profit vs. non-profit, global vs. local, corporate vs. DOE laboratory. He will also describe the basic pharmaceutical scientific pipeline, his work and focus at NIBR, the challenges in the industry, and some of the potential for collaboration and interaction. This will be an informal talk with plenty of opportunity for questions, answers, and discussion.
SUMMARY:Working in the \'Real World\'
UID:737
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090930T130000
DTEND:20090930T140000
DTSTAMP:20091122T063007Z
LOCATION:Cafeteria Conf. Rm. B, Argonne National Labortory
DESCRIPTION:Parallab is the unit for High Performance Computing at the University of Bergen and operates the universities supercomputer facilities and other e-infrastructures. The group conducts research and development in scientific computing, engineering, Grid- and other e-infrastructures.\n\nIn this presentation we introduce Parallab and its activities in scientific computing.  Specialfocus will be on computational results in miscible displacement porous media flow. These processes can be described by nonlinear partial differential equations.  We will address challenges in their numerical treatment and discuss software development as well as numerical solutions strategies. Secondly, we show how results from numerical bifurcation analysis can help to understand the structure of the nonlinear solutions. Finally, we apply statistical methods in order to derive practically relevant results from the nonlinear, instable dynamics. It turns out that large\ncompute- and storage infrastructures are required to efficiently obtain these types of results.\n\n
SUMMARY:Porous Media Flow: Learning from Numerical Simulations
UID:676
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090930T130000
DTEND:20090930T140000
DTSTAMP:20091122T063007Z
LOCATION:Cafeteria Conf. Rm. B, Argonne National Labortory
DESCRIPTION:Parallab is the unit for High Performance Computing at the University of Bergen and operates the universities supercomputer facilities and other e-infrastructures. The group conducts research and development in scientific computing, engineering, Grid- and other e-infrastructures.\n\nIn this presentation we introduce Parallab and its activities in scientific computing.  Specialfocus will be on computational results in miscible displacement porous media flow. These processes can be described by nonlinear partial differential equations.  We will address challenges in their numerical treatment and discuss software development as well as numerical solutions strategies. Secondly, we show how results from numerical bifurcation analysis can help to understand the structure of the nonlinear solutions. Finally, we apply statistical methods in order to derive practically relevant results from the nonlinear, instable dynamics. It turns out that large\ncompute- and storage infrastructures are required to efficiently obtain these types of results.\n\n
SUMMARY:Porous Media Flow: Learning from Numerical Simulations
UID:677
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20090930T130000
DTEND:20090930T140000
DTSTAMP:20091122T063007Z
LOCATION:Cafeteria Conf. Rm. B, Argonne National Labortory
DESCRIPTION:Parallab is the unit for High Performance Computing at the University of Bergen and operates the universities supercomputer facilities and other e-infrastructures. The group conducts research and development in scientific computing, engineering, Grid- and other e-infrastructures.\n\nIn this presentation we introduce Parallab and its activities in scientific computing.  Specialfocus will be on computational results in miscible displacement porous media flow. These processes can be described by nonlinear partial differential equations.  We will address challenges in their numerical treatment and discuss software development as well as numerical solutions strategies. Secondly, we show how results from numerical bifurcation analysis can help to understand the structure of the nonlinear solutions. Finally, we apply statistical methods in order to derive practically relevant results from the nonlinear, instable dynamics. It turns out that large\ncompute- and storage infrastructures are required to efficiently obtain these types of results.\n\n
SUMMARY:Porous Media Flow: Learning from Numerical Simulations
UID:678
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091002T094500
DTEND:20091002T104500
DTSTAMP:20091122T063007Z
LOCATION:Bldg. 240, Conference Rom 6C2, Argonne National Laboratory
DESCRIPTION:The recent advent of agent-based modeling (ABM) and the availability of software platforms for its implementation offer a powerful alternative to model the spatiotemporal behaviors of a fishery with the consideration of heterogeneity and interactivity. This paper describes a prototype agent-based fishery management model of Hawaii’s longline fishery. The model simulates the daily fishing activities of 120 Hawaii longline vessels of diverse characteristics. Following the strategy of pattern oriented modeling (POM), we use the spatiotemporal distribution pattern of fishing efforts to calibrate the model. While POM has a record of success in ecology, the present application to socioeconomic systems such as fishing and fishery management is almost unprecedented.\n\nWe also use the calibrated model to evaluate three alternative fishery regulatory policies in Hawaii’s longline fishery: 1) no regulation; 2) annual cap of 17 turtle interactions; and 3) close the north central area year round, with respect to their impacts on fishing productivity and by-catch of protected sea turtle. The prototype model, constructed using 1999 data, appears to be able to capture the responses of the fishery to these alternative regulations reasonably well, suggesting its potential as a management tool for policy evaluation in Hawaii’s longline fishe
SUMMARY:A Prototype Agent Based Model for Policy Evaluation in Hawaii\'s Longline Fishery
UID:687
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091007T110000
DTEND:20091007T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 202, Room B169, Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:The Evolution of ADP-glucose Pyrophosphorylase Subunits
UID:688
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091002T103000
DTEND:20091002T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Room 2C2, Argonne National Laboratory
DESCRIPTION:As large-scale numerical simulations permeate science and industry, the resulting deluge of data brings about an urgent need for effective analysis tools to help researchers turn this information into actual insight. Scientific visualization plays an important role in this process by creating a visual interface to massive dataset sets that affords an intuitive basis for interpretation,\nassessment, and decision making. However, the rapidly growing size and complexity of scientific datasets put an increasing emphasis on the ability of visualization methods to clearly convey a high-level picture of the data by characterizing its inherent structure across spatial and temporal scales. In this talk I will describe a general strategy built upon a principled mathematical framework to identify salient structures in vector and tensor fields, which are ubiquitous in practical scenarios. Our methodology combines concepts from topology and dynamical systems, differential geometry, and computer vision to extract important features from large-scale multivariate\ndatasets, thus producing a concise geometric signature that lends itself to automatic processing and insightful visual representations. I will illustrate this basic approach in the context of problems ranging from computational fluid dynamics and solid mechanics to fusion research and medical image analysis. I will also present our ongoing work on the application of a novel Lagrangian method to the structural analysis and interactive multi-scale exploration of transient flows.
SUMMARY:Structural Analysis of Vector and Tensor Fields for Effective Visualization
UID:689
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091118T150000
DTEND:20091118T160000
DTSTAMP:20091122T063007Z
LOCATION:1404&1405, Conference Center, Bldg 240, Argonne National Laboratory
DESCRIPTION:This talk deals with two quadratic inverse eigenvalue problems that arise in mechanical vibration and structural dynamics. The &#64257;rst one, Quadratic Partial Eigenvalue Assignment Problem(QPEVAP), arises in controlling dangerous vibrations in mechanical structures, such as buildings, bridges, highways, automobiles, air and space crafts, and others. QPEVAP concerns with &#64257;nding two feedback matrices such that a small amount of the eigenvalues of the associated quadratic eigenvalue problem are reassigned to suitably chosen ones while keeping the remaining large number of eigenvalues and eigenvectors unchanged. For robust and economic control design, these feed-back matrices must be found in such a way that they have the norms as small as possible and the condition number of the modi&#64257;ed quadratic inverse problem is minimized. These considerations give rise to two nonlinear unconstrained optimization problems, known respectively, as the Robust Quadratic Partial Eigenvalue Assignment Problem (RQPEVAP) and Minimum Norm Quadratic Partial Eigenvalue Assignment Problem (MNQPEVAP). The other one, Finite Element Model Updating Problem (FEMUP) arising in the design and analysis of structural dynamics, refers to updating an analytical &#64257;nite element model so that a set of measured eigenvalues and eigenvectors from a real-life structure are reproduced and the physical and structural properties of the original model are preserved. A properly updated model can be used in con&#64257;dence for future designs and constructions. Another major application of FEMUP is the damage detections in structures. Solutions \nof FEMUP also give rise to several constrained nonlinear constrained optimization problems.\n\nWe will give an overview of the recent developments on computational methods for these difficult nonlinear optimization problems and discuss directions of future research. The talk is interdisciplinary in nature and will be of interests to mathematicians, computational and applied mathematicians, specialists in optimizations, and engineering researchers and practicing engineers.
SUMMARY:Computational and optimization methods for quadratic inverse eigenvalue problems in finite element model updating
UID:693
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091005T133000
DTEND:20091005T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Room 1406 and 1407, Argonne National Laboratory
DESCRIPTION:Ever increasing research and development in science and engineering is based on I/O and data intensive simulations and/or analysis of observational data, requiring the use of high-performance computing (HPC) systems. Traditional\ninterfaces in file systems and storage systems are designed to handle the worst-case scenarios for conflicts, synchronization, locking, coherence checks, and other issues, which adversely affect the I/O performance. In\nmany cases, the problem is not that of having insufficient I/O capacity or bandwidth, but it is the excessive synchronization of I/O accesses at the I/O layer, generated by massively parallel applications.\n\nWe have designed and implemented an I/O delegate system that uses a subset of processes to carry out the I/O tasks for an application. By placing the I/O system close to the applications and allowing the applications to pass the high-level data access information, the I/O system has more opportunity to provide better performance. One of the most important features of the I/O delegate system is that it allows communication among delegates and enables their collaboration for further optimizations, such as collaborative caching, I/O aggregation, load balancing, and request alignment. We achieved I/O Bandwidth improvement percentages ranging from 25 &#37; to 260 &#37; by allocating 2-3 &#37; additional compute nodes to be used as I/O delegate nodes.\n\nUsing I/O delegate system as the basic infrastructure, we have developed a method that assigns disjoint file regions to the I/O delegates such that, lock conflicts and overlapping accesses are resolved at the delegate system.\nFor example, Lustre file system has a server-based locking protocol, we configure I/O delegates to have one-to-one or one-to-many mapping to the I/O servers. This strategy of having persistent pairing between servers and clients reduces the number of lock acquisitions to only one, eliminates lock contention altogether, produces more effective data prefetching, and less cache coherence control overhead. By allocating only 1/8th of additional\ncompute nodes as I/O delegates, we achieved I/O Bandwidth improvement percentages ranging from 100 &#37; to 10000% for applications using MPI Independent I/O operations.
SUMMARY:Optimizing I/O for Large-Scale Scientific Applications using I/O Delegation
UID:694
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091009T110000
DTEND:20091009T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 203 Auditorium, Argonne National Laboratory
DESCRIPTION:During the last several years there has been an increasing awareness that exascale (1018 operations/sec) computer systems may be feasible by the end of the next decade.   This community awareness began through a series of town hall meetings held at Argonne, Berkeley and Oak Ridge in the spring of 2007, a series of DARPA sponsored workshops and study groups looking at challenges for exascale hardware and software and most recently a series of eight DOE workshops covering applications ranging from climate, to high-energy and nuclear physics to biology.   DOE has launched a joint planning effort between the Office of Science and the National Nuclear Security laboratories to develop the science case and a roadmap that includes technology research and development, hardware platform development, programming models and software development and science code development.   While it is generally assumed in the science community that there are many problems whose solution can be advanced by access to three orders of magnitude more computing capability than exists today, it is unclear at this point how many problems will actually be able to effectively utilize the systems that will be possible to build.   In this talk I will describe the technical barriers (e.g. device power, optics, packaging, concurrency, etc.) to developing exascale systems, the current approaches to attack those barriers and the science that we hope will drive the venture.
SUMMARY:Building the Science Case for Exascale Computing
UID:695
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091008T133000
DTEND:20091008T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:The Petascale Active Data Store (PADS) project is a National Science Foundation (NSF) Major Research Infrastructure grant. Using the funds from NSF and the University of Chicago the project will acquire and operate a substantial data storage (~500 terabytes) and analysis system (9 teraflop/s) for the Computation Institute community.  \n\nThis talk will provide an overview of the PADS project, including an update on the state of hardware and software. It will introduce the upcoming seminar series being held this fall and the class on data intensive computing to be held winter quarter. Finally it will open up for discussion the research issues associated with the project. 
SUMMARY:PADS Overview and Update
UID:697
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091015T133000
DTEND:20091015T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:As HPC systems have approached petascale, the demands on storage and I/O throughput of HPC workloads have brought about highly developed storage systems with unprecedented performance.  Likewise, data intensive computing has driven new approaches to storage architectures that meet the needs of those programming models. This seminar presents the Parallel Virtual File System, its role as a software component in the petascale storage architecture, and as a platform that supports development of a variety of storage models and architectures.
SUMMARY:Maximizing throughput of Petascale Storage with PVFS
UID:706
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091209T150000
DTEND:20091209T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 (TCS) Conference Center, Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:Parallel scripting with Swift
UID:707
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20100106T150000
DTEND:20100106T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 (TCS) Conference Center, Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:TBA
UID:708
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091023T153000
DTEND:20091023T163000
DTSTAMP:20091122T063007Z
LOCATION:TBA, Argonne National Laboratory
DESCRIPTION:The optimal Jacobian accumulation problem is one of the original\ncombinatorial problems arising in automatic differentiation.\nThe vast majority of approaches to this problem have attempted to\nexploit its similarity to the problem of minimizing fill during LU\nfactorization of sparse, unsymmetric matrices.\nIn this talk, we take a complexity-theoretic approach to Jacobian accumulation.\nSpecifically, we explore relationships between this problem and others\nthat occur in the context of algebraic and Boolean complexity,\nas well as discuss the results that are implied by these relationships.
SUMMARY:New Complexity Results for Jacobian Accumulation
UID:709
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20100127T150000
DTEND:20100127T160000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:TBA
UID:710
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091111T150000
DTEND:20091111T160000
DTSTAMP:20091122T063007Z
LOCATION:1404&1405, Conference Center, Bldg 240, Argonne National Laboratory
DESCRIPTION:Message passing via MPI is widely used in single-program, multiple-data (SPMD) parallel programs.  Existing data-flow frameworks do not model the semantics of message-passing SPMD programs, which can result in less\nprecise and even incorrect analysis results.  We present a data-flow analysis framework for performing interprocedural analysis of message-passing SPMD programs. The framework is based on the MPI-ICFG representation, which is an interprocedural control-flow graph augmented with communication edges between possible send and receive pairs and context-sensitivity. We demonstrate our techniques on the nonseparable analysis, activity analysis.  Activity analysis is a domain-specific analysis used to reduce the computation and storage requirements for automatically differentiated MPI programs. Our experimental results have shown that using the MPI-ICFG data-flow analysis framework improves the precision of activity analysis and as a result significantly reduces memory requirements for the automatically differentiated versions of a set of parallel benchmarks.
SUMMARY:Improving the Precision of Activity Analysis on MPI Programs
UID:711
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091023T103000
DTEND:20091023T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 / Room 1C2, Argonne National Labortory
DESCRIPTION:We describe the development of graphics processor (GPU) accelerated iterative methods and preconditioners for solving linear systems arising in science and engineering applications. Krylov subspace methods including GMRES and TFQMR have been implemented on the GPU using Nvidia Cuda.  The performance of these algorithms is intimately related to the performance of matrix-vector multiplies and sparse-matrix storage formats.  The convergence of an iterative solver is most often determined by the preconditioner employed. The data-parallel architecture of the GPU computing platform must be considered when selecting a preconditioner.  We also report on the development of a set of preconditioners, working together with GPU accelerated iterative solvers, to provide significant acceleration. These include, but are not limited to, block Jacobi, algebraic multigrid (AMG) with novel smoothing techniques, sparse approximate inverses and CPU based ILU(k) preconditioners that work with GPU solvers.
SUMMARY:GPU Accelerated Krylov Subspace Methods and Preconditioners
UID:712
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091029T133000
DTEND:20091029T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:Increasingly massive datasets produced by tomorrow\'s simulations beg the question: How will we connect this data to the computational and display resources that support visualization and analysis?  This question is driving research into new approaches to allocating computational, storage, and network resources. Some of these approaches rest on creating and exploiting ways to optimally couple these resources in real time.\n\nExamples of what we mean by resource-coupled computations abound.  For example, remote visualization is an activity which may couple data and large computation resources at the shared facility to client software and display hardware at the remote site. In situ analysis and visualization contemporaneously merges simulation and analysis onto the shared resource of the supercomputing platform.  Co-analysis approaches will directly couple simulations running on a primary supercomputer to live analysis running on an optimized visualization and analysis platform over a high performance network.\n\nConsequently, we are working on a systems approach to modeling the end-to-end activity of extracting understanding from computational models.  In this paper we will present our models and results from experiments designed to test them.
SUMMARY:Modeling Resource-Coupled Computations
UID:713
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091022T133000
DTEND:20091022T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:Scripting languages let users rapidly compose assemble existing programs into more powerful applications.  In parallel scripting, users apply parallel composition constructs to existing sequential or parallel programs to develop highly parallel applications.\n\nParallel scripts are quite flexible and portable, and can run efficiently on platforms ranging from multicore workstations to petascale supercomputers. For many applications, like parameter sweeps and data analysis, parallel scripting is easier, more accessible, and more productive than tightly-coupled parallel programming.\n\nIn this talk, we will describe how the Swift parallel scripting system (www.ci.uchicago.edu/swift) is used to run scientific applications on petascale systems like IBM Blue Gene/P and Sun Constellation. We’ll present case studies, discuss architectural challenges of large-scale systems in the areas of scheduling and data management, and examine solutions that are also relevant to effectively using the PADS system.
SUMMARY:Parallel Scripting for Science Applications at the Petascale and Beyond
UID:714
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091105T133000
DTEND:20091105T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:The Petascale Active Data Store (PADS) Fall Seminar Series is a forum for discussions of data intensive computing. Our first series held Fall 2008 introduced the National Science Foundation funded PADS system, its hardware and software infrastructure, and highlight some of the scientific domain partners and how they plan to use the environment.\n\nThis week\'s lecture is with CI Faculty and Fellow, Gordon Kindlmann.
SUMMARY:Particle Systems for Robust Feature Sampling and Visualization of Three-Dimensional Imaging
UID:715
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091112T133000
DTEND:20091112T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:Montage is an astronomical image mosiacking tool that has been used in a variety of infrastructures.  This talk will discuss the history of the application and how it has been used on single processor systems, clusters, and grids, including discussing performance on these systems.  More recently, we have looked at some general questions about distributed applications, using Montage as a sample application.  We have some initial ideas on objectives for developing, deploying, and executing distributed applications, and we have attempted to begin using these ideas for Montage, and will discuss this work, which includes running Montage on a mix of grids an
SUMMARY:Using Montage, an Astronomical Mosaicking Application, to Explore Data-Oriented Distributed Computing
UID:716
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091124T133000
DTEND:20091124T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Room 1404-1405, Argonne National Laboratory
DESCRIPTION:Interactions among individuals are often modeled as social networks\nwhere nodes represent individuals and an edge exists if the\ncorresponding individuals have interacted during\nthe observation period. The model is essentially static in that the\ninteractions are aggregated over time and all information about the time\nand ordering of social interactions is discarded. We show that such\ntraditional social network analysis methods may result in incorrect\nconclusions on dynamic data about the structure of interactions and the\nprocesses that spread over those interactions.\n\nWe have extended computational methods for social network analysis to\nexplicitly address the dynamic nature of interactions among individuals.\nWe have developed techniques for identifying persistent communities,\ninfluential individuals, and extracting patterns of interactions in\ndynamic social networks. We will discuss computational properties of the\nanalysis problems and algorithms for solving them. Time permitting, we\nwill demonstrate the applicability of the techniques by analyzing zebra\nsocial networks.\n
SUMMARY:Computational Analysis of Dynamic Networks
UID:741
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091203T133000
DTEND:20091203T143000
DTSTAMP:20091122T063007Z
LOCATION:Searle Lab, room 240, University of Chicago
DESCRIPTION:The Petascale Active Data Store (PADS) Fall Seminar Series is a forum for discussions of data intensive computing. Our first series held Fall 2008 introduced the National Science Foundation funded PADS system, its hardware and software infrastructure, and highlight some of the scientific domain partners and how they plan to use the environment.
SUMMARY:Characterizing Economic Forecast Uncertainty with Ensemble Simulations and Large Scale Analysis in CIM-EARTH
UID:718
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091023T110000
DTEND:20091023T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Conference Center Rooms 1406 & 1407, Argonne National Laboratory
DESCRIPTION:The talk will cover the development of cluster ion beam technology, including historical background, fundamental characteristics of cluster ion to solid surface interactions, emerging industrial applications, and identification of some of the significant events which occurred as the technology has evolved into what it is today.  The new ion beam processes, using cluster ions which consist of substantial numbers of atoms or molecules, are very different from those produced by impact of conventional ions comprised of single atoms or molecule. Cluster-surface collisions produce important non-linear effects which are being applied to shallow junction formation, to etching and smoothing of semiconductors, metals, and dielectrics, to assisted formation of thin films with nano-scale accuracy, and to other surface modification applications. Some of the unique industrial applications which have been done by a Japanese large-scale government project (METI/NEDO) will also be presented.  
SUMMARY:Cluster ION Beam Technology for Nano-scale Surface Processing
UID:719
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091021T133000
DTEND:20091021T143000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Room 3C1, Argonne National Laboratory
DESCRIPTION:Storage systems on leadership-class machines can deliver tens of gigabytes of performance at peak, yet applications frequently see much less performance in practice.  High Level I/O libraries such as HDF5 can bridge the gap between application I/O and the storage system. This seminar will give an introduction to using the HDF5 library, with a focus on parallel I/O and performance tuning options.\n\nQuincey has been with The HDF Group since its founding and started with the HDF team in 1991, when it was still part of the  National Center for Supercomputing Applications. He serves as the Director of Software Development, overseeing the design and architecture of the HDF5 software, as well as providing software engineering leadership. Quincey received his Bachelor’s degree in Electrical Engineering \nfrom the University of Illinois and is pursuing his Master\'s degree in Computer Science from the U of I.
SUMMARY:Parallel I/O with HDF5: Overview and Tuning
UID:720
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091029T103000
DTEND:20091029T113000
DTSTAMP:20091122T063007Z
LOCATION:Bldg: 240, Conference Room 1404, 1405, and 1406, Argonne National Laboratory
DESCRIPTION:Autotuning technology has emerged recently as a systematic process for evaluating alternative implementations of a computation to select the best-performing solution for a particular architecture. At a LANS seminar in May, I introduced compiler-based empirical performance tuning and presented my success of applying it to a dense matrix-multiply kernel for small, rectangular matrices. \n\nIn this talk, I will begin with a summary of the talk, and then present my recent progress since then. A major result is that I could use the same technique to tune a higher-level kernel which is a loop with a call to a dense matrix multiply routine for small matrices. The kernel performance is up to 82% of peak on an AMD Phenom processor. With the tuned higher-level kernel and the library of tuned matrix multiply routines produced earlier, the whole Nek5000 program achieves 21% speedup on 256 nodes of the Cray XT5 at Oak Ridge National Laboratory. Also, I will show the overheads and fluctuations in measurements and how I overcame them for this experiment.
SUMMARY:Speeding up Nek5000 with Autotuning and Specialization
UID:723
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091028T110000
DTEND:20091028T120000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, TCS Conference Center (1416), Argonne National Laboratory
DESCRIPTION:Doug Kothe is the director of science for the NCCS at ORNL, responsible for guiding the multidisciplinary research teams using the center’s leadership computing systems. Doug has more than 20 years of experience in computational science research. His research interests and expertise have centered on developing physical models and numerical algorithms for simulating physical processes in the presence of incompressible and compressible fluid flow. A leader in modeling interfacial flows, he has been the principal developer of broadly disseminated scientific simulation tools. His most notable contribution has been the development of methods for flows possessing interfaces, especially free surfaces.Before joining the NCCS, Doug was deputy program director for Theoretical and Computational Programs in the Advanced Simulation and Computing (ASC) Program at Los Alamos National Laboratory (LANL). He served for several years as the leader of ASC’s Telluride Project, which developed the advanced manufacturing simulation tool “Truchas” for the Department of Energy complex. He joined the technical staff at LANL in 1988 as a member of the Fluid Dynamics Group, in which he helped develop the Ripple, Pagosa, and CFDLIB computational fluid dynamics codes. He later worked in the Structure/Relations Group and was group leader of the Continuum Dynamics Group.\n\nDoug received his B.S. in chemical engineering from the University of Missouri–Columbia and his M.S. and Ph.D. in nuclear engineering from Purdue University. He is the author of more than 60 refereed publications and has written more than a half-million lines of source code.\n
SUMMARY:Progress & Challenges in the High-Fidelity Modeling of Interfacial Flows in Scalable Multi-Physics Applications
UID:724
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091028T140000
DTEND:20091028T150000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Room 5178, Argonne National Laboratory
DESCRIPTION:Radar-based Observations of Convection
SUMMARY:Radar-based Observations of Convection - A Tale of Two Cities
UID:725
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091029T080000
DTEND:20091029T000008
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Rooms 1404, 1405, Argonne National Laboratory
DESCRIPTION:Ray Bair, LCRC director will cover how employees may obtain Fusion accounts, computer time and support. Fusion is intended for laboratory-wide use and is located in the Theory and Computing Sciences Building
SUMMARY:LCRC Supercomputer Briefing
UID:726
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091105T103000
DTEND:20091105T113000
DTSTAMP:20091122T063007Z
LOCATION:1406&1407, Conference Center, Bldg 240, Argonne National Laboratory
DESCRIPTION:A particle-based nonlinear filtering scheme will be presented. This algorithm is based on implicit sampling, a new sampling technique related to chainless Monte Carlo method. Posterior densities are represented by pseudo-Gaussians and the filter is designed to focus particle paths sharply so as to reduce the number of particles needed in the nonlinear data assimilation. Examples will be given.
SUMMARY:Implicit sampling for nonlinear filters
UID:727
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091103T103000
DTEND:20091103T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, Conference Room 1406 and 1407, Argonne National Laboratory
DESCRIPTION:This talk presents the design and implementation of an asynchronous data-staging strategy for \nfile accesses based on ROMIO, the most popular MPI-IO distribution, and ZOID, the I/O forwarding component \nof ZeptoOS, an open source operating system solution for Blue Gene systems. We describe and evaluate \na two-level file write-back and prefetching solution. The experimental results demonstrate that our\napproach achieves high performance through a high degree of overlap between computation, communication, \nand file I/O.
SUMMARY:Design and evaluation of multiple level file write-back and prefetching for Blue Gene/P
UID:728
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091104T103000
DTEND:20091104T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 / Room 1172 (1C2), Argonne National Labortory
DESCRIPTION:Recent advances in computer technology combined with new theoretical methodology and algorithms have allowed for dramatic improvement in the computation of molecular properties. This has allowed computational chemistry to become a rapidly growing field of research, which plays a key role in many different areas of chemistry ranging from the interpretation of experiments, understanding of species that can be difficult or impossible to study experimentally (e.g. arsenic containing compounds and interstellar molecules), and chemical reactivity, to name just a few. Unfortunately, even with these advances, the extensive computational cost (i.e. computer time, memory, and disk space) of the sophisticated methods required to achieve a high level of accuracy effectively limits the size of molecules that can be studied to fewer than 10-15 atoms.  Several approaches have been developed to help reduce the computational cost of expensive ab initio methods, and I will discuss several such methods including the correlation consistent Composite Approach (ccCA), hydrogen basis set truncation, and local correlation. 
SUMMARY:Reducing the Computational Cost of Ab Initio Methods
UID:731
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091104T103000
DTEND:20091104T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 / Room 1172 (1C2), Argonne National Labortory
DESCRIPTION:Recent advances in computer technology combined with new theoretical methodology and algorithms have allowed for dramatic improvement in the computation of molecular properties. This has allowed computational chemistry to become a rapidly growing field of research, which plays a key role in many different areas of chemistry ranging from the interpretation of experiments, understanding of species that can be difficult or impossible to study experimentally (e.g. arsenic containing compounds and interstellar molecules), and chemical reactivity, to name just a few. Unfortunately, even with these advances, the extensive computational cost (i.e. computer time, memory, and disk space) of the sophisticated methods required to achieve a high level of accuracy effectively limits the size of molecules that can be studied to fewer than 10-15 atoms.  Several approaches have been developed to help reduce the computational cost of expensive ab initio methods, and I will discuss several such methods including the correlation consistent Composite Approach (ccCA), hydrogen basis set truncation, and local correlation. 
SUMMARY:Reducing the Computational Cost of Ab Initio Methods
UID:732
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091106T103000
DTEND:20091106T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240 / Room 1172 (1C2), Argonne National Labortory
DESCRIPTION:Molecular dynamics (MD) simulations offer a tantalizing window into the workings of biological systems in full atomistic detail.  The promise of this methodology for obtaining detailed understanding of biomolecular mechanisms depends in part on the ability of these simulations to reach biologically-relevant timescales.  Due to the tremendous gap between the timescales of atomistic motion and the timescales of biological processes, simulation of these processes requires extremely efficient parallel implementations of MD algorithms on high performance computing systems.  Recent implementations of MD algorithms on specialized hardware are poised to significantly increase our ability to study biological processes, as well as vigorously test the accuracy of these methods.  In this talk I will discuss, in the context of these recent developments, some of my work to facilitate the study of biological processes through molecular dynamics simulations.
SUMMARY:The Challenge of Long-Timescale Molecular Dynamics Simulations of Biological Systems
UID:733
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20100113T150000
DTEND:20100113T160000
DTSTAMP:20091122T063007Z
LOCATION:TCS Building, Argonne National Laboratory
DESCRIPTION:TBA
SUMMARY:TBA
UID:734
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091106T110000
DTEND:20091106T120000
DTSTAMP:20091122T063007Z
LOCATION:203 Auditorium,  Argonne National Laboratory
DESCRIPTION:Experiments with cold Fermi atoms provide an exciting new testing ground for our understanding of strongly-correlated matter.  Even though cold atoms can be described by extremely simple interactions the resulting physics is extremely rich.  A prototypical example is the BCS-BEC transition, where fermion pairing evolves from weak pairing of typical superfluids to very strong pairing into bosons.  May of the phenomenon observed experimentally have clear analogues in nuclear physics and related fields.  Examples include the equation of state and superfluid pairing, vortices and lattices, sound velocities and the ratio of shear viscosity to entropy.  Searches and predictions for new \'exotic\' states of polarized superfluids will also be described, as well as directions for future research.
SUMMARY:Rich Physics from Simple Interactions
UID:739
SEQUENCE:0
END:VEVENT
BEGIN:VEVENT
DTSTART:20091124T103000
DTEND:20091124T113000
DTSTAMP:20091122T063007Z
LOCATION:Building 240, TCS Conference Center (1406 & 1407), Argonne National Laboratory
DESCRIPTION:Computer simulations are currently used to predict nuclear reactor phenomena such as neutron and heat transport, fluid dynamics, and the effect or radiation on the properties of nuclear fuel elements and structural materials. An important component of the complex simulation methodology is predicting the performance of nuclear fuel elements. After a brief review of world-wide status of fuel performance codes, the presentation focuses on recent Finite Element simulations of coupled heat transfer, chemical species diffusion and thermal expansion of UO2+x fuel elements with metallic clad. The continuum simulations incorporate multi-scale models and simulations of fuel properties, such as atomistic (Molecular Dynamics) models of point defect concentration and meso-scale (Phase Field) simulations of gas bubble formation.  The continuum, coupled simulations demonstrate that including the dependence of thermal conductivity and density on local composition (oxygen and fission products content) leads to changes in the predicted centerline temperature that exceed 5%. The final part of the talk is dedicated to a discussion of national and international strategies for developing advanced, innovative models and high performance simulations for nuclear energy applications.
SUMMARY:Advanced Models and Simulations for Nuclear Energy
UID:743
SEQUENCE:0
END:VEVENT
END:VCALENDAR