The Community for Technology Leaders
SC Conference (2006)
Tampa, Florida
Nov. 11, 2006 to Nov. 17, 2006
ISBN: 0-7695-2700-0
TABLE OF CONTENTS
Introduction

SC Committee (PDF)

pp. ix
Panel

100 Years of Digital Data (PDF)

Francine Berman , San Diego Supercomputer Center
pp. xix
Architecture

The Potential Energy Efficiency of Vector Acceleration (Abstract)

Christophe Lemuet , Hewlett Packard, Palo Alto, CA
Jean Francois , Hewlett Packard, Palo Alto, CA
Norm Jouppi , Hewlett Packard, Palo Alto, CA
pp. 1

The Design Space of Data-Parallel Memory Systems (Abstract)

Jung Ho Ahn , Stanford University, Stanford, California 94305, USA
Mattan Erez , Stanford University, Stanford, California 94305, USA
William J. Dally , Stanford University, Stanford, California 94305, USA
pp. 2

A Performance Comparison Through Benchmarking and Modeling of Three Leading Supercomputers: Blue Gene/L, Red Storm, and Purple (Abstract)

Adolfy Hoisie , Los Alamos National Laboratory
Greg Johnson , Los Alamos National Laboratory
Darren J. Kerbyson , Los Alamos National Laboratory
Michael Lang , Los Alamos National Laboratory
Scott Pakin , Los Alamos National Laboratory
pp. 3
Memory

Sequoia: Programming the Memory Hierarchy (Abstract)

Kayvon Fatahalian , Stanford University
Timothy J. Knight , Stanford University
Mike Houston , Stanford University
Mattan Erez , Stanford University
Daniel Reiter Horn , Stanford University
Larkhoon Leem , Stanford University
Ji Young Park , Stanford University
Manman Ren , Stanford University
Alex Aiken , Stanford University
William J. Dally , Stanford University
Pat Hanrahan , Stanford University
pp. 4

CellSs: a Programming Model for the Cell BE Architecture (Abstract)

Pieter Bellens , Barcelona Supercomputing Center and UPC, Spain
Josep M. Perez , Barcelona Supercomputing Center and UPC, Spain
Rosa M. Badia , Barcelona Supercomputing Center and UPC, Spain
Jesus Labarta , Barcelona Supercomputing Center and UPC, Spain
pp. 5

A Memory Model for Scientific Algorithms on Graphics Processors (Abstract)

Naga K. Govindaraju , UNC Chapel Hill
Scott Larsen , UNC Chapel Hill
Jim Gray , Microsoft Corporation
Dinesh Manocha , UNC Chapel Hill
pp. 6
Interconnect Routing and Scheduling

Adaptive Routing in High-Radix Clos Network (Abstract)

John Kim , Stanford University
William J. Dally , Stanford University
J. Dally , Stanford University
Dennis Abts , Cray Inc.
pp. 7

A Near-optimal Real-time Hardware Scheduler for Large Cardinality Crossbar Switches (Abstract)

Raymond R. Hoare , Concurrent EDA, LLC
Zhu Ding , Union Switch & Signal
Alex K. Jones , University of Pittsburgh
pp. 8

Level-wise Scheduling Algorithm for Fat Tree Interconnection Networks (Abstract)

Zhu Ding , Union Switch & Signal
Raymond R. Hoare , Concurrent EDA, LLC
Alex K. Jones , University of Pittsburgh
Rami Melhem , University of Pittsburgh
pp. 9
Scalable Systems Software

Problem Diagnosis in Large-Scale Computing Environments (Abstract)

Naoya Maruyama , Tokyo Institute of Technology
Barton P. Miller , University of Wisconsin
pp. 11

From Mesh Generation to Scientific Visualization: An End-to-End Approach to Parallel Supercomputing (Abstract)

Tiankai Tu , Carnegie Mellon University
Hongfeng Yu , University of California, Davis
Leonardo Ramirez-Guzman , Carnegie Mellon University
Jacobo Bielak , Carnegie Mellon University
Omar Ghattas , University of Texas at Austin
Kwan-Liu Ma , University of California, Davis
David R. O'Hallaron , Carnegie Mellon University
pp. 12
MPI and Communications

Adaptive, Transparent Frequency and Voltage Scaling of Communication Phases in MPI Programs (Abstract)

Min Yeol Lim , North Carolina State University
Vincent W. Freeh , NSF grants CCF, Tampa, Florida
David K. Lowenthal , University of Georgia
pp. 14

Software Routing and Aggregation of Messages to Optimize the Performance of HPCC Randomaccess Benchmark (Abstract)

Rahul Garg , IBM India Research Lab, New Delhi, India
Yogish Sabharwal , IBM India Research Lab, New Delhi, India
pp. 15
MPI Tools and Performance Studies

MPI Performance Analysis Tools on Blue Gene/L (Abstract)

I-Hsin Chung , IBM Thomas J. Watson Research Center
Robert E. Walkup , IBM Thomas J. Watson Research Center
Hui-Fang Wen , IBM Thomas J. Watson Research Center
Hao Yu , IBM Thomas J. Watson Research Center
pp. 16

Quantifying the Potential Benefit of Overlapping Communication and Computation in Large-Scale Scientific Applications (Abstract)

Jose Carlos Sancho , Los Alamos National Laboratory, NM
Kevin J. Barker , Los Alamos National Laboratory, NM
Darren J. Kerbyson , Los Alamos National Laboratory, NM
Kei Davis , Los Alamos National Laboratory, NM
pp. 17

Blocking vs. Non-Blocking Coordinated Checkpointing for Large-Scale Fault Tolerant MPI (Abstract)

Camille Coti , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
Thomas Herault , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
Pierre Lemarinier , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
Laurence Pilard , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
Ala Rezmerita , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
Eric Rodriguezb , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
Franck Cappello , INRIA-Futurs / Grand-Large, Universit´e Paris-XI, France
pp. 18
Grid Allocation and Reservation

Improving Grid Resource Allocation via Integrated Selection and Binding (Abstract)

Yang-Suk Kee , University of California at San Diego
Ken Yocum , University of California at San Diego
Andrew A. Chien , University of California at San Diego
Henri Casanova , University of Hawaii at Manoa
pp. 19

Toward a Doctrine of Containment: Grid Hosting with Adaptive Resource Control (Abstract)

Lavanya Ramakrishnan , Renaissance Computing Institute
Laura Grit , Duke University
Adriana Iamnitchi , University of South Florida
David Irwin , Duke University
Aydan Yumerefendi , Duke University
Jeff Chase , Duke University
pp. 20

Grid Capacity Planning with Negotiation-based Advance Reservation for Optimized QoS (Abstract)

Mumtaz Siddiqui , University of Innsbruck, Austria
Alex Villazon , University of Innsbruck, Austria
Thomas Fahringer , University of Innsbruck, Austria
pp. 21
Grid Applications

Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications (PDF)

Mark K. Gardner , Virginia Tech
Wu-chun Feng , Virginia Tech
Jeremy Archuleta , University of Utah
Heshan Lin , North Carolina State University
Xiaosong Ma , North Carolina State University
pp. 22

Sustainable Adaptive Grid Supercomputing: Multiscale Simulation of Semiconductor Processing across the Pacific (Abstract)

Hiroshi Takemiya , National Institute of Advanced Industrial Science and Technology, Japan
Yoshio Tanaka , National Institute of Advanced Industrial Science and Technology, Japan
Satoshi Sekiguchi , National Institute of Advanced Industrial Science and Technology, Japan
Shuji Ogata , Nagoya Institute of Technology, Japan
Rajiv K. Kalia , University of Southern California, USA
Aiichiro Nakano , University of Southern California, USA
Priya Vashishta , University of Southern California, USA
pp. 23

High-Performance Dynamic Graphics Streaming for Scalable Adaptive Graphics Environment (Abstract)

Byungil Jeong , University of Illinois at Chicago
Luc Renambot , University of Illinois at Chicago
Ratko Jagodic , University of Illinois at Chicago
Rajvikram Singh , University of Illinois at Chicago
Julieta Aguilera , University of Illinois at Chicago
Andrew Johnson , University of Illinois at Chicago
Jason Leigh , University of Illinois at Chicago
pp. 24
Grid Networks and Portals

Revisiting Web Server Workload Invariants in the Context of Scientific Web Sites (Abstract)

Anne M. Faber , Indiana University, Bloomington, IN, U.S.A.
Minaxi Gupta , Indiana University, Bloomington, IN, U.S.A.
Camilo H. Viecco , Indiana University, Bloomington, IN, U.S.A.
pp. 25

Evaluating Grid Portal Security (Abstract)

David Del Vecchio , University of Virginia, Charlottesville, VA
Victor Hazlewood , San Diego Supercomputing Center, 9500 Gilman Dr, La Jolla, CA
Marty Humphrey , University of Virginia, Charlottesville, VA
pp. 27
Grid Scheduling and Protocols

Supporting Dynamic Migration in Tightly Coupled Grid Applications (Abstract)

Liang Chen , Ohio State University, Columbus OH
Qian Zhu , Ohio State University, Columbus OH
Gagan Agrawal , Ohio State University, Columbus OH
pp. 28

Evaluation of a Workflow Scheduler Using Integrated Performance Modelling and Batch Queue Wait Time Prediction (Abstract)

Daniel Nurmi , University of California, Santa Barbara
Anirban Mandal , Rice University
John Brevik , University of California, Santa Barbara
Chuck Koelbel , Rice University
Rich Wolski , University of California, Santa Barbara
Ken Kennedy , Rice University
pp. 29

Benchmarking XML Processors for Applications in Grid Web Services (Abstract)

Michael R. Head , State University of New York (SUNY) at Binghamton
Madhusudhan Govindaraju , binghamton.edu
Robert van Engelen , Florida State University
Wei Zhang , Florida State University
pp. 30
Grid Resource Management

CRUSH: Controlled, Scalable, Decentralized Placement of Replicated Data (Abstract)

Sage A. Weil , University of California, Santa Cruz
Scott A. Brandt , University of California, Santa Cruz
Ethan L. Miller , University of California, Santa Cruz
Carlos Maltzahn , University of California, Santa Cruz
pp. 31

CycleMeter: Detecting Fraudulent Peers in Internet Cycle Sharing (Abstract)

Zheng Zhang , Purdue University
Y. Charlie Hu , Purdue University
Samuel P. Midkiff , Purdue University
pp. 32

Designing a Runtime System for Volunteer Computing (Abstract)

David P. Anderson , UC Berkeley
Carl Christensen , University of Oxford, UK
Bruce Allen , University of Wisconsin
pp. 33
Data Management and Query

Hypergraph Partitioning for Automatic Memory Hierarchy Management (Abstract)

Sriram Krishnamoorthy , Ohio State University
Umit Catalyurek , Ohio State University
Jarek Nieplocha , Pacific Northwest National Laboratory
Atanas Rountev , Ohio State University
P. Sadayappan , Ohio State University
pp. 34

Multiple Range Query Optimization with Distributed Cache Indexing (Abstract)

Beomseok Nam , University of Maryland
Henrique x Henrique Andradeç, , IBM T. J. Watson Research Center, NY
Alan Sussman , University of Maryland
pp. 35

Estimating Query Result Sizes for Proxy Caching in Scientific Database Federations (Abstract)

Tanu Malik , Johns Hopkins University
Randal Burns , Johns Hopkins University
Nitesh V. Chawla , University of Notre Dame
Alex Szalay , Johns Hopkins University
pp. 36
Imaging and Visual Analysis

Toward Real-Time Image Guided Neurosurgery Using Distributed and Grid Computing (Abstract)

Nikos Chrisochoides , College of William and Mary, VA
Andriy Fedorov , College of William and Mary, VA
Andriy Kot , College of William and Mary, VA
Neculai Archip , Harvard University
Peter Black , Harvard University
Olivier Clatz , Harvard University
Alexandra Golby , Harvard University
Ron Kikinis , Harvard University
Simon K. Warfield , Harvard University
pp. 37

Large Image Correction and Warping in a Cluster Environment (Abstract)

Vijay S. Kumar , Ohio State University
Benjamin Rutt , Ohio State University
Tahsin Kurc , Ohio State University
Umit Catalyurek , Ohio State University
Joel Saltz , Ohio State University
Sunny Chow , University of California San Diego
Stephan Lamont , University of California San Diego
Maryann Martone , University of California San Diego
pp. 38

Detecting Distributed Scans Using High-Performance Query-Driven Visualization (Abstract)

Kurt Stockinger , University of California Berkely
E. Wes Bethel1 , University of California Berkely
Scott Campbell , University of California Berkely
Eli Dart , University of California Berkely
Kesheng Wu , University of California Berkely
pp. 39
Biology

PBPI: a High Performance Implementation of Bayesian Phylogenetic Inference (Abstract)

Xizhou Feng , Virginia Polytechnic Institute and State University
Kirk W. Cameron , Virginia Polytechnic Institute and State University
Duncan A. Buell , University of South Carolina
pp. 40

Locality and Parallelism Optimization for Dynamic Programming Algorithm in Bioinformatics (Abstract)

Guangming Tan , Graduate School of Chinese Academy of Sciences
Shengzhong Feng , Institute of Computing Technology, Chinese Academy of Sciences
Ninghui Sun , Institute of Computing Technology, Chinese Academy of Sciences
pp. 41

Computing Large Sparse Multivariate Optimization Problems with an Application in Biophysics (Abstract)

Emre H. Brookes , University of Texas at San Antonio
Rajendra V. Boppana , University of Texas at San Antonio
Borries Demeler , University of Texas Health Science Center at San Antonio
pp. 42
Molecular Dynamics

Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters (Abstract)

Kevin J. Bowers , D. E. Shaw Research, LLC, New York, NY
Edmond Chow , D. E. Shaw Research, LLC, New York, NY
Huafeng Xu , D. E. Shaw Research, LLC, New York, NY
Ron O. Dror , D. E. Shaw Research, LLC, New York, NY
Michael P. Eastwood , D. E. Shaw Research, LLC, New York, NY
Brent A. Gregersen , D. E. Shaw Research, LLC, New York, NY
John L. Klepeis , D. E. Shaw Research, LLC, New York, NY
Istvan Kolossvary , D. E. Shaw Research, LLC, New York, NY
Mark A. Moraes , D. E. Shaw Research, LLC, New York, NY
Federico D. Sacerdoti , D. E. Shaw Research, LLC, New York, NY
John K. Salmon , D. E. Shaw Research, LLC, New York, NY
Yibing Shan , D. E. Shaw Research, LLC, New York, NY
David E. Shaw , D. E. Shaw Research, LLC, New York, NY
pp. 43

Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics (Abstract)

Blake G. Fitch , IBM Thomas J. Watson Research Center
Aleksandr Rayshubskiy , IBM Thomas J. Watson Research Center
Maria Eleftheriou , IBM Thomas J. Watson Research Center
T.J. Christopher Ward , IBM Thomas J. Watson Research Center
Mark Giampapa , IBM Thomas J. Watson Research Center
Michael C. Pitman , IBM Thomas J. Watson Research Center
Robert S. Germain , IBM Thomas J. Watson Research Center
pp. 44
Particles and Continuum

Nested OpenMP for Efficient Computation of 3D Critical Points in Multi-Block CFD Datasets (Abstract)

Andreas Gerndt , RWTH Aachen University, Germany
Samuel Sarholz , RWTH Aachen University, Germany
Marc Wolter , RWTH Aachen University, Germany
Dieter an Mey , RWTH Aachen University, Germany
Christian Bischof , RWTH Aachen University, Germany
Torsten Kuhlen , RWTH Aachen University, Germany
pp. 46

Modeling Pulse Propagation and Scattering in a Dispersive Medium: Performance of MPI/OpenMP Hybrid Code (Abstract)

Robert Rosenberg , Naval Research Laboratory
Guy Norton , Naval Research Laboratory
Jorge C. Novarini , Planning Systems, Inc.
Wendell Anderson , Naval Research Laboratory
Marco Lanzagorta , ITT, Advanced Engineering and Sciences
pp. 47

Performance Modeling and Optimization of a High Energy Colliding Beam Simulation Code (Abstract)

Hongzhang , Lawrence Berkeley National Laboratory
Erich Strohmaier , Lawrence Berkeley National Laboratory
Ji Qiang , University of California at Berkeley
David H. Bailey , Lawrence Berkeley National Laboratory
Kathy Yelick , Lawrence Berkeley National Laboratory
pp. 48
Tools and Techniques for Performance

Architectures and APIs: Assessing Requirements for Delivering FPGA Performance to Applications (Abstract)

Keith D. Underwood , Sandia National Laboratories
K. Scott Hemmert , Sandia National Laboratories
Craig Ulmer , Sandia National Laboratories
pp. 49

Exploiting the Performance of 32 bit Floating Point Arithmetic in Obtaining 64 bit Accuracy (Revisiting Iterative Refinement for Linear Systems) (Abstract)

Julie Langou , University of Tennessee, Knoxville TN
Julien Langou , University of Tennessee, Knoxville TN
Piotr Luszczek , University of Tennessee, Knoxville TN
Jakub Kurzak , University of Tennessee, Knoxville TN
Alfredo Buttari , University of Tennessee, Knoxville TN
Jack Dongarra , University of Tennessee, Knoxville TN
pp. 50

FFT Program Generation for Shared Memory: SMP and Multicore (Abstract)

Franz Franchetti , Carnegie Mellon University
Yevgen Voronenko , Carnegie Mellon University
Markus Puschel , Carnegie Mellon University
pp. 51
Blue Gene System Software

Topology Mapping for Blue Gene/L Supercomputer (Abstract)

Hao Yu , IBM Thomas J. Watson Research Center, NY
I-Hsin Chung , IBM Thomas J. Watson Research Center, NY
Jose Moreira , IBM Thomas J. Watson Research Center, NY
pp. 52

Designing a Highly-Scalable Operating System: The Blue Gene/L Story (Abstract)

Jose Moreira , IBM Thomas J. Watson Research Center, NY
Michael Brutman , IBM Systems and Technology Group, Rochester, MN
Jose Castano , IBM Thomas J. Watson Research Center, NY
Thomas Engelsiepen , IBM Almaden Research Center, San Jose
Mark Giampapa , IBM Thomas J. Watson Research Center, NY
Tom Gooding , IBM Systems and Technology Group, Rochester, MN
Roger Haskin , IBM Almaden Research Center, San Jose
Todd Inglett , IBM Systems and Technology Group, Rochester, MN
Derek Lieber , IBM Thomas J. Watson Research Center, NY
Pat McCarthy , IBM Systems and Technology Group, Rochester, MN
Mike Mundy , IBM Systems and Technology Group, Rochester, MN
Jeff Parker , IBM Systems and Technology Group, Rochester, MN
Brian Wallenfelt , GeoDigm Corporation, Chanhassen, MN
pp. 53

Design and Implementation of a One-Sided Communication Interface for the IBM eServer Blue Gene (Abstract)

M. Blocksome , IBM Systems Group, Rochester MN
C. Archer , IBM Systems Group, Rochester MN
T. Inglett , IBM Systems Group, Rochester MN
P. McCarthy , IBM Systems Group, Rochester MN
M. Mundy , IBM Systems Group, Rochester MN
J. Ratterman , IBM Systems Group, Rochester MN
A. Sidelnik , IBM Systems Group, Rochester MN
B. Smith , IBM Systems Group, Rochester MN
G. Almasi , IBM Thomas JWatson Research Center, Yorktown Heights, NY
J. Castanos , IBM Thomas JWatson Research Center, Yorktown Heights, NY
D. Lieber , IBM Thomas JWatson Research Center, Yorktown Heights, NY
J. Moreira , IBM Thomas JWatson Research Center, Yorktown Heights, NY
S. Krishnamoorthy , Ohio State University
V. Tipparaju , Pacific Northwest National Laboratory, Richland, WA
J. Nieplocha , Pacific Northwest National Laboratory, Richland, WA
pp. 54
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