The Quarterly Publication of the NASA 

Advanced Supercomputing Division

NAS researchers have developed an innovative

visualization system, the ‘hyperwall,’ which

allows scientists to view complex datasets 

and multiple parameters. See page 11

Nanotechnology: Simulating the Future of Computing – 8

Special Section: NASA At SC2002 – 1A

Fall 2002

www.nas.nasa.gov

NASA’s IPG Team Develops New Tools – 4

New NAS Parallel Benchmarks Released – 14
Vol. 3, No. 3 • Fall 2002

Executive Editor: John Ziebarth

Editor: Nicholas A. Veronico

Writers: Holly A. Amundson

Jill A. Dunbar

Julie Jervis

Rob Van Der Wijngaart

Graphic Designer: Sue Kim

Illustrator: Cliff Williams

Photographer: Michael Boswell

Contact the Editor:

Nicholas A. Veronico

Gridpoints

M/S 258-6

Moffett Field, CA 94035-1000

Tel. (650) 604-3046 • Fax (650) 604-4377

nveronico@mail.arc.nasa.gov

Gridpoints is a quarterly publication of the NASA

Advanced Supercomputing Division at NASA

Ames Research Center. The division’s staff includes

government employees and contractors from

Advanced Management Technology Inc., Computer Sciences Corp., Cray Inc., Eloret, Raytheon Co.,

and SGI.

Gridpoints acknowledges that some words, model

names and designations mentioned herein are the

property of the trademark holder. Gridpoints uses

them for identification purposes only.

The staff of Gridpoints would like to

thank the following people for their assistance in preparing this publication:

Michael Aftosmis, M.P. Anantram, Asen

Asenov, Marsha Berger, Glenn Deardorff,

Daniel Dorney, Reynaldo Gomez, TR

Govindan, Chris Henze, Thomas Hinke,

Vee Hirsch, Marjorie Johnson, William

Johnston, Randy Kaemmerer, Creon

Levit, Anthony Lisotta, Nagi Nicholas

Mansour, John Melton, Parviz Moin,

George Myers, Chuck Niggley, Marcia

Redmond, Tim Sandstrom, Karim

Shariff, Warren Smith, Judith Utley, Rob

Van Der Wijngaart, Arsi Vaziri, Anne

Woods, Jerry Yan, Pamela Walatka

On The Cover:

Subscribe to Gridpoints

Subscriptions to Gridpoints are complimentary.

Please send e-mail with your name, company

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Note: Subscribers outside the United States 

can access Gridpoints on the web in PDF

format at: http://www.nas.nasa.gov/gridpoints

The Quarterly Publication of the NASA 

Advanced Supercomputing Division 4

8

Features

Nanotechnology: Simulating

the Future of Computing

NAS scientists demonstrate how the laws of 

quantum mechanics affect transistor and 

device miniaturization.

Julie Jervis

Mars terrain data displayed on the NASA Ames-developed ‘hyperwall” – a seven-by-seven cluster

of flat panel screens, each driven by its own dual-CPU computer with high-end graphics card.

Each row in this visualization projected on the hyperwall depicts the same 48-degree swath along

Mars’ equator from 180 degrees West to 180 degrees East. See page 11 for details.

(Dataset courtesy MOLA science team ; visualization by Glenn Deardorff)

NASA At SC2002

A look at NASA exhibits, events, and

speakers at the annual high-performance

networking and computing conference,

SC2002, in Baltimore, Maryland,

November 17-21, 2002.

NASA’s IPG Team Develops 

New Tools

NASA’s IPG team meets another of its milestones,

creating tools to simplify job submission to 

distributed grid resources.

Holly A. Amundson

1A

Also in this issue:

1 News From NAS

1 From the Division Chief

6 CTR Summer Program

14 New NAS Parallel

Benchmarks Released

17 Calendar

The Vision Behind 

the ‘hyperwall’

NAS researchers have developed an 

innovative visualization system that

allows scientists to view complex datasets

and multiple parameters.

Julie Jervis

11
For fifteen years, the NAS Division has taken a leadership role in support of the annual supercomputing

conference, this year known as SC2002. Many of the

division’s research highlights shown in this issue of

Gridpoints will be displayed at SC2002. (Details begin on page 1A.)

I am proud to announce that the division’s researchers were recently honored

with two prestigious awards. The Cart3D development team was the recipient of NASA’s Software of the Year Award (see page 3), and the division’s computational fluid dynamics research on the DeBakey Ventricular Assist Device

(VAD) was recognized as NASA’s Invention of the Year for 2001, announced

in spring 2002 (see Gridpoints, Summer 2002, page 3). This award-winning

work by our research teams is the culmination of more than a dozen years of

computational science research and development for both products.

In addition to the Cart3D and DeBakey VAD highlights, division researchers

will present a number of new tools and applications at SC2002 that form

the infrastructure of NASA’s Information Power Grid (IPG). The IPG team

recently demonstrated the CODE (Control and Observation in Distributed

Environments) framework, which enables researchers to control multiple

resources, services, and applications in the grid environment (see page 4). To

support the CODE framework, the IPG team also developed a grid abstraction tool that presents information from the MDS in a uniform manner.

Furthering our development of a robust infrastructure for the IPG, the division has released new versions of the NAS Parallel Benchmarks. GridNPB3.0

consists of four sets of problems that represent applications on computational grids for measuring grid performance (see page 14).

NAS researchers recently received an Information Sciences and Technology

Directorate grant to develop the “hyperwall,” a problem-solving environment

consisting of a seven-by-seven cluster of flat-panel screens, each driven by its

own dual-CPU computer. The hyperwall will help scientists use their own

perceptive skills to analyze data by recognizing patterns, detecting features and

changes, and sorting relationships between datasets.

NAS scientists are modeling the characteristics of electron flow in a wide variety of nanostructures, in an effort to demonstrate how the laws of quantum

mechanics affect transistor miniaturization. These laws will aid researchers in

building nanoscale transistors with an eye toward developing smaller-scale

computers for future NASA space missions (see page 8).

From the need to solve fluid flows within the VAD, and during the development cycle of Cart3D, many important collaborations were established with

researchers at other NASA centers, commercial companies, and numerous academic institutions. SC2002 provides our scientists with a venue to display

their research while seeking new collaborators to help further NASA’s mission goals.

I hope you enjoy this issue, and, as always, I welcome your feedback.

John Ziebarth

jziebarth@mail.arc.nasa.gov

From The Division Chief

NAS Mission

To lead the country in the research,

development, and delivery of revolutionary, high-end computing services

and technologies, such as applications

and algorithms, tools, system software, and hardware to facilitate NASA

mission success.

News

From

NAS

Gridpoints 1

NAS Scientist Receives

International Award

NAS senior scientist Deepak

Srivastava recently received the

Eric Reissner Medal for distinguished

work in computational nanosciences.

The medal, awarded in August at the

International Conference on Computational & Experimental Engineering

and Sciences (ICES), cites Srivastava’s

“distinguished work in computational

nanosciences and carbon nanotubes.”

The award, given by an international forum of scientists and engineers, recognizes

Srivastava’s contributions in broadening the understanding of the nanomechanics and electronic behavior of carbon nanotubes. It also signals an international acceptance of nanotechnology

as the next growth area in the broader scientific and engineering communities.

Srivastava is technical lead of the NAS

Division’s computational nanotechnology investigations, and has concentrated

his work on computational nanotechnology in nanomaterials, nanoelectronics, and nanodevices. Possible applications include ultra-strong, light-weight

composite materials and molecular electronics devices for computing and sensing

purposes, as well as concepts and materials for solid-state quantum computers.

Srivastava’s new focus area will include

state-of-the art implementation of

Continued on page 2
simulation algorithms on NAS supercomputers, in a user

friendly way. Srivastava hopes this area of research will pave

the way for NAS to become a service provider for simulations in nanomaterials and molecular electronic devices and

systems to other NASA centers, and to industry and university customers. NASA Ames’ nanotechnology program plays

a significant role in steering nanotechnology developments

both within and outside NASA. 

The Eric Reissner Medal is awarded every two years by ICES

for excellence in computational mechanics research. Reissner,

who passed away in 1996, was a noted teacher, researcher,

and author, who expanded the foundations of the theory of

mechanics, leading to advances in the design of both civil

engineering and aerospace structures.

Biologists, Nanotechnologists, and

Information Technologists Gather

Nearly 100 experts gathered at NASA Ames Research

Center October 7-9 for the Biology, Information

Science, Nanotechnology Fusion and NASA Missions Invitational Workshop to explore cross-disciplinary approaches

to solving the science and technology challenges facing

future NASA missions. Organized by Ames Research Center

and the Universities Space Research Association (USRA), the

workshop was the first of its kind, designed to explore the

emerging fusion of these three fields of science.

“Our goal was to start a conversation and gather new ideas,”

says T.R. Govindan, NASA Advanced Supercomputing Division senior scientist and co-chair of the workshop. “This is a

very diverse group of people, and everyone speaks their own

language, but the presentations gave us excellent examples of

what this research might accomplish for NASA missions.”

Experts from universities, industry, and government agencies

throughout the United States joined NASA personnel for

three days of presentations, panel talks, and discussions covering topics that included the use of biology to solve information technology challenges, life detection and sensors,

computational biology and bioinformatics, and nanotechnology assembly.

By inviting mission experts from all NASA enterprises to talk

about their needs and challenges, the workshop leaders began

the task of matching these nascent research areas to NASA’s

mission needs.

Participants Baruch Blumberg, director of the NASA Astrobiology Institute, and Michael Storrie-Lombardi of NASA’s

Jet Propulsion Lab both agreed the meeting was an important first step in bringing these sciences together, and hoped

it would lead to a concentrated effort to follow up on the

leads and themes discussed. Govindan says the next step will

be to publish a report detailing the themes, ideas, and suggestions that emerged from the workshop, and provide a

framework for planning. “Based on the level of enthusiasm

and interest in the fusion of these three fields, it’s likely that

this kind of conference might become a regular event,” he

says. For more information visit: http://binfusion.arc.nasa.gov

News From NAS

Continued from page 1

2 Gridpoints

Representative Mike Honda (second from right), of the 15th

Congressional District in Silicon

Valley, toured the NASA Advanced

Supercomputing (NAS) Facility at

Ames Research Center on August 23.

The facility houses NASA Ames’ new

Aviation Security Laboratory, a mock

airport setting designed to investigate

where information technology can be

applied to the flow of passengers

through an airport, to detect potential

security concerns. Aviation Systems

Division Chief Tom Edwards, (far

right), and Thomas Hinke, lead scientist for the Ames Aviation Security

Lab (second from left), look on as Bill Thigpen, NAS Engineering Branch chief, explains how the system works.

Honda serves on the House Budget Committee, the

House Committee on Science, including its subcommittee on Research, and on the Transportation and Infrastructure Committee, including its subcommittees on

Aviation, Highways and Transit, and Water Resources

and Environment. (NASA/Tom Trower)

Representative Honda Visits Ames’ Aviation Security Laboratory
www.nas.nasa.gov/gridpoints Gridpoints 3

Recognizing Leadership in Scientific Computing

Every year NASA recognizes outstanding accomplishments of the agency’s research community by presenting the NASA Software of the Year award. This year, the

prestigious award was placed in the hands of the NASA

Advanced Supercomputing (NAS) Division’s Michael

Aftosmis, John Melton of NASA’s Aerospace Directorate,

and Marsha Berger of the Courant Institute, New York

University. The team was recognized for their long-time

work on Cart3D, a design and analysis software package

for complex aerospace vehicles (see Gridpoints, Summer

2000, page 4).

Co-sponsored by NASA’s Chief Information Officer and

NASA’s Inventions and Contributions Board, the Software

of the Year award is judged by the NASA Software Advisory Council. To meet eligibility requirements, software

must be supported, adopted, sponsored, or used by NASA,

it must be significant to the NASA mission, and be of

commercial grade. In addition to Cart3D, a Direct Simulation Monte Carlo software package, called DAC, from

NASA’s Johnson Space Center, Houston, was named cowinner of the annual award.

What sets Cart3D apart from other Cartesian mesh generation packages is its ability to accept geometry of arbitrary

complexity and process it in a fully automated manner.

Reynaldo Gomez, the Space Shuttle aerodynamics subsystem manager at NASA Johnson is especially pleased

with the robustness of Cart3D: “The real power of

Cart3D lies in its simplicity of use. Historically, computational fluid dynamics (CFD) codes required a lot of manual intervention and training to develop grid systems and

to run the flow solver. With Cart3D, I’ve actually taken a

third-year Air Force cadet who had no background in

CFD, no knowledge of UNIX or CAD systems, and within a period of about a week, he was able to generate grids,

start running the flow solver, and begin postprocessing

results for Space Launch Initiative configurations.”

In addition to its applications in NASA programs such as

the Space Launch Initiative, Cart3D has significant relevance in the commercial world. In September 2001,

ICEM CFD Engineering, Inc. of Berkeley, Calif., was

granted an exclusive license by NASA Ames’ Commercial

Technology Office in the areas of aerospace, automotive

engineering, and turbomachinery. Since then, the company has also been granted a non-exclusive license in the areas

of electronics, electromagnetics, and the process industry –

injection molding and casting.

Another company based in Seattle, Washington, also has a

commercial license for Cart3D, and is using the grid generation software to investigate the American Airlines

Airbus crash on November 2001 on Long Island, New

York. “This kind of ‘virtual flight’ capability allows people

to do aero forensics on this type of crash,” explains

Aftosmis. The Airbus crash analysis includes estimations of

aerodynamic loads imposed by turbulence from other aircraft in the area. 

Cart3D’s ease of use and automation makes it possible to

carry out virtual flight, where every permutation of a

design is explored over the complete range of expected

flight conditions. “Cart3D provides designers with the

trend information they need in order to understand how

their designs are going to operate, not just under a single

condition, but over a wide range of flight conditions,”

explains Melton. “Cart3D makes the computational fluid

dynamics process fast enough to replace lower-order design

methods with high-fidelity techniques – the key to streamlining the design and analysis process of complex aerospace

vehicles,” adds Aftosmis.

The level of automation demonstrated by Cart3D has

sparked international interest in Cartesian mesh generation. “It is very gratifying to see this line of research being

picked up by other researchers worldwide,” says Berger.

The team hopes to continue generating interest in Cartesian meshes as they add new capabilities to Cart3D.

For more information about the Cart3D software package,

visit: www.nas.nasa.gov/~aftosmis

NASA researchers Michael Aftosmis (left) and John Melton

(right) and Marsha Berger, from New York University’s

Courant Institute, co-developed Cart3D

(Michael Boswell)
4 Gridpoints

NASA’s IPG Team Develops 

New Tools

NASA’s IPG team meets another of its milestones, creating tools 

to simplify job submission to distributed grid resources.

NASA’s Information Power Grid (IPG) team has

taken another step toward making the agency’s prototype grid environment more user-friendly. To support the Computing, Information, and Communications

Technology (CICT) Program’s Computing, Networking,

and Information Systems (CNIS) Project in reaching one of

its major milestones in September, the IPG team delivered a

grid programming environment consisting of the Globus

Toolkit and tools developed by the IPG team. Coincidentally, the tools developed for the CNIS milestone enabled

the IPG team to meet one of its own goals. In addition, the

IPG team’s development work provided access to as many as

17 grid resources at seven locations. The heterogeneous computer resources included Sun, Linux, Linux cluster, and SGI

machines running Irix, Solaris, and Linux operating systems.

CICT researchers used 13 resources at four locations to meet

the milestone – 10 resources in four locations was the measure of the milestone’s success.

In achieving this goal, IPG team members at NASA Ames,

Glenn, and Langley Research Centers collaborated with researchers at the National Center for Supercomputing Applications (NCSA) in Illinois, Information Sciences Institute (ISI)

at the University of Southern California in Marina Del Rey,

and Argonne National Laboratory (ANL) in Argonne, Illinois. Together, these organizations provided the support and

expertise needed to make the resources available from multiple locations. To make it easier for users to take advantage

of these geographically distributed resources, several new

grid tools were developed and deployed. These tools use

the Globus Toolkit, which provides a uniform interface to

the resources.

The tools created for simplifying the process of submitting

jobs to the distributed grid resources include a job manager

to run specified jobs and track job progress, an abstraction

tool for handling job scheduler information on multiple machines, and a resource broker for selecting grid resources (see

figure, page 5). Standard grid security measures were also put in

place on every resource, ensuring the secure transfer of all data.

Tools of the Trade

To oversee all the “transactions” taking place among the grid

resources, the IPG team used an existing framework called

Control and Observation in Distributed Environments, or

CODE (see Gridpoints, Summer 2002, page 18). The

CODE framework, created to provide a standardized process

for making observations and performing actions on remote

computer systems, served as the basic communication mechanism for the CICT milestone. “We had to accommodate

Java and Perl clients, so we needed a communication framework that could do both – CODE was the answer,” explains

IPG team member Warren Smith, who developed the framework. CODE was also used to manage events – automatic

notifications were sent to users alerting them upon completion of a task, or when a machine became unavailable.

The job manager delivered to IPG users is designed to submit, track, and cancel jobs. Users describe the set of files

they want to stage (transfer) before they run their job,

which application they want to execute, and where they

want their files to end up when the jobs are complete. “The

job manager is really tuned to be able to run jobs reliably,

once users define what they want to accomplish and where

they want the results to go,” says Smith. To move files from

one machine to another within the grid environment, the job

manager takes advantage of the GridFTP mechanism, a

method for transferring files. To execute applications on grid

machines, the job manager utilizes the Globus Resource

Allocation Manager (GRAM), a service that enables remote

job submission.

The information abstraction tool, also developed for the

milestone, is intended to take the “noise,” or extra details, out

of using grid resources. The abstraction tool comprises components that represent information about computers, networks, and schedulers, and encapsulates information from a

hierarchy of servers called the Monitoring and Discovery

Service (MDS). “The problem is that the format of the information in the MDS changes periodically, and this is a nuisance to users. The abstraction tool hides these changes, providing a consistent view of the information needed by users

to run their jobs,” explains Smith.

To handle resource selection within the grid environment,

the IPG team also created a resource broker. To utilize the

resource broker, users are only required to describe the job

they want to run by specifying the number of CPUs needed,
www.nas.nasa.gov/gridpoints Gridpoints 5

the amount of memory needed, the operating system

requirements, and any other information unique to

their jobs. Once this information is collected, the

broker uses the description and data from the abstraction tool to determine which machines satisfy their

job requirements. The broker then generates a list of

machines capable of running the job, prioritized by

current loads on the machines’ processors. “Our

application utilized the IPG resource broker software

to select the right compute host for each computation, greatly simplifying our submission process,”

says NAS researcher Stuart Rogers.

Lessons Learned 

“This milestone provided us with a great opportunity to study the interoperability of grids, helping

uncover some grid management problems. This will

lead to future work in making grids more compatible

with one another,” explains NAS IPG task lead Tony

Lisotta. One of the biggest challenges the IPG team

faced while working to meet this milestone was

ensuring the use of compatible grid software so the

resources could “talk” to one another. Contributing to

this challenge, the grid community was in the middle

of a Globus upgrade. During this transitional period,

a lot of backward compatibility issues surfaced – centers were using different versions of the Globus

Toolkit, preventing resources from communicating

with one another. 

To promote communication about Globus Toolkit versions

and other issues that came up during the process of meshing

the various grid environments, several practices were put into

place. E-mail lists were established so that everyone involved

had access to information about problems and solutions;

weekly meetings were held for researchers working on the

applications portion of the milestone; and regular conference

calls were conducted to encourage communication among all

participants. 

“Coordination and collaboration are some of the most critical challenges in managing a grid. Lessons learned with this

milestone are being shared in the grid community as IPG

takes a lead role in making grids work, and work well together,” explains IPG team member Judith Utley. IPG team members and collaborators plan to write a “lessons learned” paper

addressing grid management, which will be submitted to the

Global Grid Forum (GGF) for discussion. In addition, a new

group, dedicated to addressing grid management issues, and

co-chaired by Utley, has been formed within GGF. “This will

contribute to the overall grid community in the long run, as

we identify areas where standards and agreements are necessary,” adds IPG team member George Myers.

Promising Future for Grids

While not all the tools and practices used to meet this milestone will become standard grid practices, integrating some

of these new tools into the IPG environment will make it

more robust and increase its capabilities. “Given what we’ve

learned about these tools, we are reviewing them to see how

they should be changed, and what we can do with them. The

job manager, for example, will be extended a bit to add some

more functionality,” says Smith. “The effort to meet the

milestone led to the development of tools that will continue

making the IPG easier to use – that has been our goal from

the beginning, and will continue to be the theme as we develop the tools we envision,” says Myers. 

The September milestone provided the IPG team with an

opportunity to demonstrate its ability to contribute to the

advancement of grids. Says Myers: “I think it was an amazing accomplishment to bring together such an array of

diverse organizations, and it says something about the power

of grid technology that we could pull it all together.”

— Holly A. Amundson

Editor’s note: The AeroDB group, part of the CICT/CNIS

Project, used tools provided by the IPG team for this milestone to

implement an application for automating large CFD parameter

studies. This application enabled the AeroDB group to analyze a

flight vehicle over a wide range of flight conditions. Look for an

article outlining this portion of the milestone in the Winter 2003

issue of Gridpoints.

This diagram represents a conceptual view of the IPG software environment, including software components developed by the IPG team used to

meet the requirements of a Computing, Information, and Communications Technology (CICT) Program milestone. The IPG resource broker

obtains information from the various components of the Monitoring

and Discovery Service, an information service containing resource information, in order to suggest where to run jobs. To execute applications

on grid resources, the job manager utilizes the Globus Resource Allocation Manager, a service that enables secure remote job submission, and

the GridFTP mechanism to securely transfer files between grid resources.
6 Gridpoints

Center for Turbulence Research

Summer Program Making

Worldwide Waves

Presentations and papers from the popular NASA-Stanford

University program attract international attention.

After four weeks of intense collaborative study, participants in the Center for Turbulence Research (CTR)

summer 2002 program presented their findings

before a large international audience at Stanford University.

The August presentation ceremony marked the final step

before publication and worldwide distribution later this year.

Since its first session in 1987, CTR’s biennial summer program has attracted research proposals from laboratories all

over the world; each evaluated according to its relevance and

match with NASA’s interests. This year,

the 46 selected participants came from

11 countries, nine states, and 40 institutions across the globe. Research focused

on nine areas of CTR’s expertise – turbulence acoustics, Reynolds-Averaged

Navier-Stokes (RANS) modeling, large

eddy simulation (LES), numerical methods for LES, turbulence fundamentals,

stratified shear flow turbulence, flow

optimization, nanofluidics and biology,

and turbulent combustion and sprays.

A cooperative program between Stanford University and NASA Ames Research Center, CTR serves as a consortium for turbulence research by bringing theorists and experimentalists together in a number of research programs. The

NAS Division co-manages and supports CTR by providing supercomputing power and access to its huge archive

of raw field data, enabling researchers to test their ideas.

NAS scientists are also involved in several individual CTR

research projects.

“The summer program is a cost-effective way for researchers

to get a first cut at their ideas, which are typically brand new,

exploratory, and often high risk,” says Parviz Moin, CTR’s

director. Each of the 32 projects conducted this year were

based on the researchers’ own proposals, some of which used

the full potential of NAS’ supercomputing resources. “NAS

had to increase CTR’s allocation of computer time threefold to accommodate their use of visualization facilities, networks, and data archives,” says Nagi Mansour, CTR’s

deputy director and lead of NAS’ Physics Simulation and

Modeling Office.

“Historically, turbulence researchers have been preoccupied

with generating data to test ideas and take measurements,”

explains Moin. “The numerical simulation techniques pioneered at Ames provide raw field data, so researchers do

not have to worry about producing the data. This is

being emulated all over Europe, as it

provides a single standard for independent testing.”

This year’s program started with registration on July 28, followed by an

intense work schedule that included

kick-off presentations, midterms, tutorials, and final presentations. The endof-term presentations included an

overview of methods, investigations,

comparisons, and conclusions, while

the research teams faced close scrutiny

and intense questioning from experts

in the audience. These experts included guests from other institutions and

government agencies that might be interested in funding the

participant to continue the research at their home institute.

Moin says that past findings from the program have had a

major impact in the field of turbulence control and modeling, resulting in methodologies used for standard code

throughout the world in the areas of simulation technology

and database diagnostic tools. This year, the monthly journal, Physics of Fluids, published by the American Institute of

Physics, will publish a summary of the findings.

Karim Shariff is a NAS research scientist who has been involved with the program from the start when he participated

as a graduate student. Over the years, he has participated in

several successful projects, including Simulation and Modeling

“The summer program is

a cost-effective way for

researchers to get a first

cut at their ideas, which

are typically brand new,

exploratory, and often

high risk.”

—Parviz Moin

Center for Turbulence Research
www.nas.nasa.gov/gridpoints Gridpoints 7

of the Elliptic Streamline Flow in

1996, which was the first study of

turbulence in this type of flow. This

summer, Shariff was one of 26 hosts

from Stanford and NASA, and guided a study on contrail formation in aircraft wakes.

“I’ve always been interested in aircraft trailing vortices,” says

Shariff. “Atmospheric scientists have suspected for some time

that airplane contrails, those two lines that come out like

smoke behind an aircraft, have an impact on climate.

Basically, contrails are clouds of ice that form when soot or

aerosols from engines cause condensation of water vapor

present in the engine exhaust and in the atmosphere.

Contrails artificially increase cloudiness and trigger the formation of cirrus clouds, which in turn alters the climate on

local and global scales.”

The proposal to study the conditions that cause the formation of contrails came from Roberto Paoli, a post-doctorate

scientist with the Computational Fluid Group at CERFACS,

the European Centre for Research and Advanced Training in

Scientific Computation, in France. Paoli’s research project

simulated the interaction of jet exhaust with the vortex of the

aircraft and tracked representative soot particles to show

when ice begins to accumulate, what the radius of the ice is

going to be, and how the distribution of ice particles evolves

over time. Using prior knowledge gained by researchers in

the Earth Science Division at Ames, who have been doing

flight studies of cloud formation and contrails for many

years, the scientists were able to identify the areas of the

parameter space that are important.

After completing his calculations, Paoli concluded that vapor

first supersaturates at the edges of the engine jet exhaust,

then the vortex increases the mixing of water vapor and air,

which favors condensation. Paoli also concluded that as ice

particles form, they decrease the amount of vapor in the

atmosphere, resulting in a significant deviation from the classical theory of a mixing line. These kinds of results will ultimately be used by Earth scientists as models in simulations

of the global climate.

Like all the participants in CTR’s summer program, Shariff

hopes to see more research coming out of this new and innovative project. Among the many offshoots from this summer’s work, Paoli is planning further study into how jet mixing is suppressed within the vortices, a study that Shariff will

find useful for his own work on the radar detection of aircraft

trailing vortices (see Gridpoints, Fall 2001, page 14). 

“This is really the first time this type of simulation has been

done,” says Shariff. “If it were not for the summer program,

Paoli would be working on it in Europe, and I might never

hear about it. This is a wonderful opportunity for people

doing cutting-edge research in different but related fields to

come together, bring each other up to speed, and benefit

from sharing valuable experience and knowledge.”

— Julie Jervis

CTR Summer program participant

Daniele Carati, of Brussels University in Belgium, presents his group’s

findings on Large Eddy Simulations.

CTR invited 46 scholars to participate in the summer program. They

represented 40 institutions from nine

U.S. states and 11 countries.

For more information on the Center for Turbulence

Research, visit:

http://ctr.stanford.edu

Shariff’s work on aircraft wake vortex detection can be

viewed at:

http://people.nas.nasa.gov/~shariff
8 Gridpoints

Nanotechnology: Simulating the

Future of Computing

NAS scientists demonstrate how the laws of quantum mechanics

affect transistor and device miniaturization.

S

ince transistors were invented in 1947, their miniaturization and large-scale integration have been so rapid,

that chip designers have been able to double computer

processing power approximately every 18 months. This ruleof-thumb is commonly known as Moore’s Law, after Gordon

Moore first made this observation in 1965. Today, microprocessors the size of a fingernail contain tens of millions

of transistors and are used in supercomputers with enough

processing power to simulate complex models of Earth’s climate system.

At the same time, developing expertise for modeling and

understanding the characteristics of electron flow in a wide

variety of nanostructures is a goal that NAS scientists hope

will one day enable them to send a supercomputer the size of

a briefcase into space. With such sophisticated computing

power, a spacecraft would be more autonomous, be able to

self-diagnose, self-repair, and better guide mission control on

Earth into making the right decisions in outer space.

As transistor miniaturization has led to faster and more powerful chips, chip designers are now facing new challenges

from the laws of physics. In its 2001 International Technology

Roadmap for Semiconductors, the Semiconductor Industry

Association predicted that transistors will shrink to tens of

nanometers within the next decade (see How Small Is Nanoscale?). This raises concern among researchers and industry

that, as the laws of quantum mechanics take over, current

methods of lithographic chip etching will be inadequate and

devices may not work as expected. Quantum mechanics is

the science that deals with the behavior of matter and light

at the atomic and subatomic scales. This dictates a different

realm of physics than the one we are used to in the real

world, causing tiny transistors to behave in a completely different manner than their conventional, larger siblings.

Industry is turning to the research community for critical

studies into new analytical modeling techniques, and to

ensure a full understanding of the physics and chemistry

involved at the quantum level.

“Part of our focus is to downscale semiconductor technology

and model the current voltage characteristics of transistors

with channel lengths less than 25 nanometers in size,” says

NAS research scientist M.P. Anantram. “We can simulate

these transistors on the computer, determine the ideal design

parameter space, and predict device characteristics. This can

then guide experimentalists to build these transistors in a

reproducible manner.”

Together with colleagues Alexei Svizhenko and NAS Senior

Scientist T. R. Govindan, Anantram is harnessing the power

of NAS’ parallel supercomputers to conduct the complex

and highly sophisticated calculations necessary for nanoscale

modeling. The process involves running thousands of calculations on potential transistor models, solving large sets of

equations, and then using the results to continually refine

the model (see figure on page 10). Just to compute the current voltage characteristics of one device can take as much as

ten hours of computing time on 64 processors of an SGI

Origin 3800 supercomputer.

NAS’ supercomputing power has been instrumental in attracting international collaboration and advancing research

in the field. Asen Asenov, head of the Department of

Electrical Engineering at the University of Glasgow in Scotland is one of NAS’ collaborators in the field of nanotransistors. “We chose NASA Ames for collaboration because they

have, in my view, the most sophisticated and accurate quanHow Small Is Nanoscale?

• One inch is equal to 25.4 million nanometers.

• The average width of a human hair measures 100,000

nanometers.

• One human red blood cell measures 10,000 nanometers wide.

• A single streptococcus (strep throat) group A bacteria

measures 600 to 1,000 nanometers in diameter.

• A single HIV virion measures 80-100 nanometers in

diameter.
www.nas.nasa.gov/gridpoints Gridpoints 9

tum transport simulator in the world, and the necessary

computing power to run meaningful design-oriented simulations,” says Asenov.

Asenov’s team specializes in developing 3-D statistical simulations to understand fluctuations in the electrical characteristics of nanoscale devices. For each device, the Glasgow scientists use the results from NAS scientists’ advanced 2-D

quantum mechanical simulations to determine the appropriate parameters to use in their less sophisticated but faster 3-

D atomistic quantum device simulator. 

Asenov is planning to introduce more of the advanced quantum simulation methods developed by NASA Ames into the

university’s simulation tools, and to continue collaboration,

especially in developing new, close to first-principle simulation techniques to describe the complex transport properties

of atomic-scale devices.

Another successful aspect of Anantram, Govindan, and

Svizhenko’s work has been examining many of the physics

issues concerning the flow of electrons in atomic-scale carbon

nanotubes. Building devices using carbon nanotubes is a

new, alternative approach that assembles larger objects from

molecules, rather than starting with something large and trying to define smaller and smaller patterns. “Carbon atoms

form a long tubular structure, which can either be a metal or

a semiconductor, depending on the chirality, or ‘twist,’ of the

tube,” explains Anantram. Copper wire is not atomically precise, and therefore subject to defects, which cause scattering

and reduces its current-carrying capacity. Carbon nanotubes

are atomically precise, and the NAS researchers are exploring

issues such as the ultimate current-carrying capacity, coupling to metal contacts and their electromechanical properties. “Chirality is a degree of freedom that nature offers to us,

and we are interested in studying the best chiral angles for

various nano-device applications,” explains Anantram.

More recently, the NAS researchers have modeled the

electromechanical properties with nano-sensor applications

in mind. These investigations have yielded significant results

in the scientific community. Working in collaboration with

Amitesh Maiti of Accelrys Inc., a San Diego-based provider

of simulation and informatics software and services,

Anantram and Svizhenko were able to offer an explanation

for an experiment published in the journal Nature in June

2000. In the paper, “Reversible Electromechanical Characteristics of Carbon Nanotubes under Local Probe Manipulation,” conducted at Stanford University, scientists set a carbon nanotube between two metal contacts and pressed down

on the middle of the tube using an Atomic Force Microscope

(AFM) tip. They were surprised to find that this strain

caused the current to decrease by a factor of 100, and theorized that the nanotube becomes a bad conductor of electricity because the bond structure changes in the area where the

tip strikes the tube.

“We wanted to find out why this happened in the experiment, and predict what would happen if the experimentalists

used nanotubes of other chiralities and diameters of nanotubes,” says Anantram. The team began by modeling a nanotube made from a few thousand carbon atoms, simulating

the effect of the AFM tip, and then examining the new configuration of atoms. They were particularly interested in seeing how this effect varied from just bending a nanotube.

“What we found was that stretching was more important

than bending,” says Anantram. “The change in conductance

is actually due to the ‘rubberband effect’ – strain across the

entire tube – and not just because of the deformation in the

central region by the AFM tip, as previously theorized.”

The results of the team’s collaborative study were published in

a paper titled, “Electronic Transport through Carbon

NAS scientists have developed models to demonstrate how the

laws of quantum mechanics affect transistor and device miniaturization. The top model depicts a nanotube between source

and drain contacts, where its ultimate current-carrying capacity, metal-nanotube coupling, and electromechanical/nano-sensor properties are being studied. The center model is a DNA

strand used in transport experiments where the physics of conduction is being explored. At bottom is a nano-transistor, where

2-D doping profiles, polysilicon depletion, source-to-drain and

gate tunneling, and the role of scattering are being studied.

(M.P. Anantram/Cliff Williams)
10 Gridpoints

Nanotubes: Effects of Structural Deformation and Tube Chirality” in the

American Physics Society’s journal,

Physical Review Letters, March 25, 2002.

This study continues to be the focus of

ongoing research into the metallic and

semiconductor properties of carbon

nanotubes. 

A third and more controversial paradigm

for device design is the nascent research

into conductivity in DNA. NAS scientists are interested in this form of nanotechnology for two main reasons: Currently, experimentalists around the

world are getting contradictory results

from their studies, providing a major

challenge in establishing the true nature

of DNA. In addition, they are interested

in learning whether the arbitrary

sequences that can be reproducibly

designed by biochemists can be exploited in nanotechnology.

DNA has four building blocks: A, T, C,

and G, which biochemists can arrange

within the DNA structure in any arbitrary and reproducible manner – a huge

attraction for nanotechnologists. The

challenge has been isolating individual

strands from the millions that are produced at one time, and locating them in

an experiment. However, experimentalists have recently been

able to take strands approximately 8-100 nanometers long

and place them between metal electrodes to measure the current as a function of voltage, as though it were a nanodevice.

“These experiments have been very controversial,” says

Anantram. “One group in the Netherlands finds the strands

are semiconducting in nature, and another in Switzerland finds they are metallic.

Their experimental techniques differ and

they have slightly different ways of doing

these measurements, so the challenge is

for us theory and modeling researchers to

find out what is really happening.”

So far, Anantram says, calculations performed in collaboration with NAS postdoctoral fellow Christophe Adessi (now a

faculty member at the University of

Lyon, France), and Steve Walch from the

Center for Nanotechnology at NASA

Ames, indicate DNA is, at best, a semiconductor. In addition, as the length of

the DNA increases, it becomes an

extremely poor conductor of electricity.

The resistance increases much more rapidly than linearly with length. Though

the researchers have two papers in review

explaining some aspects of the experimental work, Anantram says that the

physics of conduction in DNA is far from

resolved, and there is much to be understood – for example, how the currentvoltage characteristics change as a function

of DNA sequence, and can DNA design

obtain specific device characteristics.

As an overlap in the fields of information

science and biology continues to grow,

NAS scientists are developing the theory and simulations

that will provide a deeper understanding of what will work

and why. “Large scale simulations give us a better understanding of these emerging fields,” says Anantram. “Technology is interrelated, and nanomachines will help us make

the next leap forward.”

— Julie Jervis

The heart of modeling electronic nanotransistor devices is

the Metal Oxide Semiconductor Field Effect Transistor

(MOSFET), commonly recognized as the workhorse of

modern-day computing. The MOSFET works like a superefficient switch with three terminals: source, drain, and gate

(see models on page 9). The gate is an electrode attached to

the base of the transistor with a piece of positively charged

(p-type) semiconductor in the middle and a thin layer of an

insulator, such as silicon dioxide. When low voltage is

applied to the gate, electrons in the form of current are able

to flow freely from the source to the drain. But applying

high voltage to the gate has the same effect as standing on a

flexible water hose – electrons are repelled and fewer can

flow through (see Gridpoints, Summer 2000, pages 10-13).

In conventional MOSFET design, technical issues such as

current leakage and electron tunneling can be solved using

classical physics equations, but in devices that are less than

100 nanometers in size, these equations no longer describe

the physics of resistance. Anantram, Govindan, and

Svizhenko’s work has been to simulate charge flow in tiny

MOSFETs using quantum mechanical equations, and to

provide answers to complex technical issues without the billion-dollar cost of building machinery and fabrication

plants. “Going forward, no one knows whether silicon will

be the best material for nanotransistors,” says Anantram.

“Our modeling effort can provide answers and guidelines

that could eventually help companies by focusing on technologies that have a high chance of success.”

Semiconductor Modeling

Scientists use this process for

running quantum mechanical calculations of the current-voltage characteristics of

a potential transistor profile.

(Cliff Williams)
SC2002 High Performance Networking and Computing

A special section of

 Gridpoints Magazine, Fall 2002

A look at NASA exhibits,

 events, and speakers at SC2002
SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

Welcome, SC2002 participants.

I’m pleased to welcome you to a conference that represents everything NASA is all

about: pioneering the future, pushing the envelope, and doing what has never been

done before.

The city of Baltimore will provide a wonderful setting for productive professional

interchange about the latest developments in information architectures, scalable computing, data analysis, applications, and collaborative technologies.

For our part, NASA will demonstrate at SC2002 how we are utilizing advanced

supercomputing technologies to improve aviation safety and efficiency, probe more

deeply into the mysteries of the universe, model terrain and pinpoint possible spacecraft landing sites on Mars, and work to better understand the dynamics of Earth’s climatic system. 

We’re also delighted to showcase how the adept use of computational science was a key factor in the development of

the NASA-(Dr. Michael) DeBakey Ventricular Assist Device, NASA’s Commercial Invention of the Year. NASA

computational techniques that normally model rocket fuel flow helped to perfect this miniature heart assist pump,

which promises to improve the lives of thousands of heart patients.

When we think about touching lives, clearly the kind of work all of us are engaged in has the potential to help

inspire the next generation of explorers, which not so coincidentally is one of NASA’s core mission goals. Given the

fact that fewer young people are choosing to enter technical fields, I’m very pleased that this conference offers excellent programs that will help teachers apply the exciting work of computational research into classroom activities. By

assisting teachers in their efforts to connect students to the technology frontiers you explore on a daily basis, I

believe that SC2002 will help in immeasurable ways to build a better America.

—Sean O’Keefe

Bill Ingalls/NASA

Sean O’Keefe

NASA Administrator

NASA is showcasing many of its exciting scientific research

projects at SC2002. The following are descriptions of demonstrations, paper presentations, videos, and panel discussions

listed by participating NASA centers and collaborators.

Ames Research Center

Mountain View, California

Ames Research Center (ARC) and its personnel work to develop technologies that enable the Information Age, expand the

frontiers of knowledge for aeronautics and space, improve

America’s competitive position, and inspire future generations.

Ames specializes in research geared toward creating new knowledge and new technologies that span the spectrum of NASA

interests.

Atomistic Simulations on USA and Japan Grid 

Researchers will demonstrate results from multiscale quantum-mechanical and/or classical atomistic simulations on a

grid of geographically distributed PC clusters, to study environmental effects of water molecules on fractures in silicon.

The multiscale simulation approach seamlessly combines

atomistic simulations based on the molecular dynamics

(MD) method and quantum mechanical (QM) calculations

based on the density functional theory. The multiscale

MD/QM simulation code has been grid-enabled using a

modular additive hybridization scheme; multiple QM clustering; and computation/communication overlapping. A

preliminary code run has achieved a parallel efficiency of 94

percent on 25 PCs distributed over three PC-clusters in the

United States and Japan. A video trip through a silicon

crack tip shows water-silicon reactions.

Cart3D: A Package For Automated Grid 

Generation and Aerodynamic Database Creation

Cart3D, NASA’s Software of the Year for 2002, is a software

package for fully automated geometry processing and computational fluid dynamics (CFD) simulation. The software

enables users with access to networked computing clusters

or supercomputers to synthetically generate the types of

aerodynamic databases typically obtained only through

extensive wind tunnel testing. SC2002 attendees can select

and manipulate pre-built vehicle geometries, and watch

while meshes suitable for CFD analysis are automatically

generated on demand. An entire suite of CFD runs for the

chosen configuration can then be submitted for processing

on NASA’s Information Power Grid. These simulation results constitute a synthetically generated aerodynamic database that gives analysts information needed for design.

Animations, images, and results from previously computed

simulation suites will also be available for playback, discussion, and demonstration. Additional information is available on the web at: www.nas.nasa.gov/~aftosmis/cart3d

2A NASA Research Centers: Ames • Glenn • Goddard • Jet Propulsion Laboratory • Langley
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www.nas.nasa.gov/SC2002 3A

The Hyperwall: A Multiple Flat-Panel Display

Wall For High-Dimensional Visualization

The NASA Ames “hyperwall” consists of a seven-by-seven

matrix of flat panel displays driven by 49 rack-mounted

dual-CPU nodes, each with its own high-end graphics card.

The hyperwall emphasizes displaying multiple independent but related images, and provides useful means for composing and controlling these image sets. In place of elaborate software or hardware crossbar switches, researchers rely

on the human visual system for integration, synthesis, and

pattern discrimination in complex and high-dimensional

data spaces.

The tabular layout of the hyperwall supports many existing

“multiview” visualization paradigms, including spreadsheetstyle approaches, multidimensional/multivariate techniques,

and brushing/linking.

DeBakey Ventricular Assist Device

NASA’s Invention of the Year – 2001

The use of computational fluid dynamics (CFD) technology has led to several major design improvements on the

NASA-DeBakey Ventricular Assist Device (VAD). NASA

Ames scientists Cetin Kiris and Dochan Kwak employed

NASA Shuttle main engine technology and CFD modeling

capabilities, coupled with the NASA Advanced Supercomputing (NAS) Division’s high-performance computing

technology, to make several design modifications that vastly

improved this miniature heart pump’s performance. To date,

it has been successfully implanted in 170 individuals in

Europe, Asia, and the United States. In April 2002, the

NASA-DeBakey VAD was named NASA’s Commercial

Invention of the Year for 2001.

Information Power Grid

Grids are an emerging technology that provide seamless

and uniform access to geographically dispersed computational, data storage, networking, instruments, and software

resources needed for solving large-scale scientific and engineering problems.

NASA’s Information Power Grid (IPG) project is developing and deploying such a computing and data grid, and its

goal is to use NASA’s remotely located computing and data

system resources to build distributed systems that can

address problems too large or complex for a single site.

IPG Job Manager

The IPG Job Manager allows IPG users to reliably execute

applications on remote computer systems specified by users.

The Job Manager provides the following functionalities:

moving files between file servers before an application

begins executing (pre-staging) – a typical use of this is to

move input data files to a computer system where an application will be run; moving files between file servers after an

application completes executing (post-staging) – a typical

use of this is to move output data files from a computer system where an application was run to a repository of project

data; and reliably executes an application. The IPG Job

Manager handles a variety of software and hardware failures; monitors the progress of the execution of a job; and

maintains a history of the execution of an application that

is available to users after the application finishes executing. 

IPG Resource Broker

A computational grid such as the IPG consists of a large

number and variety of computer systems. Users may not be

familiar with all the available resources and their current

state, so it can be difficult for users to select where to run an

application. The purpose of the IPG Resource Broker is to

provide suggestions for which computer system should be

used to execute an application. Users provide: the number

of CPUs and the amount of memory required; the executables to use for different operating systems; job execution

parameters such as command line arguments, environment

variables, scheduling queue, project, etc.; and the files to

pre- and post-stage (optionally qualified by host name).

From this input, the Resource Broker suggests where to run

an application in the form of Job Manager Jobs. Each Job

Manager Job contains all the information needed to execute

the application, including the suggested computer system.

The broker suggests systems by considering: the candidate

hosts and operating systems (if any) that the user specified;

the number of CPUs and amount of memory specified

by the user; and the current status and load on the systems;

the predicted completion times of the application on different systems.

Performance Prediction

Performance grids allow users to access a large number and

variety of computer systems. This leads to the question of

where users should run their applications. The NASA IPG

team provides predictions of application execution and

completion times to assist users in making this decision.

Using CFD analysis, NAS researchers found that major design

modifications to the NASA-DeBakey Ventricular Assist Device

were necessary. The result of these changes: overall efficiency of

the device was increased by 22 percent.

(MicroMed Technology)
SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

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SPECIAL EDITION : NASA at SuperComputing 2002

4A NASA Research Centers: Ames • Glenn • Goddard • Jet Propulsion Laboratory • Langley

The team predicts execution times of applications on spaceshared parallel computers using instance-based learning

techniques. This tool maintains a database of experiences,

called an experience base. The prediction for a query is

formed using the outcomes of experiences in the database

that are similar to the query. Experiences are job descriptions consisting of characteristics such as user name, number of CPUs, and executable name.

Access to most large computer systems is scheduled using

queues and a scheduling algorithm that decides when to

start jobs. Completion times of applications are predicted

by simulating the operation of scheduling algorithms, given

the jobs currently in the queues, and predictions of how

long those jobs will execute.

Multi-level Parallelization and

Optimization Environment

NASA researchers show three prototype tools working

together to transform serial codes into multi-level parallel

codes. Depicting a typical parallelization scenario, it starts

with a serial cloud-modeling code and uses CAPO, a tool

for assisting in parallelization, to produce an OpenMP version of the code. User inputs during parallelization are

incorrect, and the resulting program does not produce the

same answers as the original serial code. An automatic

debugging tool is then applied, which uses information

from CAPO to isolate the cause of the differences. Once the

problem is fixed, the Paraver tool is used to demonstrate

how to analyze performance of the parallel program. The

scenario concludes with a visualization of the data computed by the program. Visit: www.nas.nasa.gov/Tools

Programmable Visualization of EOS DAAC Data

This demonstration shows programmable visualization

components for the Earth Observing System (EOS)

Distributed Active Archive Center (DAAC) data. The components include a central data model (“Field Model”), a

metadata model (“Active Metadata”), and modules capable

of interfacing to various data formats, including HDF-EOS

files. The components can easily be assembled within a

framework based on the Python programming language.

Python includes numerous modules for web data access,

offering the potential for automated access of DAAC data.

The interactive visualization modules, coupled with the programmability of Python, enables users to complement the

insights gained by interactive techniques with the efficiencies of programmable analysis. More information is available

at: http://field-model.sourceforge.net

*-Ray: Large-Scale Data Rendering Software

Pronounced star-ray, *-Ray is a multi-threaded software

package developed by researchers at the University of Utah

and is capable of rendering large-scale scientific data sets at

interactive rates. Star-ray rendering is entirely software based,

taking advantage of the ccNUMA architecture of the SGI

Origin series. Star-ray is able to achieve near linear scaling in

performance, based on the number of pixels rendered and

number of processors used. Ray tracing also provides an

ideal framework for rendering large-scale data, because the

rendering time scales sublinearly with scene complexity. The

primary limitation on data size is main memory. With

NASA’s SGI Origin 3000, researchers will demonstrate the

ability to interactively render datasets ranging from gigabytes to hundreds of gigabytes.

Simulation-Based Medical Planning 

for Vascular Surgery

The current paradigm for cardiovascular surgery planning

relies exclusively on diagnostic imaging data to define the

present state of the patient, empirical data to evaluate the

The visualization of the U.S. Gulf Coast region is based on

Level One-B swath data acquired September 29, 2000, by the

Moderate Resolution Imaging Spectroradiometer (MODIS)

instrument aboard the Terra satellite. Terra is the flagship in

NASA’s Earth Observing System. The datasets are made available by the Distributed Active Archive Center based at

Goddard Space Flight Center, Greenbelt, Maryland.

IPG’s performance prediction architecture enables users to predict how an application will run on the grid, and how long

the task will take. (NASA)
SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

www.nas.nasa.gov/SC2002 5A

effectiveness of prior treatments for similar patients, and the

judgment of the surgeon to decide on a preferred treatment.

Researchers at Stanford University and NASA are working

to create a simulation-based medical planning system for

cardiovascular disease that uses computational methods to

evaluate alternative surgical options prior to treatment,

using patient-specific models of the vascular system. The

blood flow simulations enable a surgeon to see the flow features resulting from a proposed operation and to determine

if they pose potential adverse effects such as increased risk

of atherosclerosis and blood clot formation. Further details

on this research can be found at:

www.med.stanford.edu/school/vascular

John H. Glenn Research Center

Cleveland, Ohio

As a diverse team working in partnership with government,

industry, and academia to increase national wealth, safety, and

security, protect the environment, and explore the universe, the

John H. Glenn Research Center develops and transfers critical

technologies that address national priorities through research,

technology development, and systems development for safe and

reliable aeronautics, aerospace, and space applications.

Coupling Engineering Applications on

NASA’s IPG: A CORBA-Based Approach

Researchers will demonstrate the results of an engineering

parameter study that pairs NASA Langley Research Center’s

VULCAN (Viscous Upwind aLgorithm for Complex flow

ANalysis) code with CORBA-based services and applications developed at Glenn. The demo will feature this

CORBA-based environment transferring data and executing the VULCAN code on IPG resources.

A secondary benefit of this research is the ability to couple

CORBA-IPG middleware to Glenn’s Numerical Propulsion

System Simulation (NPSS) CORBA Component Developer’s Kit (CCDK). This capability enables VULCAN to

function as a service to both NPSS and stand-alone IPG

client applications.

Interactive Large-Screen Visualizations

NASA Glenn researchers will showcase recent activities in

adapting interactive large-screen visualizations of scientific

and engineering research. Demonstrations will include: examples of research in space communications and distributed supercomputing solutions using advanced propulsion

models; fuel cell design and research; biotechnology; and

microgravity science, all supported by NASA’s Computing,

Information, and Communication Technologies Program.

Goddard Space Flight Center

Greenbelt, Maryland

Goddard Space Flight Center (GSFC) seeks to expand knowledge of the Earth and its environment, the solar system, and the

universe through observations from space. High-performance

computing interprets observational data both by processing it

into understandable forms and by simulating observed and

unobserved phenomena.

Modeling the Earth’s Atmosphere at 

the Data Assimilation Office (DAO)

The NASA finite-volume General Circulation Model

(fvGCM) is the DAO’s next-generation modeling system. It

is based on a unique, state-of-the-art finite-volume dynamical core and community-built physical parameterizations

and land surface model. A highly efficient application of

the MPI-2 remote memory access message-passing paradigm has been implemented within the NASA fvGCM.

This implementation improves the throughput by as much

as 39 percent, compared to the MPI-1 non-blocking communication paradigm. The NASA fvGCM produces highresolution global forecasts capable of resolving atmospheric

Flow simulations are performed for each preoperative plan

and quantities of interest (such as wall shear stress, particle residence time) are calculated. (Stanford University)

Glenn Research Center’s interactive visualization theater will

feature demonstrations of interactive computational research.
SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

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6A NASA Research Centers: Ames • Glenn • Goddard • Jet Propulsion Laboratory • Langley

motions from meso- to planetary-scale with a high throughput on multiple-processor, distributed memory computing

platforms. For more information about the Data Assimilation Office, visit: http://dao.gsfc.nasa.gov

Ultra-High Resolution Astronomy: Phasing of

Arrays of Formation Flying Spacecraft

Goddard Space Flight Center researchers are investigating

arrays of multiple spacecraft, phased together and flying in

formation. Systems of this type would enable ultra-high resolution science, including resolution of the stellar disks of

nearby stars, as well as the planets around these stars.

Systems with baselines (largest distance between spacecraft)

of up to 500 meters are currently under study. GSFC scientists are researching and developing tools for systems modeling to determine the system design drivers, set science

goals, and ascertain system performance. This is inherently

a large-scale computing problem, both in terms of modeling and in terms of the algorithms to actively control the

system. It is likely that such systems would also require autonomous on-board computing.

http://code935.gsfc.nasa.gov/cube%20Folder/OSCAR/

index.html

IBEAM: Interoperability-Based Environment 

for Adaptive Meshes

IBEAM’s technology goals are to develop a community

framework for scalable astrophysical modeling simulations

that promotes code interoperability. Design constraints require that the framework enable adaptive

mesh refinement techniques; support interoperability of astrophysical modeling

codes; be componentoriented; promote

Object Oriented Design (OOD) concepts

to enhance code reusability; and be

coded in F90+MPI to

promote performance and portability.

The testbed problem

is modeling gammaAdaptive mesh refinement simulation

of a relativistic shock wave interacting with a dense gas cloud. (NASA)

Chombo Framework for BlockStructured AMR Applications

Researchers are developing a software framework for implementing block-structured adaptive mesh refinement (AMR) algorithms to solve targeted problems in star formation, microgravity

research, and space physics. The Chombo framework is a basis

for this effort. Chombo is a set of object-oriented C++ libraries

for implementing AMR applications that use MPI to support

distributed memory computing.

Algorithm components in development include finite-volume

techniques for representing irregular geometries and multi-fluid

interfaces, along with techniques for particles in incompressible

fluids.

The ChomboVis tool provides an interpretive environment for

manipulating and visualizing AMR data in the Chombo framework. ChomboVis is built using the Python scripting language

and the Visualization Tool Kit, enhancing portability to a variety

of architectures. Both Chombo and ChomboVis use HDF5

(Hierarchal Data Format) for input and output. For more details,

visit: http://seesar.lbl.gov/ANAG/NASA

Adaptive mesh refinement (AMR) simulation of two

co-rotating vortex rings (indicated by the yellow rings).

Green lines show streamlines of the flow, while white

boxes show where finer resolution is used to better

capture details of the flow. Coherent vortices like

those shown here are the principal means for mixing

fluids in microgravity environments.

Snapshot of a three-dimensional animation of a hurricane

developing in the Gulf of Mexico created from a 0.5- x 0.625-

degree, 32-level run of the NASA fvGCM. (NASA)
SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

www.nas.nasa.gov/SC2002 7A

ray burst fireballs and afterglows. Project participants

include NASA GSFC, University of Illinois, University of

Chicago, SUNY Stony Brook, and the Universities Space

Research Association. Details of this research can be found

at: www.ibeam.org

The Parallel Virtual File System Version 2

PVFS is a parallel file system for Linux clusters. It harnesses commodity storage and network technology to provide

concurrent access to data that is distributed across a (possibly large) collection of servers. PVFS serves as both a testbed for parallel I/O research and as a freely available, production-level parallel file system for use in the cluster community. Development and support is carried out with collaboration between Clemson University, GSFC, and

Argonne National Laboratory. For more information, visiit: www.parl.clemson.edu/pvfs

Coven Software Development Framework

Coven is a framework for component-based collaborative

software development. Its goals are to provide extensibility

and usability, and to produce high-performance code. Extensibility is achieved through pluggable modules representing individual algorithms. Modules are connected to

form a dataflow graph, created with assistance from a

graphical user interface. Environments using this framework can build additional graphical components, which

tailor to the specific needs of that problem domain (such as

dataset visualizers, performance analyzers, debuggers, database query tools). Coven has been used to build environments for satellite remote sensing, n-body problems,

molecular dynamics problems, and CFD fluid flow and

heat transfer problems. For more information, visit:

www.parl.clemson.edu/Coven

Beowulf/Mini-Grid System Software

A mini-grid is a campus-wide version of a computational

grid, featuring a private switched network interconnecting

grid resources where performance is not limited by Internet

connections. All resources on the Clemson grid are

Beowulf/Linux clusters. The Scyld Beowulf Linux OS has

been modified to support the mini-grid with the addition

of Balloc, the Beowulf node Allocator, which allows large

jobs to transparently “borrow” nodes from adjoining clusters. Traffic for jobs on borrowed nodes runs through a private network, which means performance can be predicted.

A single job can use all processors in the grid. The software

project is funded by Goddard. Details are on the web at:

www.parl.clemson.edu/minigrid

Cost-Effective Advanced Computing Technologies

Researchers at NASA are working on the use of reconfigurable logic to provide ultra-high-performance computing

in both space-based and ground-based systems. Techniques

include implementing applications directly in reconfigurable hardware, implementing specialized assist logic in

reconfigurable hardware, and using reconfigurable logic

blocks inside of an otherwise standard microprocessor.

Information on this NASA/Clemson University collaboration is available at: www.parl.clemson.edu

Sci-Interactives: Science Outreach from Truth-N-Beauty Software and NASA 

The advent of broadband Internet access together with high-speed processors for commercial PCs, has opened significant

new avenues for communicating science to the general public. Truth-N-Beauty Software, a science ‘e’- outreach and education company, has partnered with

NASA’s Computational Technologies

(CT) Project to develop digital tools for

teaching the public about the latest

results of NASA Earth and space science research.

Sci-Interactives are web-based applications that let the science speak for itself.

These tools give people access to the

real equations and data behind NASA

science with intuitive, graphically

sophisticated tools and games. 

Current projects include story development and Sci-Interactives for Discover

Magazine’s website. Tools explore the

collapse of rotating interstellar clouds

and the creation of aurora in the Earth’s

magnetosphere. Details of NASA’s latest Earth and space science research can

be found at www.truth-n-beauty.com Simulation screen for a collapse and rotation Sci-Interactive.
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8A NASA Research Centers: Ames • Glenn • Goddard • Jet Propulsion Laboratory • Langley

Jet Propulsion Laboratory (JPL)

Pasadena, California

The Jet Propulsion Laboratory’s mission is to enable the nation

to explore space for the benefit of humanity. The lab’s mission

is: to explore our own and neighboring planetary systems; to

search for life outside the Earth’s confine; to further our understanding of the origins and evolution of the Universe and the

laws that govern it; to make critical measurements to understand our home planet and help protect its environment; to

apply JPL’s unique skills to solve problems of national security

and national significance; and to inspire the next generation

of explorers.

Shuttle Radar Topography Mission(SRTM):

Science Processing on a Supercomputer 

NASA researchers have developed software to process raw

data acquired by the Shuttle Radar Topography Mission

(SRTM), as part of an effort to generate a global digital elevation model database. The large amount of data required

to form the mosaic was processed on Alhena, the SGI

Origin 2000 supercomputer at JPL, using 32 processors in

parallel. Digital elevation models are used for scientific

applications in geophysics, geology and hydrology, as well as

practical applications, such as highly detailed 3-D maps for

civilian and military user communities. Information about

this project, co-sponsored by NASA and the National

Imagery and Mapping Agency, can be viewed at:

http://photojournal.jpl.nasa.gov.

Dusty Rings: Signposts of Recent Planet Formation

Every planetary system forms in a thin disk of gas and dust

around a young star. Web-based animations show the evolution of bright rings of dust in a disk where planets form.

Planets grow from collisions and mergers of smaller bodies,

called planetesimals, embedded in a disk of gas and dust in

orbit around the star. Each visualization starts with the same

initial conditions,

roughly 10 billion

billion planetesimals

1-100 meters across,

embedded in a disk

that extends from

the orbit of Neptune

to the outer edge of

the Kuiper belt. The

colors represent the

intensity of the dust

grains from low (dull

reds) to high (blue/

white). Individual aniEstimating the Circulation and Climate of the Ocean:

The Circulation Pathway of Subtropical-Tropical Exchange

JPL researchers are investigating mechanisms of subtropical-tropical water mass exchange in the Pacific Ocean, using an

animation of a simulated passive tracer and its adjoint tracer. The forward passive tracer and adjoint passive tracer can be

identified as describing where the tracer-tagged water mass goes to and where it comes from, respectively. The exchange

plays a central role in the decadal change of El Niño, and is examined by explicitly tracing the water of the eastern

Equatorial Pacific. In contrast to previous theoretical expectations, the exchange is found to be an “open-circuit,” in which

the origin is distinct from the destination. Temporal variability in ocean circulation is found to be fundamental in determining the pathway of the water mass, “short-circuiting” the otherwise circuitous route. Details of this research are available on the Internet at: http://ecco.jpl.nasa.gov/external 

The image at left illustrates the average distribution of the water mass (depth integrated content) that reaches the eastern

Equatorial Pacific five years prior to its terminal instant. The right panel shows the same data, except when the time-mean circulation is assumed. The difference between the two illustrates the significance of the circulation’s temporal variability.
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SPECIAL EDITION : NASA at SuperComputing 2002

www.nas.nasa.gov/SC2002 9A

mations depict a passage of time of 2 billion years. In the

“weaker bodies” animation, the bodies fragment easier than

the stronger bodies, and thus produce more dust and

brighter rings when they collide. The figure shown on page

8A depicts nine snapshots of the disk in one calculation.

The bright point at the center is the star. The inner edge of

the disk is at the orbit of Neptune. The outer edge is at the

outer edge of the Kuiper Belt in our solar system. The top

row of frames corresponds to a time, t = 0, 3, and 10 million years (Myrs); the middle row is t = 30, 100 and 300

Myrs; the bottom row is t = 600 Myrs, 1 billion years

(Gyrs) and 2 Gyrs. Further details can be found at:

http://cfa-www.harvard.edu/~kenyon/pf/sp/index.html

Using Hollywood for Science: Animation of a

Proposed NASA Mission using Maya 4.0

The Satellite Test of the Equivalence Principle (STEP) was

a proposed NASA small explorer mission which would test

the principle that all masses, regardless of size or composition, will experience the same acceleration in a given

3-D Adaptive Grid: MHD Simulations of the 

Global Heliosphere

The visualizations show the interaction of the interstellar

medium and the solar wind. The solar system is moving

through the local interstellar medium. This complex system involves three different discontinuities: the termination shock, the heliopause, and the bow shock. In

the visualization, the interstellar wind flows from the left

and impinges on the solar wind. The sun is located at

the center.

The code uses BATS-R-US, developed at the University

of Michigan. It is a 3-D magnetohydrodynamics adaptive grid code. It uses an adaptive Cartesian grid made of

a rectangular block of cells. The solar wind and the interstellar wind are modeled, including both magnetic fields

and the plasma in a self-consistent way. The simulation

used 4.5 million cells and 11 levels of refinement. The

minimum size of the cells is 0.5 Astronomical Units

(AU), and the maximum size is 36 AU.

Above: This graph shows the contours of the density. In this

figure the interstellar medium flows from the left, with the

Sun at the center of the figure. Black denotes different

refined areas of the mesh. Also indicated: the location of the

Bow shock (BS), Heliopause (HP), and the Termination

shock (TS).

Left: Contours of the magnetic field are shown with blue

representing the minimum intensity of the magnetic field

and red depicting maximum intensity. The white lines indicate magnetic field lines. At the center, the solar magnetic

field (the Parker spiral), can be seen with the Sun at the center. The interstellar medium flows from the left.

Using Hollywood for Science: Animation of a proposed NASA

Continued on page 10A mission using Alias Wavefront’s Maya 4.0 software. 
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10A NASA Research Centers: Ames • Glenn • Goddard • Jet Propulsion Laboratory • Langley

gravitational field. This principle is a fundamental assumption in Einstein’s General Theory of Relativity. The movie

contains a simulation of the relative motion of two test

masses in the experiment in orbit about the Earth when the

Equivalence Principle is violated, followed by an animation

of the assembly of the various parts of the experiment. The

modeling, animation, and rendering of the movie were performed using Alias Wavefront’s Maya Complete software

package, and took approximately three hours on eight

processors of JPL’s SGI Origin 2000 supercomputer.

Further details on this research project can be found at:

http://sc.jpl.nasa.gov/success_stories/slides/slide44.html

Common Component Architecture: A Demonstration of the CCA Forum Technologies

The Common Component Architecture (CCA) Forum is a

group of researchers from national labs and academic institutions committed to defining a standard component architecture for high-performance computing. 

In the last year, researchers began testing the Common

Component Architecture (CCA), designed for large, collaborative, high-performance computing applications. The

testing is designed specifically for its suitability to NASA

applications, such as climate simulations. Further details

can be found at: http://pat.jpl.nasa.gov/public/projects

NASA Participation: Technical Papers, Tutorials,

and Panel Discussions

Several NASA scientists (both contractor and civil service

personnel) are participating on SC2002 committees, panels,

tutorials, and other conference events. 

Paper Presentation

Collaborative Simulation Grid: Multiscale QuantumMechanical/Classical Atomistic Simulations on

Distributed PC Clusters in the USA and Japan

Hideaki Kikuchi (Louisiana State University), Rajiv K. Kalia,

Aiichiro Nakano, Priya Vashista (University of Southern

California), Hiroshi Iyetomi (Niigata University), Shuji

Ogata, Takahisa Kouno (Yamaguchi University), Fuyuki

Shimojo (Hiroshima University), Kenji Tsuruta (Okayama

University), and Subhash Saini (NASA Ames).

A multidisciplinary, collaborative simulation has been performed on a grid of geographically distributed PC clusters.

The multiscale simulation approach seamlessly combines

atomistic simulation based on the molecular dynamics (MD)

method and quantum mechanical (QM) calculation based

on the density functional theory, so that accurate but less

scalable computations are performed only where they are

needed. The multiscale MD/QM simulation code has been

grid-enabled using a modular, additive hybridization

scheme, multiple QM clustering, and computation-communication overlapping. The ‘gridified’ MD-QM simulaLangley Research Center

Hampton, Virginia

In alliance with industry, other agencies, academia, and the

atmospheric research community, Langley Research Center

(LaRC) undertakes innovative, high-payoff aerospace and scientific activities beyond the risk limit or capability of commercial enterprises and delivers validated

technology, scientific knowledge, and

understanding of the Earth’s atmosphere.

The center’s success is measured by the

extent to which its research results

improve the quality of life.

Biological Metaphors for

Feature Extraction 

in Large Datasets 

This demonstration describes a new

visualization metaphor for quickly

extracting and visualizing features in

large datasets. The data swarming

metaphor is a biologically based collection of agents that move through space

interacting with local data. Although

each agent follows a few simple rules,

the collection of agents can find complex patterns in the dataset. In particular, this demonstration portrays a general agent architecture

that can be used to create unique visualization tools as well

as support common visualization techniques. The data

swarming paradigm is applied to computational fluid

dynamics visualization (below), and is implemented as a

virtual environment that runs on immersive displays. 

Continued from page 9A
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www.nas.nasa.gov/SC2002 11A

tion code has been used to study environmental effects of

water molecules on fractures in silicon. A preliminary run

of the code has achieved parallel efficiency of 94 percent

on 25 PCs distributed over three PC clusters in the United

States and Japan. A larger test involving 154 processors on

five distributed PC clusters is in progress.

Tutorial S11

November 18, 8:30 a.m. – 12:00 p.m.

Requirements Analysis for 

Scientific Applications

Scientific applications are increasingly complex and collaborative. In order to coordinate, plan, and validate scientific software, it is useful to gather requirements before

development begins. In this tutorial, developers of the

Earth System Modeling Framework explore how requirements analysis can improve development efficiency and

reduce misunderstandings and defects. They will look at

how requirements collection can be implemented for distributed collaborations; review sample requirements documents and templates; and discuss how the requirements

process impacts other aspects of software development,

such as design and verification. Throughout this process

they will emphasize sensitivity to the unique aspects of the

research-oriented HPC computing environment. More

information about the Earth System Modeling Framework

is at: http://www.esmf.ucar.edu

Tutorial S3

November 16, 8:30 a.m. – 5:00 p.m.

Component Software for High-Performance

Computing: Using the Common 

Component Architecture

Rob Armstrong, Jaideep Ray (Sandia National Laboratories),

David Bernholdt, Wael Elwasif, Jim Kohl (Oak Ridge

National Laboratory), Lori Freitag, Lois McInnes, Boyana

Norris (Argonne National Laboratory), Dan Katz (NASA–

Jet Propulsion Laboratory), Gary Kumfert (Lawrence

Livermore National Laboratory), Craig Rasmussen (Los

Alamos National Laboratory)

This tutorial will introduce the Common Component

Architecture (CCA) at both conceptual and practical levels.

Components are software objects that encapsulate useful

functionality and interact with other components only

through well-defined interfaces. Component-based approaches to software development, including the CCA,

provide a means to manage the complexity of large-scale

software applications and facilitate the reuse and interoperability of code. 

The component concept is widely used in the commercial

and business world (e.g., CORBA, COM, and Enterprise

JavaBeans) and is popular in visualization as well (e.g., Data

Explorer), but none of these environments is well suited to

use in high-performance computing environments. The

CCA was designed specifically with the needs of highperformance scientific computing in mind, including the

existence of large bodies of existing code that cannot easily

be rewritten. The tutorial will cover the concepts of components and the CCA in particular; the tools provided by

the CCA environment – including the Babel system for

language interoperability; the creation of CCA-compatible

components; and their use in scientific applications. A

combination of traditional presentation, and live demonstration will be used during the tutorial. After the session,

participants will be able to download the tools and software

to reproduce the live examples in their local environment.

For more information, see:

www.cca-forum.org/tutorials/sc02.html.

Panels

November 22, 8:30 – 10:00 a.m.

Are Designer Supercomputers an 

Endangered Species?

Moderator: Aruna Ramanan (IBM)

Panelists: Thomas Sterling (Center for Advanced Computing

Research, California Institute of Technology and Jet

Propulsion Laboratory); Gita Alaghband (University of

Colorado, Denver); Jamshed Mirza (IBM Corporation);

Tadaski Watanabe (NEC Corporation); and Candace

Culhane (NSA) 

At the dawn of the high-performance computing era, all

supercomputers were “designer machines.” Every aspect of

these machines was designed specifically to lend the highest performance level achievable, using the state of the art

technology available at the time. While the attention to

design still remained, the focus changed from exploiting

fine-grained parallelism using vector processors to coarsegrained parallelism using “massive parallel processors” or

MPPs. The emergence of MPPs changed the focus from

the processor to the interprocessor communication network. The systems were still designer systems. Then came

the shift to specially designed clusters. 

More recently, “Components Off the Shelf” or COTS clusters, have emerged in a big way. Strides in the cyber communication infrastructure, together with the narrowing gap

between the computing world and the networking world

has opened up the possibility of grid computing and peerto-peer computing. The SETI@home project has demonstrated the power of utilizing distributed resources. These

developments have led many to believe less and less in

designer supercomputers and more and more in constructing high-performance systems using widely available components used in mainstream computing. But the emergence of the Japanese Earth Simulator as the top performer

has stirred up the high-performance computing community. This panel will explore the strategies needed to transform terabytes of information into insights, and examine

the challenges that need to be addressed by the two different approaches to supercomputing. 
Immersive 

Workbench

1

2

3

4

Information

hyperwall

1

2

3

4

8

10

14

11

12

5

6

7

Immersive Workbench

• Biological Metaphors for Feature Extraction in Large 

 Datasets

• IBEAM: Interoperability-Based Environment for 

 Adaptive Meshes

• Interactive Large Screen Visualizations

• Coupling Engineering Applications on the Information 

 Power Grid: A CORBA-Based Approach

• 128-Node Information Power Grid Cluster

• Simulation-Based Medical Planning for Vascular Surgery

• Common Component Architecture (CCA): A Demonstration

 of the CCA Forum Technologies

• Dusty Rings: Signposts of Recent Planet Formation

• Estimating the Circulation and Climate of the Ocean: The

 Circulation Pathway of Subtropical-Tropical Exchange

• Shuttle Radar Topography Mission (SRTM): Science

 Processing on a Supercomputer

• 3D Adaptive Grid: MHD Simulations of the Global 

 Heliosphere

• Using Hollywood for Science: Animation of a Proposed

 NASA Mission Using Maya 4.0

• AeroDB: Automated CFD Parameter Studies on

 Distributed Parallel Computers

• Information Power Grid (IPG)

• IPG Job Manager

• IPG Resource Broker

• Performance Prediction

• Tool Agent Framework-Java (TAF-J) - Connecting 

 Aerospace Analysis Tools with the Information Power Grid

• Multi-Level Parallelization and Optimization Environment

• Atomistic Simulations on USA and Japan Grid 

• Cart3D: A Package for Automated Grid Generation and

 Aerodynamic Database Creation

• Beowulf/Mini-Grid System Software

• Coven Parallel Programming Framework

• The Parallel Virtual File System Version 2

• Reconfigurable Computing Technology

• Programmable Visualization of EOS DAAC Data

• Real-Time Ray Tracing with the University of Utah

• The hyperwall: A Multiple Flat-Panel Display Wall for

 High-Dimensional Visualization 

• Modeling the Earth's Atmosphere at the Data

 Assimilation Office

• Sci-Interactives: Innovative Science Outreach from 

 Truth-N-Beauty Software and NASA CT

• Ultra-High-Resolution Astronomy: Phasing of Arrays of

 Formation Flying Spacecraft

• Chombo Framework for Block-Structured AMR Applications

• IBEAM: Interoperability-Based Environment for 

 Adaptive Meshes

5

6

7

8 & 9

10

11

14 Video and Poster Wall

• SC2002 Conference Opening Video

• Capability Computing at the NASA Ames Research Center: Solving the 

 Toughest Computational Problems

• Cart3D: 2002 NASA Software of the Year

• Computational Science at Goddard Space Flight Center

• Computing, Information, and Communications Technology Program (CICT)

• Computing, Networking, and Information Systems Project (CNIS)

• Consolidated Supercomputing Management Office (CoSMO)

• HiMAP: High-Fidelity Multidisciplinary Analysis Process

• Information Power Grid (IPG) Accomplishments - 2002

• MU-SPIN: Extending Computing Opportunities to Minority Institutions

• NASA-DeBakey Ventricular Assist Device (VAD) - 2001 NASA Commercial

 Invention of the Year

• NASA Research Highlights Video

• NASA/SGI Develops 1,024-Processor Coherent Shared-Memory Origin 3000

• Numerical Propulsion System Simulation (NPSS)

• Supercomputing at Goddard Space Flight Center 12

9

13

13

SC2002

SPECIAL EDITION : NASA at SuperComputing 2002

BOOTH MAP

12A NASA Research Centers: Ames • Glenn • Goddard • Jet Propulsion Laboratory • Langley
www.nas.nasa.gov/gridpoints Gridpoints 11

The Vision Behind the ‘hyperwall’

The flow field around an aircraft as it soars through the

skies. A dynamic model of cloud formation. A molecule undergoing bond-breaking in quantum mechanical fields. All of these complex simulations are typical

examples of how today’s supercomputers are generating more

data than ever before. And as the quantity of available data

increases, advances in computational science have improved

the quality of that data. Whereas computing the flow around

an aircraft at a given speed and altitude was once considered

a large and sophisticated process, today’s supercomputers can

readily compute the flow around a whole family of vehicle

designs, with a wide range of different speeds, altitudes,

flight profiles, and other variables. 

A team of NAS scientists has developed a new tool to help

researchers display, analyze, and study these high-dimensional datasets in meaningful ways – the hyperwall. Inspired by

the sight of endless panels of images pinned to researchers’

walls, desks, and corridors, the hyperwall is a seven-by-seven

cluster of flat panel screens, each driven by its own dualprocessor computer with high-end graphics card. Unlike

powerwalls or caves – large projection systems that have to

coordinate separate machines to tile images, the hyperwall

allows each computer to process and display its own data.

This essential difference

enables researchers to harness

that computer power and provides the flexibility to display

data, while allowing their own

human perceptual apparatus –

the eye-brain system, to perform

the functions it does best –

feature detection, pattern recognition, and sorting.

“The hyperwall provides a

problem-solving environment

where we can use different tools,

different viewpoints, even different graphics parameters, to

display the same data or relationships within a dataset,”

explains the system’s developer,

NAS Senior Scientist Chris Henze. Together with NAS scientists Timothy Sandstrom, Creon Levit, and David

Ellsworth, Henze received a grant from the Information

Sciences and Technology Directorate at NASA Ames in April

2002 to put the system together and demonstrate the basic

proof-of-principle. Today, the hyperwall’s power and versatility are already attracting attention from research teams both

within and outside the NASA Ames community.

The hyperwall team recently demonstrated that power by

showing a visiting group of researchers from NASA’s Goddard Space Flight Center how the hyperwall can be used to

display Goddard’s models of cloud data. “The anatomy of

clouds is incredibly complex,” explains Henze. “Goddard’s

cloud models involve a wide range of hydrometeor classes

(different forms of water and ice), which intermingle within a

cloud. If you try to show them in a single image, it just looks

a mess. On the hyperwall, we were able to show the researchers separate classes on different screens along one column of

the wall, with different time steps running from left to right,

so they could see the evolution of these different fields.”

Although the hyperwall can display a single image distributed across all of its screens, the team has focused on developing software to enhance

the system’s ability to display sets of related images.

Its strength, they believe, lies

in its ability to take one simulation and look at many

different quantities, crosssections, magnifications, and

time steps, while keeping the

whole image, or images, visible in subarrays, for example

on three-by-three screens in

the corner. “It’s like a visualization spreadsheet. The array

of displays is a giant spreadsheet with the user defining

which operations happen in

each cell, or row, or column,”

says Henze.

Why Seven-by-Seven? “And finally, what about the magical number seven? What

about the seven wonders of the world, the seven seas, the

seven deadly sins, the seven daughters of Atlas in the

Pleiades, the seven ages of man, the seven levels of hell, the

seven primary colors, the seven notes of the musical scale,

and the seven days of the week? What about the seven-point

rating scale, the seven categories for absolute judgment, the

seven objects in the span of attention, and the seven digits in

the span of immediate memory? For the present I propose to

withhold judgment. Perhaps there is something deep and

profound behind all these sevens, something just calling out

for us to discover it. But I suspect that it is only a pernicious,

Pythagorean coincidence.”

George Miller

The Magical Number Seven, Plus or Minus Two;

Some limits on our Capacity for Processing Information

NAS researchers have developed an innovative visualization system that

allows scientists to view complex datasets and multiple parameters.
12 Gridpoints

To perform these endless combinations of tasks, the hyperwall uses a standard Linux operating system on the master

node and on each CPU, or slave node. The master controls

each screen by broadcasting script commands to copies of the

programs running on each of the slave nodes. Using the

team’s ‘growler’ framework (see Gridpoints, Fall 2000, page

11), a system designed for distributed programming, the user

is able to determine the location of processes and images with

the master computer or the hyperwall serving as the graphical

user interface. In addition, with a 100-gigabyte disk on each of

the 49 slave nodes and even more on the master, the system

has approximately five terabytes of aggregate disk space and

more than 50 gigabytes of RAM.

As the project moves beyond the proof-of-concept stage,

members of the hyperwall team are developing new ideas

for mapping, manipulating, and managing data, including an enhancement that will allow different cooperating

simulations to communicate, share, and display their composite information. But the team is also sensitive to their

need to talk to researchers and to understand the application requirements.

“Visualization researchers are notorious for telling scientists

the best way to display their data, when all the scientists want

is a 2-D plot,” says Creon Levit. “Our approach is to understand their demands exactly, ask questions, and see how we

fit in. The hyperwall team has a wide range of experience and

expertise that not only covers graphics, programming, and

scientific visualization, but also includes research fields such

as biochemistry, nanotechnology, fluid dynamics, and quantum mechanics.”

This multidisciplined approach was instrumental in determining some of the human factors behind the seven-byseven array. With an eye to George Miller’s 1956 paper, The

Magical Number Seven, Plus or Minus Two: Some Limits on

our Capacity for Processing Information, as well as budget

and space constraints, the team discovered that, at a comfortable distance, the 49 screens fit naturally in the overlap

field of vision. “We were originally going for eight-by-eight,”

explains Levit. “Computer scientists naturally gravitate

toward powers of two, but at a natural distance, this sevenby-seven array of monitors has a resolution of just over 64

million pixels – that’s about the same resolution as your eye.

So, if you have perfect vision in a dark room, theoretically

you could almost tell the difference between single pixels.” 

Another human factor considered by the team is the issue of

a seamless display. Powerwalls typically use several projectors

to display a single image, and try to minimize the seams by

lining up pixels and balancing colors. However, such systems

are often difficult to calibrate and, although the borders are

less obvious than the one-inch or so bezel around the hyperThe NASA Ames hyperwall consists of 49 flat panel displays driven by an equal number of rack-mounted dual-CPU nodes. The

tabular layout of the hyperwall supports many existing “multiview” visualization models, including spreadsheet-style approaches,

multidimensional/multivariate techniques, and brushing/linking. (Art Joly)
www.nas.nasa.gov/gridpoints Gridpoints 13

wall’s screens, the team found that faint boundaries were

often more bothersome. “Compare the difference between a

poorly constructed picture window with seams and ripples,

versus a multi-paned window,” says Levit. “People don’t mistakenly think that the outside world is really broken up when

they look through a multi-paned window.”

Each screen is mounted on a custom-designed rack, and can

be adjusted individually or by column or row to accommodate different viewing requirements and distances. The rack’s

design also allows users to compensate for the monitors’

directional field of view, or make other viewing arrangements, such as gently curved display areas. And because the

entire system is based on commodity technology rather than

highly specialized and expensive projection equipment, the

hyperwall team is confident the system will be easy to scale

in the future and will decrease in cost.

In the meantime, the team continues to focus on providing

compelling problem-solving environments for various research teams and pursuing software development based on

individual application requirements. “We have somewhat of

a symbiotic relationship with scientists,” explains Sandstrom.

“They need our tools, and we need their data. Their very large

and complex datasets drive the capabilities of our software, so

we have this leapfrog approach. They challenge us with bigger and more complex data, and we respond with better techniques. The closer computer scientists can work with the research

scientists, the better results we can get for everyone.”

—Julie Jervis

The hyperwall emphasizes displaying multiple independent, but related, images, and providing useful means for composing and

controlling these image sets. In place of elaborate software or hardware crossbar switches, scientists rely on the human visual system

for integration, synthesis, and pattern discrimination in complex and high-dimensional data spaces. Recently, the hyperwall was

used to display Mars surface terrain images. Each row shows the same 48-degree swath along the equator from 180 degrees West to

180 degrees East. The rows show various data maps of that swath, and from top to bottom display: 1) the visible surface, 2) surface elevations, 3) geologic units, 4) thermal inertia (analogous to granularity), 5) basalt distribution, and 6) hematite distribution. This visual layout facilitates rapid intercomparison of features in different data maps. (Dataset courtesy MOLA Science Team,

D. H. Scott et al., M. Mellon et al., J. L. Bandfield et al., P. R. Christensen et al.; Glenn Deardorff, NASA Ames Research Center)
14 Gridpoints

New NAS Parallel Benchmarks

Release Addresses Grid Computing

One of the NAS Division’s widely recognized research

products is the NAS Parallel Benchmarks (NPB).

The division recently released a major new version of the benchmarks, which incorporates several important

aspects of computing not covered by the previous release (see

page 19). Included are benchmarks for new languages, disk

access (input/output, I/O), and grid computing.

First conceived in 1991, NPB is a collection of standard tasks

that are representative of classes of computational applications important to NASA and to its research and industry

partners. An important NPB goal was to provide a level playing field for the myriad of high-performance computer architectures and parallelization paradigms and tools available at

that time. Organizations like NASA needed to evaluate the

performance of such systems without giving undue advantage to any particular vendor or tool developer, and to provide sensible targets for all. Therefore, NPB was originally formulated as paper-and-pencil problems, with very few restrictions on how they ought to be implemented and executed. The

computing community embraced this concept, and submitted many results for evaluation by NAS.

In the mid-1990s, computer architectures began to converge

and standards for parallel computing emerged, so NAS researchers decided to develop an implementation of NPB that

could be executed on high-performance computers worldwide. This implementation, predominantly in Fortran and

using the first widely accepted parallelization standard,

Message Passing Interface (MPI), was released in 1996 under

the name NPB2. Several versions followed, and the final version of all eight benchmark problems, NPB2.3, was released

in 1997.

Since then, high-performance computer systems have grown

significantly in processor count and capabilities. Cache and

memory capacities have increased, clock rates have gone up,

compiler technology has improved, network bandwidths

have increased, and total numbers of processors have gone

up. Consequently, more challenging benchmark sizes have

become necessary to rate the performance of computer systems. At the same time, other important parallelization

methods have been standardized, warranting alternate source

code implementations. 

As parallel computing matured, practitioners also started to

pay attention to more practical issues, most notably how to

store and process the results of their computations; writing

and accessing computed solutions on disk proved a major

bottleneck, and ways to assess the efficiency of proposed

solutions to this I/O problem became necessary.

Recently, the new field of grid computing has gained popularity. As pioneering efforts are underway to make these grids

usable and efficient, NAS researchers have already recognized

the need for yardsticks to rate their performance.

To meet these needs, NAS researchers have developed new

versions of and extensions to NPB. These have been released

in three packages, NPB2.4, NPB3.0, GridNPB3.0, which

are available for worldwide distribution and can be downloaded from the NAS Software Repository: www.nas.nasa.gov/

Software. More details can be found in NAS technical reports,

available on the web at www.nas.nasa.gov/Research/Reports/

techreports.html, and efforts are underway to streamline the

process for submitting and viewing new results online. For

information on NPB, visit www.nas.nasa.gov/Software/NPB.

Editor’s Note: Michael Frumkin, Henry Jin, and Parkson

Wong also contributed to this article.

Figure 1: Schematic of Visualization Pipe, one of four grid

benchmark problems. Computation (in this case computational

fluid dynamics or CFD), post-processing (Smooth), and visualization (FFT) are carried out cyclically. (Van Der Wijngaart)

By Rob Van Der Wijngaart
www.nas.nasa.gov/gridpoints Gridpoints 15

NPB2.4: Larger problems, I/O benchmark

A relatively straightforward extension of the NPB MPI

implementation, NPB2.4-MPI provides class D, a new set

of problem sizes that involves approximately 20 times as

much computational work as NPB2.3’s class C. Dataset

sizes have simultaneously been increased by a factor of 16

to keep up with the larger cache memories. In addition, an

I/O benchmark program, previously called BTIO, is now

being released under the name NPBIO2.4-MPI.

This version is virtually the same as the BT benchmark program in NPB2.4-MPI, but also writes the computed solution to disk at set intervals, using any of four methods to

expedite the process. Users can select the method whose

performance they want to rate, one of which is based on

high-level, efficient I/O operations defined in the most

recent version of the MPI standard. NPB2.4-MPI and

NPBIO2.4-MPI are released together in a package called

NPB2.4.

NPB3.0: New parallelizations, new language

While MPI was the first widely accepted standard for parallelizing scientific programs, computational scientists have

since proposed several other paradigms, which has led to

some new NPB implementations. Prototypes of these

codes were initially included in a limited distribution, then

called Programming Baseline for the NAS Parallel

Benchmarks (PBN). For more information on this, see

NAS News, Summer 1999, on the web at:

www.nas.nasa.gov/About/Gridpoints/PDF/nasnews_V04_

N03_1999.pdf.

Now that these new parallelization standards have reached

a significant level of acceptance and maturity, NAS

researchers have decided to incorporate them into a full,

worldwide NPB release. The researchers based their efforts

on an improved NPB version without message passing constructs, designated NPB3.0-SER (SER stands for “serial,”

that is, written in conventional, non-parallel Fortran), and

which they are now releasing as a service to researchers who

want to test new parallelization tools.

The new parallel versions, called NPB3.0-OMP, NPB3.0-

HPF, and NPB3.0-JAV, are based on OpenMP, High

Performance Fortran, and Java threads, respectively.

Together with NPB3.0-SER, they are being released under

the name NPB3.0. OpenMP has become particularly popular on shared-memory systems because of its ease of program development. High Performance Fortran, generally

considered a niche programing language in high-performance computing, was recently cited in a significant fluid

flow computation on the Japanese Earth Simulator, logging

an impressive 12.5 Teraflops (floating point operations per

second). Java, though not usually associated with high-performance computing, was included because of its excellent

portability properties.

GridNPB3.0: Benchmark for grid computing

Computational grids, encompassing many high-performance systems connected in ultra-wide-area networks, have

recently been receiving a lot of attention among research

and industry groups. Several solutions have been proposed

to solve the problem of the software interface to services on

such sprawling systems, with NASA’s own effort, the Information Power Grid, an important player. Technical successes have been reported at a number of scientific meetings, but little quantitative data is readily available for use

by application engineers interested in the efficiency and

ease of use of grid computing. The NAS Grid Benchmarks

(NGB), (see Gridpoints, Summer 2002, page 5) aim to fill

that gap. They are a paper-and-pencil specification of four

families of problems that represent important applications

on computational grids, such as parameter studies involving many independent runs of the same program, each

with a different value of some problem parameter(s). 

Another important, slightly more complex problem is that

of the so-called visualization pipe, in which a sequence

of computational, postprocessing, and visualization tasks

is executed cyclically within a time-dependent calculation.

Such a process, shown schematically in the figure on page 18,

is a typical example of what users may want to run on a

grid, and is captured in one of the four benchmark problems.

While it is too early to declare a winner in the race to usable

grid software, NAS researchers decided to provide some

correct – though not necessarily efficient – reference implementations of NGB to help other groups benchmark their

systems. Called GridNPB3.0 because they use NPB3.0

components as building blocks, these implementations

consist of Fortran programs executing serially and communicating through a shared file system (GridNPB3.0-SHFSER), or of Fortran or Java programs executing fully concurrently (both inter- and intra-task parallelism), communicating through the Java Remote Method Invocation

(Grid NPB3.0-JAV-OMP/JAV).

NAS Grid Benchmarking Software

Now Available On Web
NAS Technical Training Seminars

Many of the seminars presented at the NASA Advanced

Supercomputing (NAS) Facility are videotaped, and

can be borrowed by sending e-mail to the NAS Documentation Center (doc-center@nas.nasa.gov). The seminars

highlighted below are all available on videotape. Please reference the date code when ordering.

Microphysics, Radiation, and 

Surface Processes

Wei-Kuo Tao from NASA Goddard Space Flight Center’s

Laboratory for Atmospheres spoke about “Microphysics,

Radiation and Surface Processes in the Goddard Cumulus

Ensemble (GCE) Model” at a New Technology Seminar. The

GCE Model has been developed and improved at Goddard

over the past two decades, and has been used to understand

a variety of climate phenomena. These include: water and

energy cycles and their roles in the tropical climate system;

the vertical redistribution of ozone and trace constituents

over various spatial scales by individual clouds and wellorganized convective systems; the relationship between the

vertical distribution of latent heating (phase change of water)

and the large-scale (pre-storm) environment; and the validity of assumptions used in the representation of cloud microphysical processes and their interaction with radiative forcing

over tropical and mid-latitude regions. Tao discussed five

major GCE improvements, as well as their performance.

(September 17)

Cluster Approaches to Solvation 

and Surface Chemistry

Mark Gordon from the Department of Chemistry and the

Ames Laboratory for Scalable Computing at Iowa State

University discussed “Cluster Approaches to Solvation and

Surface Chemistry.” For the past several years, researchers at

Iowa State University have been developing methods to

approach condensed phase behavior, starting from a molecular, as opposed to a continuum basis. This has resulted in the

effective fragment potential (EFP) model, which has been

applied most extensively to problems in which water is the

solvent. Gordon discussed an embedded cluster method for

treating surface chemistry known as the surface integrated

molecular orbital-molecular mechanics (SIMOMM) method, which integrated quantum mechanics with molecular

mechanics. (September 12)

Higher Order Godunov Finite-Volume

Approximation of PDEs

Tim Barth, from the NASA Advanced Supercomputing

Division at Ames Research Center, described his research

“Genuine Error Estimates for the Higher Order Godunov

Finite-Volume Approximation of Partial Differential Equations (PDE)” at a new technology seminar. Barth presented

a-posteriori error estimates for high-order Godunov finitevolume methods which exploit the inherent two-solution

representations. He also discussed important issues such as

the treatment of nonlinearity and postprocessing of dual

data. In addition, Barth presented numerical results for linear and nonlinear conservation laws to verify the analysis.

(August 22)

Tool Support for OpenMPI

Barbara Chapman, associate professor of Computer Science

at the University of Houston, discussed “Tool Support for

the OpenMPI API.” Chapman noted that OpenMP is the

language of choice for shared memory parallel programming

and, having undergone minor revisions within the past two

years, is now relatively stable. OpenMP is also strongly supported by the major vendors. Chapman believes that tools

are needed to support application developers who use

OpenMP, whether they are using it alone or in conjunction

with MPI for better portability. At this time, however, relatively few commercial tools are available. Chapman presented a technology to help researchers create and share tools that

support the creation and optimization of OpenMPI programs. (July 8)

Computational Nanotechnology of 

Nanomaterials and Devices

Deepak Srivastava, senior scientist and task lead in the NAS

Division’s computational nanotechnology group, was the

invited speaker at the Information Sciences and Technology

Directorate’s monthly “IT Forum.” Srivastava spoke on

“Computational Nanotechnology of Nanomaterials and

Devices.” The role of computational nanotechnology in

advancing the possibilities in nano-materials, electronics,

sensors, and machines was described as was the use of carbon

nanotubes and fullerenes and how they apply to NASA’s missions. Using large-scale classical atomistic and quantum

molecular dynamics and transport simulations, Srivastava

discussed the nanomechanics of carbon and boron-nitride

nanotubes in ultra-light and very strong functional composite materials; branched carbon nanotube structures for biomimetic molecular electronics and sensing applications;

endo-fullerenes and doped diamond nanocrystals for solidstate quantum computers; and model operations of molecular gears and motor systems. Large-scale physics and chemistry-based modeling and simulation tools and capabilities

have a critical role to play in the development of nanotechnology and new frontiers at the interface of info-bio-nano

technologies. Srivastava also discussed near-term requirements, and areas for pushing this growth, within a core information technology-based environment. (September 13)

16 Gridpoints
Calendar of

Events

Supercomputing 2002 (SC2002)

Baltimore, Maryland • November 16–22

“From Terabytes to Insights” is the theme for this year’s

supercomputing conference. SC2002 will bring together

scientists, engineers, designers, and managers from all areas

of high-performance networking and computing, showcasing the latest in systems, applications, and services. Check

out the conference website at: www.sc2002.org. See the special insert in this issue beginning on page 1A.

3rd International Workshop on Grid Computing

Baltimore, Maryland • November 18

This international meeting is an opportunity for the grid

community to discuss current and future work, as well as

exchange research ideas in this field. The focus of this meeting will be on grid applications. Find out more at:

www.gridcomputing.org/grid2002 

41st AIAA Aerospace Sciences Meeting

Reno, Nevada • January 6–9, 2003

The Aerospace Sciences Meeting is the largest of the AIAA

technical conferences, and is the preeminent technical gathering for computer and software technologies applicable to

the aerospace industry. Technical papers are presented by

authors chosen via a competitive selection process based on

peer review. Further details are available at: www.aiaa.org

17th Annual HPCC Conference

Newport, Rhode Island • March 25–27, 2003

The National High Performance Computing and Communications Council holds an annual High Performance

Computing and Communications Conference each spring.

This is one of the few conferences that emphasize communication between manufacturers and users, as well as academics and the government agencies which establish policy and

regulate the use of advanced technologies. Topics covered

include: wireless computing, e-government, Internet security, grid computing, mass storage, homeland cyber security,

and bioterrorism. For more information, visit: www.hpccusa. org/genconf.html

Researchers at Stanford University and NASA are working to

create a simulation-based medical planning system for cardiovascular patients that uses computational methods to evaluate

alternative surgical options prior to treatment, using patientspecific models of the vascular system. Here a patient-specific

preoperative geometric model (shown in red) is created from

3-D preoperative medical imaging data. An operative plan

(shown in green) is then created by a surgeon. This technology

will be demonstrated at the SC2002 conference in Baltimore,

November 16–22. (Stanford University) 

www.nas.nasa.gov/gridpoints Gridpoints 17

2002 NASA Information Power Grid (IPG)

Tutorial and Workshop

Palo Alto, California • December 10-12

The IPG Tutorial will be held December 10, providing an

introduction to the NASA grid and its various tools. This

is an excellent opportunity for people to become familiar

with the general capabilities of the IPG, the basic functions

available to its users, and those developing IPG applications. The tutorial requires no previous IPG experience.

In contrast to other grid workshops and events, the IPG

workshop is focused specifically on NASA's Information

Power Grid. The objectives of the IPG workshop are to

provide a forum in which: IPG system developers and

implementors can share their experiences; IPG application

developers and users can share their experiences; potential

IPG users can gain a broad understanding of its capabilities; and IPG research and development personnel and the

NSF PACI partners can report on the progress of their grid

research and development.

Presentations will include talks from research and development teams from each of the major IPG-related organizations including: NASA centers; Argonne National

Laboratory; National Computational Science Alliance; San

Diego Supercomputer Center; University of Southern

California’s Information Sciences Institute, and other participating universities.

For additional information on this event, point your

browser to: www.nas.nasa.gov/User/Training/training.html,

and click on “Workshops/Conferences,” or contact Marcia

Redmond at: mredmond@mail.arc.nasa.gov.
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NASA’s IPG Team Develops 

New Tools

NASA’s IPG team meets another of its milestones, creating tools to

simplify job submission to distributed grid resources. See page 4.

Nanotechnology: Simulating the

Future of Computing

NAS scientists demonstrate how the laws of quantum mechanics

affect transistor and device miniaturization and construction.

See page 8.

www.nas.nasa.gov/gridpoints

Proposed models of nanoscale transistors