DoD HPCMP(High Performance Computer Modernization Program) Users Group Conference 2008
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DoD HPCMP(High Performance Computer Modernization Program) Users Group Conference 2008
by IEEE
Editor’s Preface
Proceedings of the 2008 DoD HPCMP Users Group Conference
The 2008 DoD High Performance Computer Modernization Program (HPCMP) Users Group
Conference (UGC) was held July 14–17, 2008 in Seattle, WA. This annual conference enables the
Department of Defense (DoD) science and technology (S&T) and test and evaluation (T&E)
communities to share their computational science and engineering results with their colleagues and
other members of the DoD community. The conference brings together a community of scientists and
engineers with common interests, encourages the sharing of techniques and methods, and allows the
users to mix with the staff from the computer centers and HPCMP office. The users are able to gain
an appreciation of the technical breadth of the entire community and interact with their scientific and
engineering colleagues.
The UGC was organized by the program’s User Advocacy Group. That group was led by the
UAG chair Jeanie Osburn, NRL; the technical program chair was Balu Sekar, AFRL; and the technical
program co-chair was Aram Kevorkian, SPAWAR. The tutorials chair was Peter Mardahl, AFRLKirtland.
Deborah Schwartz and the HPCMP staff (Leah Glick, Suzanne Noll, Chau Nguyen, and Lisa
Powell) organized the conference arrangements. Other members of the User Advocacy Group who
helped to organize this year’s conference were: Stephen Ketcham, Stephen Schraml, Marshall
McBride, Michael Stokes, Joe Slomski, Alan Wallcraft, Matt Grismer, Peter Mardhal, and Steve Finn.
Larry Davis was the HPCMPO liaison and Cathy McDonald is the UAG Executive Secretary. Lisa
Powell edits the UGC post-proceedings.
The 2008 conference opened with a welcome by Dr. Jeanie Osburn, the conference chair. There
were six invited speakers: Captain Vic Addision, who discussed the role of supercomputers for the
Navy; Mr. Steve Scott, who summarized the advances in HPC productivity that CRAY has achieved
with their DARPA High Productivity Computing System project; Kevin Gildea, who covered the same
topic for IBM; Vice-Admiral Daniel Oliver, who discussed the role of supercomputing at the Naval
Postgraduate School; Doug Ball, who summarized the role that supercomputing played in the design
of commercial aircraft for Boeing; Dan Reed, who discussed emerging fields that supercomputing will
enable; Chris Castello, who discussed new directions for the Google Earth project; and Dave Bacon,
who summarized the status of quantum computing. Mr. Cray Henry presented the Director’s report.
Among the highlights were the new computing power that was being made available to the DoD, the
start of three new institutes (insensitive munitions, high power microwaves, and network modeling),
the plans for the next PET contract, the status of the Computational Research and Engineering
Acquisition Tools and Environments (CREATE) program, and the successful move of the program
office from Ballston to Lorton.
There were four invited presentations on technical results by DoD HPCMP users: Dr. James
Doyle, NRL-MRY, summarized his group’s progress on predicting weather for the naval battlespace
environment and the impact of those predictions; Dr. Jerry Boatz (AFRL/RZSP) presented his group’s
work on the design of energetic ionic liquids; Dr. Scott Fawaz (USAFA) presented his work on
modeling fatigue issues for aircraft; and Dr. Andrew M. Rappe (U. of Penn.) discussed his results
using computational techniques to explore the acoustic properties of complex ferroelectric oxides for
sonar applications.
xii
About one-half of the results presented at the conference are documented in these proceedings. The
papers describe the results of scientific research, engineering design studies, design optimization
studies, and the utility of various computational algorithms. The growing complexity of computer
architecture has increased the challenge of developing and running computer applications. The
papers on application profiling and optimization, and the relative performance of the HPCMP-provided
platforms address meeting these challenges. Attendance increased from 400 to 451 attendees from
last year’s conference. There were 116 technical talks, 12 Birds-of-a-feather meetings, seven
tutorials, and 57 posters. Eighty-four presenters wrote papers, an increase of eight from 2007.
The papers are written to be interesting and accessible to scientists and engineers who possess
general scientific backgrounds. They cover almost all of the unclassified scientific research and
engineering development technical areas that currently address computational techniques. The
general topics include:
Topic Number
Computational Fluid Dynamics (CFD) 12
Multi-Physics (CFD, CSM, CCM, Plasma Physics…) 12
Computational Chemistry and Materials Science (CCM) 15
Climate/Weather/Ocean Modeling and Simulation (CWO) 8
Signal/Image Processing (SIP) and Sensors; Electronics,
Networking, and Systems/C4ISR (ENS) and Testing 8
Software and Hardware Infrastructure 9
Software Performance and Performance Modeling 9
Computational Methods 9
Education 2
The papers demonstrate the continued evolutionary trend in computational science and
engineering from, exploitation of codes that treat a single isolated effect for an idealized system, to
the use of codes that integrate many different effects for complex systems. In addition, for the first
time, CFD didn’t have the most papers. However, part of the reason for this was that we recognized
that CFD was only one element of a number of multi-physics calculations.
This year, the UGC was held in conjunction with the Department of Energy’s SciDAC annual
program meeting (www.scidac.gov/). The SciDAC meeting was held about three blocks away
from the UGC and participants were cross registered so that they could attend presentations
at either conference. Next year, the UGC and SciDAC meetings will be jointly held in San
Diego, CA. This is fostering communication and collaboration between the DoD and the
DOE Office of Science HPC programs.
In summary, the papers presented at the UGC provide a good overview of the unclassified
computational science and engineering research and development in the DoD science and
technology and test and evaluation community. The format of conference allowed time for
discussions among the attending scientists and engineers during presentations and during the
breaks, at lunch, and after the day’s presentations.
—Douglass E. Post, Chief Scientist, DoD HPCMP
DoD HPCMP Users Group Conference
2008
DoD HPCMP UGC 2008
Table of Contents
Editor’s Preface…………………………………………….xii
Computational Fluid Dynamics (CFD)
A New Approach to Streambed Modeling and Simulation Using CFD …………………………………………………3
Jeffrey B. Allen, David L. Smith, Owen J. Eslinger, and Miguel A. Valenciano
Active Separation Control for Lifting Surfaces at Low-Reynolds Number
Operating Conditions …………………………………………..9
A. Gross, W. Balzer, and H.F. Fasel
An Undergraduate Computational Aerodynamics Curriculum …………………………………………………………..18
Keith Bergeron, Russell Cummings, David M. McDaniel, Robert Decker,
Jacob Freeman, Charlie Hoke, Jurgen Seidel, and Scott A. Morton
Free-Surface Proximity Effects in Developed and Super-Cavitation ………………………………………………….25
Michael P. Kinzel, Jules W. Lindau, and Robert F. Kunz
High-Fidelity Computations of Moving and Flexible Wing Sections
with Application to Micro Air Vehicles ……………………35
Raymond E. Gordnier, Miguel R. Visbal, and Marshall C. Galbraith
High-Resolution Simulations of Nonlinear Internal Gravity Waves in the South
China Sea ………………………………………………………..43
Oliver B. Fringer and Zhonghua Zhang
Modeling of Mine Countermeasure Dart Dispense ….47
Gary Prybyla, Michael Neaves, and William Dietz
Numerical Investigation of Internal and External Three-Dimensional Flow
Separation ……………………………………………………….52
A. Gross, R. Jacobi, S. Wernz, and H.F. Fasel
Numerical Simulation of Non-resonant Cavity Flow ..61
Craig A. Wagner and Scot A. Slimon
Ocean Wave Prediction Using Large-Scale Phase-Resolved Computations ………………………………………69
Wenting Xiao, Legena Henry, Yuming Liu, Kelli Hendrickson, and Dick K.P. Yue
Prediction of High-Amplitude Forces during Propeller Crashback …………………………………………………….74
Peter A. Chang, Michael P. Ebert, Jeremy Shipman, and Krishnan Mahesh
The High Speed Sea Lift (HSSL) Ships Challenge Effort …………………………………………………………………83
Joseph Gorski, Ronald Miller, Pablo Carrica, Mani Kandasamy, and Fred Stern
v
Multi-Physics (CFD, CSM, CCM, Plasma Physics)
Application of 3-D, Unsteady Navier-Stokes Simulation to Chemical
Oxygen-Iodine Laser Technology Development ……..91
Timothy J. Madden
Characterization of Hot-Wire Detonators Using Analytical Modeling
and Computational Tools …………………………………….99
Michael Lambrecht, Carl Baum, Edl Schamiloglu, and Keith Cartwright
Combustion Chamber Fluid Dynamics and Hypergolic Gel Propellant
Chemistry Simulations for Selectable Thrust Rocket Engines ………………………………………………………..103
Michael J. Nusca, Chiung-Chu Chen, and Michael J. McQuaid
Comparisons of Two-Fluid Plasma Models ………….109
B. Srinivasan and U. Shumlak
Fast and Reliable Solution of GDoF-Problems on NAVO/BABBAGE
and AFRL/HAWK Systems ………………………………..114
Scott Fawaz and Börje Andersson
Generation of Aerodynamic Coefficients Using Time-Accurate CFD and Virtual
FLy-Out Simulations ………………………………………..123
Jubaraj Sahu, Sidra Silton, James DeSpirito, Karen R. Heavey, and Mark Costello
Integrated Analysis of Scramjet Flowpath with Innovative Inlets ……………………………………………………..130
Datta V. Gaitonde, F. Joel Malo-Molina, Houshang B. Ebrahimi, and Daniel Risha
MHD Turbulence Studies Using Lattice Boltzmann Algorithms-Physical
Simulations Using 9,000 Cores on the Air Force Research Laboratory HAWK
Supercomputer ……………………………………………….138
G. Vahala, Jeffrey Yepez, Min Soe, Linda Vahala, Jonathon Carter,
and Sean Ziegler
Multidisciplinary Modeling of the CH-47 Helicopter with CFD/CSD Coupling
and Trim …………………………………………………………143
Arsenio C.B. Dimanlig, Hossein-Ali Saberi, Edward T. Meadowcroft,
Roger Strawn, and Mahendra Bagwhat
Regions of Validity for the 10-Moment, Two Fluid Plasma Model ……………………………………………………150
R. Lilly and U. Shumlak
Virtual Prototyping of Directed Energy Weapons ….154
M.T. Bettencourt, K.L. Cartwright, A.D. Greenwood, T.P. Fleming,
M.D. Haworth, N.P. Lockwood, and P.J. Mardahl
Vulnerability of Structures to Weapons Effect ………160
James Baylot, Stephen Akers, James O’Daniel, Byron Armstrong,
and Richard Weed
vi
Computational Chemistry and Materials Science (CCM)
Ab-initio Molecular Dynamics Simulations of Molten Ni-Based Superalloys ……………………………………..169
Christopher Woodward, Mark. Asta, Dallas R. Trinkle, James Lill,
and Stefano Angioletti-Uberti
Calculations of Lithium Carborane Complexes …..175
Jaroslav Vacek, Jana Chocholousova, and Josef Michl
Critical Carbon Nanotube Length in Fibers …………..180
C.F. Cornwell, D. Majure, R. Haskins, N.J. Lee, R. Ebeling, R. Maier, C. Marsh,
A. Bednar, R. Kirgan, and C.R. Welch
Crystal Structures from Nonempirical Force Fields .187
Rafał Podeszwa, Betsy M. Rice, Fazle Rob, and Krzysztof Szalewicz
Direct Quantum Mechanical Simulations of Shocked Energetic Materials
Supporting Future Force Insensitive Munitions (IM) Requirements …………………………………………………191
William D. Mattson, Radhakrishnan Balu, and Betsy M. Rice
Design of Energetic Ionic Liquids ……………………….196
Jerry A. Boatz, Mark S. Gordon, Gregory A. Voth, and Sharon Hammes-Schiffer
Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)
Simulations of the Effects of Chirality and Diameter on the Pullout Force in
a Carbon Nanotube Bundle ……………………………….201
D.L. Majure, R.W. Haskins, N.J. Lee, R.M. Ebeling, R.S. Maier, C.P. Marsh,
A.J. Bednar, R.A. Kirgan, C.R. Welch, and Charles F. Cornwell
Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics
Simulations …………………………………………………….208
In-Chul Yeh, Mark A. Olson, Michael S. Lee, and Anders Wallqvist
Modeling of Materials for Naval SONAR, Pollution Control and Nonvolatile
Memory Application …………………………………………214
Joseph W. Bennett, Ilya Grinberg, Young-Han Shin, and Andrew M. Rappe
Multiscale Simulations of High Performance Capacitors and Nanoelectronic
Devices ………………………………………………………….221
J. Bernholc, J. Jiang, V. Ranjan, L. Yu, M. Buongiorno Nardelli, and W. Lu
Novel Mechanism for the Dissociation of H2O and the Diffusion of O and H
along the aAl2O3 (0001) Surface ……………………….229
Jennifer Synowczynski, Jan Andzelm, and Dionisios Vlachos
Performance of DFT Methods in the Calculation of Optical Spectra
of Chromophores …………………………………………….235
Jan Andzelm, Adam Rawlett, Joseph Dougherty, and Niranjan Govind
PIPA: A High-Throughput Pipeline for Protein Function Annotation …………………………………………………241
Chenggang Yu, Valmik Desai, Nela Zavaljevski, and Jaques Reifman
Polynitrogen/Nanoaluminum Surface Interactions …247
Jerry A. Boatz and Dan Sorescu
Structure and Dynamics of Squalane Films on Solid Surfaces ……………………………………………………….252
Mesfin Tsige and Soumya S. Patnaik
vii
Climate/Weather/Ocean Modeling and Simulation (CWO)
Dedicated High Performance Computer Project Investment (DHPI) for
the Fleet Numerical/Air Force Weather Agency - The Navy Side ……………………………………………………259
Michael Sestak, Craig Bishop, Teddy Holt, Jason Nachamkin, Sue Chen,
Justin McLay, and James Doyle
High-Resolution Simulations and Atmospheric Turbulence Forecasting …………………………………………..262
Joseph Werne, David C. Fritts, Ling Wang, Thomas Lund, and Kam Wan
Multi-scale Predictability of High-Impact Upper Tropospheric Ice Clouds for Air
Force Platforms ………………………………………………267
Alex Mahalov
Multi-scale Predictability of High-Impact Weather in the Battlespace
Environment ……………………………………………………274
James Doyle, Carolyn Reynolds, Craig Bishop, James Goerss, Teddy Holt,
and Justin McLay
Numerical Exploration of the Stable Boundary Layer …………………………………………………………………….280
Benjamin MacCall, Patrick Haines, Edward Measure, David Marlin,
Wen-Y. Sun, Wu-Ron Hsu, and David Grove
Towards the Development of an Operational Mesoscale Ensemble System
for the DoD Using the WRF-ARW Model ……………..288
Timothy E. Nobis, Evan L. Kuchera, Scott A. Rentschler, Steven A. Rugg,
Jeffrey G. Cunningham, Chris Synder, and Joshua P. Hacker
Use of HPC to Provide Operational Mesoscale Meteorological Support
for ATEC Test Ranges ………………………………………293
John Pace, Elford Astling, Scott Halvorson, Yubao Liu, Terri Betancourt,
Josh Hacker, Jason Knievel, Scott Swerdlin, and Thomas Warner
Wave Information Studies (WIS) Pacific Regional Hindcast ……………………………………………………………299
Barbara Tracy and Deanna Spindler
Signal/Image Processing (SIP) and Sensors; Electronics, Networking,
and Systems/C4ISR (ENS) and Testing
Comparison of Turbo Decoder and Packet Acquisition Error Rates
in Frequency Hop-Spread Systems …………………….307
Everest W. Huang and Frederick J. Block
Development of Biological Warfare Sensors Using High Performance
Computer Systems ………………………………………….314
Marco Lanzagorta, Jay Eversole, and Wendell Anderson
Improved Parallel 3D FDTD Simulator for Photonic Crystal ……………………………………………………………319
Jason S. Ayubi-Moak, Stephen M. Goodnick, Dan Stanzione, Gil Speyer,
and Paul Sotirelis
viii
PVTOL: Providing Productivity, Performance and Portability to DoD Signal
Processing Applications on Multicore Processors …327
Hahn Kim, Edward Rutledge, Sharon Sacco, Sanjeev Mohindra,
Matthew Marzilli, Jeremy Kepner, Ryan Haney, Jim Daly, and Nadya Bliss
Scattering of Seismic Waves by Shallow Building Foundations Using
High-Order FEM ……………………………………………..334
Michael W. Parker, Stephen A. Ketcham, and Saikat Dey
Scattering of Urban Sound Energy from High-Performance Computations ………………………………………341
Stephen A. Ketcham, Michael W. Parker, Harley H. Cudney, and D. Keith Wilson
Signature Evaluation for Thermal Infrared Countermine and IED Detection
Systems …………………………………………………………349
John Peters, Stacy Howington, Owen Eslinger, Josh Fairley, Jerry Ballard,
Ricky Goodson, and Virginia Carpenter
Validating Simulations of Acoustic Propagation in Complex Terrain ………………………………………………..354
Harley H. Cudney, Stephen A. Ketcham, Donald G. Albert, and Michael W. Parker
Software and Hardware Infrastructure
Asymmetric Core Computing ……………………………..361
Jerry Clarke, Dale Shires, John Vines, and Eric Mark
Coprocessor Computing with FPGA and GPU ……..366
Song Jun Park, Dale R. Shires, and Brian J. Henz
HPCC Support to Campaign Level Analysis “HPCC Solving the Problem” ……………………………………….371
Steven Barnes, John Crino, and Timothy E. Smetek
Improvements to Multiple Path Secure Copy ……….376
Brian J. Guilfoos, Laura R. Humphrey, and José Unpingco
Real-Time Hardware-in-the-Loop Testing with Common Simulation Framework ………………………………379
Judith D. Gardiner
The Computational Science Environment (CSE) …..382
Jose C. Renteria and Eric R. Mark
User Friendly High Productivity Computational Workflows Using
the VISION/HPC Prototype ………………………………..387
José Unpingco
Using Mitrion-C to Implement Floating-Point Arithmetic on a Cray XD1 …………………………………………..391
Kevin K. Liu, Charles B. Cameron, and Antal A. Sarkady
Visualization of Time-Varying Features ……………….396
Mahnas Jean Mohammadi-Aragh, Sean Ziegeler, Joel Martin,
and Robert J. Moorhead
Software Performance and Performance Modeling
Enabling High Productivity Computing through Virtualization …………………………………………………………403
Juan Carlos Chaves
ix
High Performance Information Management for HPC Parallel Computing ……………………………………….409
Scot Tucker, Scott Spetka, George Ramseyer, Susan Emeny,
Dennis Fitzgerald, and Richard Linderman
High Productivity Languages for Parallel Programming Compared to MPI ……………………………………….413
Scott Spetka, Haris Hadzimujic, Stephen Peek, and Christopher Flynn
Improving Parallel Code Performance for Systems with Dual Processors ………………………………………..418
Susan Emeny, Scott Spetka, George Ramseyer, and Richard Linderman
Modeling Mixtures of Different Mass Ultracold Atoms in Optical Lattices: An
Illustration of High Efficiency and Linear Scaling on the Cray XT4 via
a Capability Applications Project at ERDC …………..424
J.K. Freericks
Observing Parallel Phase and I/O Performance Using TAU …………………………………………………………..431
Sameer Shende, Allen Malony, Alan Morris, and David Cronk
Optimization and Parallelization of DFT and TDDFT in GAMESS on DoD HPC
Machines ……………………………………………………….437
Michael E. Lasinski, Nichols A. Romero, Anthony D. Yau, Gary Kedziora,
Jean-Philippe Blaudeau, and Shawn T. Brown
Performance Evaluation of the Multi-language Helios Rotorcraft Simulation
Software …………………………………………………………442
Andrew Wissink and Sameer Shende
Performance Modeling and Mapping of Sparse Computations ……………………………………………………….448
Nadya T. Bliss, Sanjeev Mohindra, and Una-May O’Reilly
Computational Methods
A Scalability Study on Multicore Cluster Systems of an AFRL Radar
Frequency Tomography Imaging Code Written in MATLAB(r) for Parallel
Execution Using Star-P(r) ………………………………….459
Bracy H. Elton and Kevin M. Magde
Early Experiences with Algorithm Optimizations on Clusters of Playstation 3’s …………………………………468
Richard Linderman
Exploring New Architectures in Accelerating CFD for Air Force Applications ……………………………………472
Jack Dongarra, Gregory Peterson, Stanimir Tomov, Jeff Allred, Vincent Natoli,
and David Richie
Multicloud Convergence Acceleration for Complex Applications on Arbitrary
Grids ……………………………………………………………..479
Aaron Katz and Antony Jameson
Paradigms for Parallel Computation ……………………486
Gil Speyer, Natalie Freed, Richard Akis, Dan Stanzione, and Eric Mack
Parallel Implementation of Certain Robust Regression Methods Using Lazy
Evaluation in Python ………………………………………..495
José H. Unpingco
x
Progress in Applying HPC to Support Operational Use of CT-Analyst ……………………………………………..498
Gopal Patnaik, Jay Boris, Keith Obenschain, Robert Rosenberg,
Wendell Anderson, and Mabel Xu
Some Comparative Benchmarks for Linear Algebra Computations in Matlab
and Scientific Python ……………………………………….503
José Unpingco
Task and Conduit Framework for Multi-core Systems ……………………………………………………………………506
Sanjeev Mohindra, James Daly, Ryan Haney, and Glenn Schrader
Education
Educating the Educator: High Performance Computing Training Workshop
for Faculty from Under-Represented and Minority Serving Institutions …………………………………………….517
R. Mohan, N. Radhakrishnan, A. Kelkar, and V. Thomas
Women and Minorities in Information Technology …522
Virgiana Watson Ross and Valerie B. Thomas
Author Index ……………………………………………..528
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