The Community for Technology Leaders
SC Conference (2003)
Phoenix, Arizona
Nov. 15, 2003 to Nov. 21, 2003
ISBN: 1-58113-695-1
TABLE OF CONTENTS
Technical Papers
Front Matter

Front Matter (PDF)

pp. i-xxxi
Technical Papers

Parallel Multilevel Sparse Approximate Inverse Preconditioners in Large Sparse Matrix Computations (Abstract)

Kai Wang , University of Kentucky, Lexington
Jun Zhang , University of Kentucky, Lexington
Chi Shen , University of Kentucky, Lexington
pp. 1

Performance evaluation and tuning of GRAPE-6 - towards 40 "real" Tflops (Abstract)

Junichiro Makino , University of Tokyo, Japan
Eiichiro Kokubo , National Astronomical Observatory of Japan, Tokyo
Toshiyuki Fukushige , University of Tokyo, Japan
pp. 2

Efficient, Unified, and Scalable Performance Monitoring for Multiprocessor Operating Systems (Abstract)

Robert W. Wisniewski , IBM T. J. Watson Research Center
Bryan Rosenburg , IBM T. J. Watson Research Center
pp. 3

A 14.6 billion degrees of freedom, 5 teraflops, 2.5 terabyte earthquake simulation on the Earth Simulator (Abstract)

Dimitri Komatitsch , Caltech, Pasadena, California
Seiji Tsuboi , IFREE, JAMSTEC, Yokohama, Japan
Chen Ji , Caltech, Pasadena, California
Jeroen Tromp , Caltech, Pasadena, California
pp. 4

Dyn-MPI: Supporting MPI on Non Dedicated Clusters (Abstract)

D. Brent Weatherly , The University of Georgia, Athens
David K. Lowenthal , The University of Georgia, Athens
Mario Nakazawa , The University of Georgia, Athens
Franklin Lowenthal , California State University, Hayward
pp. 5

ParADE: An OpenMP Programming Environment for SMP Cluster Systems (Abstract)

Yang-Suk Kee , Seoul National University, Korea
Jin-Soo Kim , KAIST, Korea
Soonhoi Ha , Seoul National University, Korea
pp. 6

Handling Heterogeneity in Shared-Disk File Systems (Abstract)

Changxun Wu , Johns Hopkins University
Randal Burns , Johns Hopkins University
pp. 7

Improving the Scalability of Parallel Jobs by adding Parallel Awareness to the Operating System (Abstract)

Terry Jones , Lawrence Livermore National Laboratory, Livermore, CA
Shawn Dawson , Lawrence Livermore National Laboratory, Livermore, CA
Rob Neely , Lawrence Livermore National Laboratory, Livermore, CA
William Tuel , International Business Machines Corporation, Armonk, NY
Larry Brenner , International Business Machines Corporation, Armonk, NY
Jeffrey Fier , International Business Machines Corporation, Armonk, NY
Robert Blackmore , International Business Machines Corporation, Armonk, NY
Patrick Caffrey , International Business Machines Corporation, Armonk, NY
Brian Maskell , Atomic Weapons Establishment, Aldermaston Reading, UK
Paul Tomlinson , Atomic Weapons Establishment, Aldermaston Reading, UK
Mark Roberts , Atomic Weapons Establishment, Aldermaston Reading, UK
pp. 10

A Compiler Analysis of Interprocedural Data Communication (Abstract)

Yonghua Ding , Purdue University, West Lafayette, IN
Zhiyuan Li , Purdue University, West Lafayette, IN
pp. 11

Nondeterministic Queries in a Relational Grid Information Service (Abstract)

Peter A. Dinda , Northwestern University
Dong Lu , Northwestern University
pp. 12

Parallel Iterative Solvers of GeoFEM with Selective Blocking Preconditioning for Nonlinear Contact Problems on the Earth Simulator (Abstract)

Kengo Nakajima , Research Organization for Information Science and Technology (RIST), Tokyo, Japan
pp. 13

A New Parallel Kernel-Independent Fast Multipole Method (Abstract)

Lexing Ying , Courant Institute, New York University, New York
George Biros , Courant Institute, New York University, New York
Denis Zorin , Courant Institute, New York University, New York
Harper Langston , Courant Institute, New York University, New York
pp. 14

Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations (Abstract)

Makoto Taiji , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Tetsu Narumi , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Yousuke Ohno , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Noriyuki Futatsugi , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Atsushi Suenaga , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Naoki Takada , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Akihiko Konagaya , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
pp. 15

Synthesizing Realistic Computational Grids (Abstract)

Dong Lu , Northwestern University
Peter A. Dinda , Northwestern University
pp. 16

Memory Profiling using Hardware Counters (Abstract)

Marty Itzkowitz , Sun Microsystems, Inc., Menlo Park, California
Brian J. N. Wylie , Sun Microsystems, Inc., Menlo Park, California
Christopher Aoki , Sun Microsystems, Inc., Menlo Park, California
Nicolai Kosche , Sun Microsystems, Inc., Menlo Park, California
pp. 17

Early Evaluation of the Cray X1 (Abstract)

T. H. Dunigan, Jr. , Oak Ridge National Laboratory, TN
M. R. Fahey , Oak Ridge National Laboratory, TN
J. B. White III , Oak Ridge National Laboratory, TN
P. H. Worley , Oak Ridge National Laboratory, TN
pp. 18

The Tool Dæmon Protocol (TDP) (Abstract)

Barton Miller , University of Wisconsin, Madison
Ana Cortés , Universitat Autònoma de Barcelona, Spain
Miquel A. Senar , Universitat Autònoma de Barcelona, Spain
Miron Livny , University of Wisconsin, Madison
pp. 19

A Million-Fold Speed Improvement in Genomic Repeats Detection (Abstract)

John W. Romein , Vrije Universiteit, Amsterdam, The Netherlands
Jaap Heringa , Vrije Universiteit, Amsterdam, The Netherlands
Henri E. Bal , Vrije Universiteit, Amsterdam, The Netherlands
pp. 20

MRNet: A Software-Based Multicast/Reduction Network for Scalable Tools (Abstract)

Philip C. Roth , University of Wisconsin, Madison
Dorian C. Arnold , University of Wisconsin, Madison
Barton P. Miller , University of Wisconsin, Madison
pp. 21

A Configurable Network Protocol for Cluster Based Communications using Modular Hardware Primitives on an Intelligent NIC (Abstract)

Ranjesh G. Jaganathan , Clemson University, SC
Keith D. Underwood , Sandia National Laboratories, Albuquerque, NM
Ron Sass , Clemson University, SC
pp. 22

SCALLOP: A Highly Scalable Parallel Poisson Solver in Three Dimensions (Abstract)

Gregory T. Balls , University of California, San Diego
Scott B. Baden , University of California, San Diego
Phillip Colella , Lawrence Berkeley National Laboratory, Berkeley, CA
pp. 23

Grid -Based Parallel Data Streaming implemented for the Gyrokinetic Toroidal Code (Abstract)

S. Klasky , Princeton University, NJ
S. Ethier , Princeton University, NJ
Z. Lin , University of California, Irvine
K. Martins , Princeton University, NJ
D. McCune , Princeton University, NJ
R. Samtaney , Princeton University, NJ
pp. 24

MPICH-V2: a Fault Tolerant MPI for Volatile Nodes based on Pessimistic Sender Based Message Logging (Abstract)

Aurélien Bouteiller , LRI, Université de Paris Sud, Orsay, France
Franck Cappello , LRI, Université de Paris Sud, Orsay, France; INRIA Futurs, Saclay, France
Thomas Hérault , LRI, Université de Paris Sud, Orsay, France
Géraud Krawezik , LRI, Université de Paris Sud, Orsay, France
Pierre Lemarinier , LRI, Université de Paris Sud, Orsay, France
Frédéric Magniette , LRI, Université de Paris Sud, Orsay, France
pp. 25

Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP (Abstract)

Mark F. Adams , Sandia National Laboratories, Livermore, CA
Harun H. Bayraktar , University of California, Berkeley
Tony M. Keaveny , University of California, Berkeley
Panayiotis Papdopoulos , University of California, Berkeley
pp. 26

Quantifying and Improving the Availability of High-Performance Cluster-Based Internet Services (Abstract)

Kiran Nagaraja , Rutgers University
Neeraj Krishnan , Rutgers University
Ricardo Bianchini , Rutgers University
Richard P. Martin , Rutgers University
Thu D. Nguyen , Rutgers University
pp. 27

Hierarchical Dynamics, Interarrival Times, and Performance (Abstract)

Stephen D. Kleban , Sandia National Laboratories, Albuquerque, NM
pp. 28

Parallel Particle-In-Cell Simulation of Colliding Beams in High Energy Accelerators (Abstract)

Ji Qiang , Lawrence Berkeley National Laboratory, Berkeley, CA
Miguel A. Furman , Lawrence Berkeley National Laboratory, Berkeley, CA
Robert D. Ryne , Lawrence Berkeley National Laboratory, Berkeley, CA
pp. 29

The Space Simulator: Modeling the Universe from Supernovae to Cosmology (Abstract)

Michael S. Warren , Los Alamos National Laboratory, Los Alamos, New Mexico
Chris L. Fryer , Los Alamos National Laboratory, Los Alamos, New Mexico
M. Patrick Goda , Los Alamos National Laboratory, Los Alamos, New Mexico
pp. 30

Conservative Scheduling: Using Predicted Variance to Improve Scheduling Decisions in Dynamic Environments (Abstract)

Lingyun Yang , University of Chicago, IL
Jennifer M. Schopf , Argonne National Laboratory, IL
Ian Foster , University of Chicago, IL; Argonne National Laboratory, IL
pp. 31

IPSAP : A High-performance Parallel Finite Element Code for Large-scale Structural Analysis Based on Domain-wise Multifrontal Technique (Abstract)

Seung Jo Kim , Shilliom-dong Kwanak-gue, Seoul, Korea
Chang Sung Lee , Graduated Student
Jeong Ho Kim , Korean Institute of Science and Technology Information, Taejon, Korea
Minsu Joh , Korean Institute of Science and Technology Information, Taejon, Korea
Sangsan Lee , Korean Institute of Science and Technology Information, Taejon, Korea
pp. 32

A Metadata Catalog Service for Data Intensive Applications (Abstract)

Gurmeet Singh , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Shishir Bharathi , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Ann Chervenak , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Ewa Deelman , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Carl Kesselman , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Mary Manohar , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Sonal Patil , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
Laura Pearlman , Information Sciences Institute, University of Southern California, Marina Del Rey, CA
pp. 33

Remote Visualization by Browsing Image Based Databases with Logistical Networking (Abstract)

Jin Ding , University of Tennessee, Knoxville
Jian Huang , University of Tennessee, Knoxville
Micah Beck , University of Tennessee, Knoxville
Shaotao Liu , University of Tennessee, Knoxville
Terry Moore , University of Tennessee, Knoxville
Stephen Soltesz , University of Tennessee, Knoxville
pp. 34

GridSAT: A Chaff-based Distributed SAT Solver for the Grid (Abstract)

Wahid Chrabakh , University of California Santa Barbara
Rich Wolski , University of California Santa Barbara
pp. 37

Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations (Abstract)

Leonid Oliker , CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA
Andrew Canning , CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA
Jonathan Carter , CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA
John Shalf , CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA
David Skinner , CRD/NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA
Stéphane Ethier , Princeton University, NJ
Rupak Biswas , NASA Ames Research Center, Moffett Field, CA
Jahed Djomehri , NASA Ames Research Center, Moffett Field, CA
Rob Van der Wijngaart , NASA Ames Research Center, Moffett Field, CA
pp. 38

Parallel netCDF: A High-Performance Scientific I/O Interface (Abstract)

Jianwei Li , Northwestern University
Wei-keng Liao , Northwestern University
Alok Choudhary , Northwestern University
Robert Ross , Argonne National Laboratory
Rajeev Thakur , Argonne National Laboratory
William Gropp , Argonne National Laboratory
Rob Latham , Argonne National Laboratory
Andrew Siegel , Argonne National Laboratory
Brad Gallagher , University of Chicago
Michael Zingale , University of California, Santa Cruz
pp. 39

Traffic-based Load Balance for Scalable Network Emulation (Abstract)

Xin Liu , University of California, San Diego
Andrew A. Chien , University of California, San Diego
pp. 40

Enabling the Efficient Use of SMP Clusters: The GAMESS/DDI Model (Abstract)

Ryan M. Olson , Iowa State University
Michael W. Schmidt , Iowa State University
Mark S. Gordon , Iowa State University
Alistair P. Rendell , Australian National University
pp. 41

A Self-Organizing Flock of Condors (Abstract)

Ali Raza Butt , Purdue University, West Lafayette, IN
Rongmei Zhang , Purdue University, West Lafayette, IN
Y. Charlie Hu , Purdue University, West Lafayette, IN
pp. 42

The Livny and Plank-Beck Problems: Studies in Data Movement on the Computational Grid (Abstract)

Matthew S. Allen , University of California, Santa Barbara
Rich Wolski , University of California, Santa Barbara
pp. 43

Job Superscheduler Architecture and Performance in Computational Grid Environments (Abstract)

Hongzhang Shan , Lawrence Berkeley National Laboratory, Berkeley, CA
Leonid Oliker , Lawrence Berkeley National Laboratory, Berkeley, CA
Rupak Biswas , NASA Ames Research Center, Moffett Field, CA
pp. 44

An Evaluation of a Framework for the Dynamic Load Balancing of Highly Adaptive and Irregular Parallel Applications (Abstract)

Kevin J. Barker , College of William and Mary, Williamsburg, VA
Nikos P. Chrisochoides , College of William and Mary, Williamsburg, VA
pp. 45

Early Experience with Scientific Programs on the Cray MTA-2 (Abstract)

Wendell Anderson , Naval Research Laboratory
Preston Briggs , Cray, Inc.
C. Stephen Hellberg , Naval Research Laboratory
Daryl W. Hess , National Science Foundation
Alexei Khokhlov , University of Chicago
Marco Lanzagorta , Scientific & Engineering Solutions
Robert Rosenberg , Naval Research Laboratory
pp. 46

Grid-Based Galaxy Morphology Analysis for the National Virtual Observatory (Abstract)

Ewa Deelman , University of Southern California, Marina Del Rey, CA
Raymond Plante , National Center for Supercomputing Applications, Champaign, IL
Carl Kesselman , University of Southern California, Marina Del Rey, CA
Gurmeet Singh , University of Southern California, Marina Del Rey, CA
Mei-Hui Su , University of Southern California, Marina Del Rey, CA
Gretchen Greene , Space Telescope Science Institute, Baltimore, MD
Robert Hanisch , Space Telescope Science Institute, Baltimore, MD
Niall Gaffney , Space Telescope Science Institute, Baltimore, MD
Antonio Volpicelli , Space Telescope Science Institute, Baltimore, MD
James Annis , Fermi National Accelerator Laboratory, Batavia. IL
Vijay Sekhri , Fermi National Accelerator Laboratory, Batavia. IL
Tamas Budavari , Johns Hopkins University, Baltimore, MD
Maria Nieto-Santisteban , Johns Hopkins University, Baltimore, MD
William O'Mullane , Johns Hopkins University, Baltimore, MD
David Bohlender , Canadian Astrophysical Data Center, Victoria, British Columbia
Tom McGlynn , NASA High Energy Astrophysics Science Archive Research Center, Greenbelt, MD
Arnold Rots , Smithsonian Astrophysical Observatory, Cambridge, MA
Olga Pevunova , NASA Infrared Processing and Analysis Center, Pasadena, CA
pp. 47

Visualizing Very Large-Scale Earthquake Simulations (Abstract)

Kwan-Liu Ma , University of California at Davis
Aleksander Stompel , University of California at Davis
Jacobo Bielak , Carnegie Mellon University
Omar Ghattas , Carnegie Mellon University
Eui Joong Kim , Carnegie Mellon University
pp. 48

Identifying and Exploiting Spatial Regularity in Data Memory References (Abstract)

Tushar Mohan , Lawrence Berkeley National Laboratory, Berkeley, CA
Bronis R. de Supinski , Center for Applied Scientific Computing, Livermore, CA
Sally A. McKee , Cornell University, Ithaca, NY
Frank Mueller , North Carolina State University, Raleigh, NC
Andy Yoo , Center for Applied Scientific Computing, Livermore, CA
Martin Schulz , Cornell University, Ithaca, NY
pp. 49

Optimizing 10-Gigabit Ethernet for Networks of Workstations, Clusters, and Grids: A Case Study (Abstract)

Wu-chun Feng , Los Alamos National Laboratory (LANL), NM
Justin (Gus) Hurwitz , Los Alamos National Laboratory (LANL), NM
Harvey Newman , California Institute of Technology (CalTech), Pasadena
Sylvain Ravot , California Institute of Technology (CalTech), Pasadena
R. Les Cottrell , Stanford Linear Accelerator Center (SLAC), Menlo Park, CA
Olivier Martin , European Organization for Nuclear Research (CERN), Geneva, Switzerland
Fabrizio Coccetti , Stanford Linear Accelerator Center (SLAC), Menlo Park, CA
Cheng Jin , California Institute of Technology (CalTech), Pasadena
Xiaoliang (David) Wei , California Institute of Technology (CalTech), Pasadena
Steven Low , California Institute of Technology (CalTech), Pasadena
pp. 50

Automatic Type-Driven Library Generation for Telescoping Languages (Abstract)

Arun Chauhan , Rice University, Houston, TX
Cheryl McCosh , Rice University, Houston, TX
Ken Kennedy , Rice University, Houston, TX
Richard Hanson , Rice University, Houston, TX
pp. 51

High Resolution Forward And Inverse Earthquake Modeling on Terascale Computers (Abstract)

Vokan Akçelik , Carnegie Mellon University, Pittsburgh, Pennsylvania
Jacobo Bielak , Carnegie Mellon University, Pittsburgh, Pennsylvania
George Biros , New York University, NY
Ioannis Epanomeritakis , Carnegie Mellon University, Pittsburgh, Pennsylvania
Antonio Fernández , Carnegie Mellon University, Pittsburgh, Pennsylvania
Omar Ghattas , Carnegie Mellon University, Pittsburgh, Pennsylvania
Eui Joong Kim , Carnegie Mellon University, Pittsburgh, Pennsylvania
Julio López , Carnegie Mellon University, Pittsburgh, Pennsylvania
David O'Hallaron , Carnegie Mellon University, Pittsburgh, Pennsylvania
Tiankai Tu , Carnegie Mellon University, Pittsburgh, Pennsylvania
John Urbanic , Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania
pp. 52

An Efficient Data Location Protocol for Self.organizing Storage Clusters (Abstract)

Hong Tang , University of California, Santa Barbara
Tao Yang , University of California, Santa Barbara
pp. 53

Scalable Hardware-Based Multicast Trees (Abstract)

Salvador Coll , Technical University of Valencia, Spain
José Duato , Technical University of Valencia, Spain
Fabrizio Petrini , Los Alamos National Laboratory, NM
Francisco J. Mora , Technical University of Valencia, Spain
pp. 54

The Case of the Missing Supercomputer Performance: Achieving Optimal Performance on the 8,192 Processors of ASCI Q (Abstract)

Fabrizio Petrini , Los Alamos National Laboratory, New Mexico
Darren J. Kerbyson , Los Alamos National Laboratory, New Mexico
Scott Pakin , Los Alamos National Laboratory, New Mexico
pp. 55

BCS-MPI: A New Approach in the System Software Design for Large-Scale Parallel Computers (Abstract)

Juan Fernández , Los Alamos National Laboratory, NM, Universidad de Murcia, Spain
Eitan Frachtenberg , Los Alamos National Laboratory, NM
Fabrizio Petrini , Los Alamos National Laboratory, NM
pp. 57

Performance Comparison of MPI Implementations over InfiniBand, Myrinet and Quadrics (Abstract)

Jiuxing Liu , The Ohio State University, Columbus
Balasubramanian Chandrasekaran , The Ohio State University, Columbus
Jiesheng Wu , The Ohio State University, Columbus
Weihang Jiang , The Ohio State University, Columbus
Sushmitha Kini , The Ohio State University, Columbus
Weikuan Yu , The Ohio State University, Columbus
Darius Buntinas , The Ohio State University, Columbus
Peter Wyckoff , Ohio Supercomputer Center, Columbus, OH
D K Panda , The Ohio State University, Columbus
pp. 58

Scalable NIC-based Reduction on Large-scale Clusters (Abstract)

Adam Moody , The Ohio State University, Columbus
Juan Fernandez , Los Alamos National Laboratory, NM
Fabrizio Petrini , Los Alamos National Laboratory, NM
Dhabaleswar K. Panda , The Ohio State University, Columbus
pp. 59

Fast Parallel Non-Contiguous File Access (Abstract)

Joachim Worringen , NEC Europe Ltd., Germany
Jesper Larsson Träff , NEC Europe Ltd., Germany
Hubert Ritzdorf , NEC Europe Ltd., Germany
pp. 60

Application Steering in a Collaborative Environment (Abstract)

John Brooke , University of Manchester, UK
Thomas Eickermann , Research Centre Juelich, Germany
Uwe Woessner , University of Stuttgart, Germany
pp. 61
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