The Quarterly Publication of the NASA 

Advanced Supercomputing Division

Computational methods are now being used to

create preoperative surgical models for 

heart bypass patients. See page 10

Visualizing Uncertainty in EOS Satellite Data – 6

Marsoweb: Analyzing the Mysteries of Mars – 15

Summer 2002

www.nas.nasa.gov

CODE Framework Brings Structure to Grids – 18

Setting the Standard for Grid Benchmarking – 5
Vol. 3, No. 2 • Summer 2002

Executive Editor: John Ziebarth

Editor: Nicholas A. Veronico

Writers: Holly A. Amundson

Jill A. Dunbar

Julie Jervis

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:

John Adams, Dick Anderson, Bryan

Biegel, Kathleen Cain, Glenn Deardorff,

Jennifer Dungan, Valerie Favier, Michael

Frumkin, Chris Gong, T.R. Govindan,

Virginia Gulick, Chris Henze, Esther

Johnson, Randy Kaemmerer, David Kao,

Stephanie Langhoff, Jeff Leibow, Tony

Lisotta, George Myers, Marcia Redmond,

Cynthia Rodriguez, Warren Smith, Allan

Snavely, Deepak Srivastava, Charles A.

Taylor, Rob Van Der Wijngaart, David

Walford, Mary Walsh, Steven Zornetzer

On The Cover:

Subscribe to Gridpoints

Subscriptions to Gridpoints are complimentary.

Please send e-mail with your name, company

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

The Quarterly Publication of the NASA 

Advanced Supercomputing Division 6

10

Features

Computational Models to

Predict Outcome of 

Vascular Surgery

Scientists at NASA’s Center for Turbulence Research

and Stanford University are using magnetic resonance

imaging data to create numerical flow simulations of

blood flow through vessels of patients with cardiovascular disease.

Holly A. Amundson

Computational simulation of a pig’s aorta with an implanted bypass graft, during the acceleration phase (systole) of the cardiac cycle. The curved model represents a 2-D slice of the

velocity magnitude, plus an iso-surface for a given value of the velocity magnitude. Red

defines the outside of the artery wall, while green denotes high blood flow velocity.

(Visualization by Valerie Favier)

Marsoweb: Analyzing the

Mysteries of Mars

The Marsoweb website offers researchers a onestop shop for Mars images and data, including

tools for evaluating the best landing sites for the

next Mars mission.

Julie Jervis

Visualizing Uncertainty in

Earth Observing System

Satellite Data

NASA researchers are developing sophisticated

visualization tools for displaying statistical 

summaries that will help Earth scientists 

interpret variations in satellite data.

Julie Jervis

18

CODE Framework Brings

Structure to Grids

IPG development team applies standards and 

protocols established in the Grid Forum to a tool

for monitoring and managing grid resources, even

from remote locations.

Holly A. Amundson

15

Also in this issue:

1 News From NAS

1 From the Division Chief

5 IPG Benchmarks

20 NAS Technical 

Training Seminars

21 Calendar
I

am honored to serve NAS and Ames Research Center

in this new capacity. For the past three years, I have

served as deputy division chief. Two years prior to that,

I was director of the Consolidated Supercomputing Management Office. During this time, the capabilities of our

high-end computers has increased tremendously, enabling our researchers to

make significant progress in computational sciences. This progress is reflected

in a number of the division’s highlights, which are listed below and detailed

within the pages of this issue:

In April, the DeBakey Ventricular Assist Device (VAD) was named NASA’s

Commercial Invention of Year for 2001 (see page 3). NAS Division researchers developed and implemented a number of modifications for the VAD using

computational fluid dynamics, enabling the device to run without failure for

more than 120 days.

Additionally, the HiMAP (High Fidelity Multidisciplinary Analysis Process)

software tool, developed by division researchers, has received the NASA Space

Act Software Release award (see page 2). The American Institute of Aeronautics and Astronautics’ Fluid Dynamics Technical Committee named a

NAS collaborative paper, “Multilevel Error Estimation and Adaptive hRefinement for Cartesian Meshes with Embedded Boundaries,” best paper for

2002 (see page 4). 

In the hardware arena, Chapman, our 1,024-processor machine, has been migrated from a prototype to a production machine. This is the world’s largest

single-system image supercomputer – it will enable the division to more than

quadruple the division’s computing cycles during the next year. In 2002, we

will run more than 3 million production cycles, and we expect to grant nearly 14 million in 2003. 

Recently, cracks in the Space Shuttle’s fuel delivery system liners were discovered, grounding the fleet until a solution is approved. Since the end of June, the

division has been supporting the effort of returning the Space Shuttle to flight

status. Researchers from Marshall Space Flight Center have used more than

240,000 processor hours on Chapman to determine the cause of the cracks,

their impact on safety, as well as the pros and cons of each repair choice. Selection of the final repair plans is being made as this publication goes to press.

Chapman’s computational power and multi-level parallelism programming

techniques are now being applied to POP, the Parllel Ocean Program developed by the Department of Energy’s Los Alamos National Laboratory. POP is

part of the Community Climate System Model that encompasses water circulation, sea ice, land/surface heat, atmospheric air circulation, the sun’s radiation, and Earth’s radiation into space, to simulate how the world’s oceans

affect the Earth’s climate. NAS Division researchers have scaled the code to

run on all 1,024 of Chapman’s processors, and are working to further optimize the code. Today, it runs on 900-processors, and can simulate data for

three-quarters of a year per day – an order of magnitude improvement over

previous runs. 

I hope you enjoy this issue, and 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.

Continued on page 2

News

From

NAS

Gridpoints 1

Ziebarth Appointed Acting

Division Chief

The NAS Division welcomed John

Ziebarth to its helm as Acting

Division Chief in April, following the

move of Bill Feiereisen to director of

Computer and Computational Sciences at Los Alamos National Laboratories. Ziebarth has been NAS’s deputy

division chief since 1999 and promises

to move the division forward in its mission to serve as the flagship of supercomputing innovation.

“John Ziebarth comes to the acting

division chief position with a wealth of

experience in high-end computing

(HEC) and networking,” says Steven F.

Zornetzer, director of Information

Sciences and Technology at Ames.

“John’s leadership is important during

this dynamic period of changing paradigms from vector to parallel machines

and architectures and the rapid evolution in the Information Power Grid

community. The NAS Division has a

rich heritage of national and international leadership in HEC, which needs

to be reasserted. We look to John to

provide this leadership.”

Ziebarth obtained his doctorate in

Aerospace Engineering from Mississippi State University in 1983 and formerly served as director of the NASA

Consolidated Supercomputing Management Office (CoSMO) and an associate
director at the National Center for Supercomputing Applications (NCSA). 

“My background in high-end computing and computational engineering and science will allow me to work well with the

top-notch scientists in this division,” says Ziebarth. “Many firsts

have come out of the division, and I think part of our goal is

to continue to be innovators and leaders in the HEC field.”

Ziebarth says he’s confident that NAS will continue to

achieve significant milestones while supporting research projects throughout the agency, despite the challenges of declining budgets and changes in the way NASA does business. To

support Ziebarth in his leadership role, John Parks has agreed

to take on the post of acting deputy, bringing with him more

than 20 years of experience in HEC systems at Ames.

Drawing on Parks’ experience for daily operations issues,

Ziebarth says, will allow him to spend more time on the

research side of the division.

Barth Appointed to Springer-Verlag

Editorial Board

Timothy Barth, a computer scientist in the NAS Division’s Physics and Simulation Modeling Office, has been

appointed to the editorial board of a book series published by

prestigious international scientific publisher Springer-Verlag.

Established in 1997, the series, “Lecture Notes in Computational Science and Engineering,” is a part of the publisher’s

mathematics division. Barth has been a contributing author

to two editions of the lecture series. The most recent, released

in January, is devoted to the topic of multi-scale and multiresolution methods. All editions are in some form related to

computational science and engineering (CSE), which is the

application of applied mathematics and computations. 

“Springer is really into CSE – they are embracing this as a

new subject area, even though it’s not a very focused subject.

It’s all applied mathematics with an emphasis on computations,” Barth explaines.

His duties on the editorial board include approving new

books for the series and providing input to the senior editor

about potential authors and new topics. 

Growing the Next Generation 

of Computers 

NAS researchers Deepak Srivastava and Chris Henze have

been awarded the Ames Research Center Director’s

Discretionary grant for a new proposal encompassing nano-,

bio-, and information technology. Their proposal for the

“biomimetic simulation of signal transmission in nanotubebased dendritic networks” represents an innovative step forward in the division’s work on nanotechnology. Inspired

by the structure and operations of biological neural systems,

the scientists plan to investigate the properties of a 3-D, treelike architecture of carbon nanotubes, and prove its viability.

The field of molecular electronics using carbon nanotubes

has progressed rapidly in recent years, resulting in several

newly patented technologies, which experts believe will ultimately lead to the next generation of electronic computing

devices. The National Science Foundation estimates that by

2015, the market for products manufactured using nanotechnology will reach $1 trillion, and in his latest budget

proposal, President Bush included a 17 percent increase in

spending on nanotechnology research.

Henze and Srivastava’s proposal of a 3-D, tree-like circuitry

takes a unique approach to current research by private industry and academia, which has so far focused on 2-D models.

“We recently showed that three-terminal nanotubes grown as

a y-junction serve as rectifier switches and have analog logic

capacity,” says Srivastava, senior scientist and lead of computational nanotechnology investigations at NAS. “These properties inspired us to consider the concept of a system architecture similar to the biological neural system, but made up

of synthetic material.”

Taking data derived from activating the nerve cells of crickets, Henze, a senior research scientist, can simulate their electronic behavior. Such simulations are a major tool for determining exactly how signals are transformed as they pass

through the branch structures of neurons. “What’s becoming

clear is that there’s a lot of non-linear processing going on

in the complex branching structures,” says Henze, “and it

has a lot to do with the geometry of the branching.” This

observation, combined with Srivastava’s simulations in building branched nanotube systems, led to a confluence of ideas

for the proposal that the scientists hope will ultimately

demonstrate how signals could be transmitted and processed as they pass through a branched-tree system made of

carbon nanotubes.

The Director’s Discretionary Fund is a well-established grant

that provides seed money for innovative and high-risk

research that, if successful, could lead to fundamental scientific breakthroughs. The NAS scientists hope that showing a

high level of functionality will inspire other groups to try

growing the tree and eventually lead to very complex sensing

and computing applications.

HiMAP Software Wins Space Act Award

Ateam led by Guru Guruswamy of the NAS Division at

Ames Research Center recently received the 2002

NASA Space Act Software Release award for developing

HiMAP, the High Fidelity Multidisciplinary Analysis Process.

HiMAP software efficiently integrates software analysis tools

News From NAS

Continued from page 1

2 Gridpoints
www.nas.nasa.gov/gridpoints Gridpoints 3

to solve large-scale multidisciplinary problems on massively

parallel supercomputers.

HiMAP integrates disciplines with diverse physical characteristics by retaining the efficiency of individual disciplines.

Results are demonstrated for large-scale aerospace problems

on several supercomputers. HiMAP has been successfully

used by NASA’s High Speed Civil Transport (HSCT), the

Defense Advanced Research Projects Agency’s Unmanned

Combat Air Vehicle project, the Navy’s Abrupt Wing Stall

project, as well as Boeing’s and Lockheed Martin’s Internal

Research and Development projects. “Anticipated savings

over the next fiscal year to a number of aircraft programs is

expected to be in the $100,000s. The added analysis capability due to the HiMAP software provides a capability that previously did not exist within NAVAIR,” said Dr David

Findlay, Manager, Naval Air Systems Command. Engineers

at Sun Microsystems have ported HiMAP to the latest parallel systems running Sun HPC ClusterTools 4 Software. 

HiMAP technology could prove useful in other fields such

as automotive, mechanical, civil- and bio-engineering,

where analysis of fluids and structures interactions plays an

important role. Potential future applications include analysis of floating runways (similar to that under consideration

at San Francisco airport), modern cable-stayed girder

bridges, and human hearts.

Resulting from the collaborative efforts of researchers at

NASA Ames, NASA Johnson Space Centers, and

MicroMed Technology, Inc. of Houston, a life-saving heart

pump known as the DeBakey Ventricular Assist Device

(VAD) was named NASA’s 2001 Commercial Invention of

the Year. The Invention of the Year Award program was

developed to help promote part of NASA’s mission, which

is to transfer space-based technology to the private sector.

Exclusive rights to the heart assist device were granted to

MicroMed in 1996. 

To date, the VAD has been successfully implanted in 115

individuals in Europe with no reported device failures.

Trials in the United States are currently underway – 180

implantations of the device are planned. The overwhelming

success of the heart assist device is largely due to the integration of several design modifications recommended by

computer scientists Cetin Kiris and Dochan Kwak of the

NAS Division at Ames. 

“Our involvement with the development and improvement

of the DeBakey VAD makes me extremely proud of what

we do at NASA, because this work will improve many

lives,” says Kiris. 

Drawing on previous experience with modeling fluid flow

through rocket engines, the team carefully examined seven

different designs of the assist device by simulating blood

flow patterns through the pump using NASA-developed

computational fluid dynamics (CFD) technology. Specifically, the team used unsteady turbopump simulation

technology originally developed for the Shuttle’s main

engine. “Although the technology applied here comes from

technology developed for space transportation systems

analysis, biofluid simulations require quite a bit of additional research,” explains Kwak, chief of the NAS

Applications Branch. 

Altering several components of the VAD, including cavity

shape and impeller tip clearance size, led the researchers to

propose three design modifications. One design modification was the addition of an inducer that spins with the

impeller to eliminate irregular blood flow patterns, which

led to blood clotting. The second modification was the

alteration of the cavity shape between the flow straighteners

and the inducer. The third change was the modification of

the diffuser angle to adjust the flow angle of blood exiting

the device. The combination of these three design modifications eliminated cell damage, while improving blood flow

through the device.

Currently, the device is used as a “bridge to transplant” for

heart failure patients awaiting a transplant. It is also used as

a “bridge to recovery” for those patients whose hearts are

healthy enough to heal naturally, and do not require a transplant. In the future, the team hopes to further improve the

design so that it can be permanently implanted in humans,

circumventing the need for any heart transplant.

Life Saving Device Named Invention of the Year

Using CFD analysis, NAS researchers Dochan Kwak and

Cetin Kiris found that major design modifications to the

DeBakey Ventricular Assist Device were necessary. The result

of these changes: overall efficiency of the device was increased

by 22 percent. (Courtesy MicroMed Technology)
4 Gridpoints

News From NAS

Researchers Awarded for Development of New Mesh Refinement Strategy

On June 25, the American Institute of Aeronautics and Astronautics (AIAA) recognized

the work of NAS Division researcher Michael

Aftosmis and Marsha Berger, professor and deputy director of Courant Institute at New York

University, in the area of error estimation and

adaptive meshing. The team’s paper, “Multilevel

Error Estimation and Adaptive h-Refinement

for Cartesian Meshes with Embedded Boundaries,” has been named best paper by the AIAA

Fluid Dynamics Technical Committee for 2002.

The award was presented at a special luncheon

held in conjunction with the 32nd AIAA Fluid

Dynamics Conference in St. Louis, Missouri. 

The winning technical paper describes Aftosmis’

and Berger’s development of new techniques for

error estimation and adaptive refinement for computational fluid dynamics (CFD) solutions. The

new adaptive mesh refinement, or h-refinement

technique, provides an optimal mesh refinement

strategy for flow field adaptive CFD solutions.

Meshes, or grids, are used to calculate flow fields surrounding vehicles, such as the Space Shuttle. “The novelty in our

work is that it removes the ambiguity of mesh generation

and identifies the single best solution,” says Aftosmis. 

Several features put this new h-refinement strategy a cut

above previous adaptive meshing techniques. “It is general

enough that it can be applied to any type of unstructured

or hierarchical mesh and, since it is parameter free, it can

be fully automated,” explains Aftosmis. The new meshing

strategy was also designated to remove the dependence

on user skill, making it very quick and easy to generate

meshes. CFD groups at Department of Energy laboratories, Michigan State University, and Massachusetts Institute

of Technology have been experimenting with the new error

estimator and refinement criteria. Aftosmis and Berger plan

to integrate these error estimation and refinement techniques into their grid generation and solution software

package, Cart3D, this fall.

The sequence of grids (A through D, above) surrounds two advanced

destroyer-type surface ships. These simulations were generated using

Cart3D’s flow solver module, which employs a multigrid technique to

improve the efficiency of the simulation.

(Michael Aftosmis and Donovan Mathias)

Nanotechnology Research Published

Anew take on a well-known nanotube experiment was

recently published by NAS researcher Toshishige

Yamada in Applied Physics Letters (May 2002). Yamada’s

paper, “Modeling of Kink-Shaped Carbon-Nanotube

Schottky Diode with Gate Bias Modulation,” challenges findings of a gate voltage modulation experiment by a research

group at Delft University of Technology, The Netherlands.

In 1999, the Delft researchers published the first experiment

clearly demonstrating that a transistor action principle called 

the “gate modulation effect” survives at the atomic scale as an

intermolecular device made of up only of nanotubes. However, the team could not conclude whether the nanotube was

p-type (positive-carriers rich) and where the rectification

took place. Yamada analyzed their data and clarified that the

nanotube must be n-type (negative-carriers rich), rather than

p-type, as was previously believed. He also showed that rectification occurred at the kink part of the nanotube, rather

than at the electrode contact.

Yamada’s work is meaningful from a pure physics standpoint,

and helps solve a key issue in semiconductor electronics. All

semiconductors are either p-type or n-type. Today’s semiconductor electronics require a sophisticated combination of

both types to create transistors. “Knowing whether a semiconductor is either p-type or n-type is the first step towards

nano-transistors and nano-electronics,” explained Yamada.

“The next issue to tackle is why the Delft group had an ntype nanotube, while others are seeing p-type nanotubes routinely in their laboratories.”

Other experimental nanotube devices fabricated in research

labs have all been hybrids of a semiconducting nanotube and

macroscopic metallic electrodes, and will not guarantee the

smallest miniaturization, according to Yamada. His paper

shows that the Delft device made solely of nanotubes operated with the same transistor action principle used in today’s

devices, and strongly suggests the feasibility of an “all nanomaterial transistor” in the future.

A B

C D
www.nas.nasa.gov/gridpoints Gridpoints 5

Growing enthusiasm for grid computing among the

business and research communities has prompted

participants of the Global Grid Forum (GGF) to

turn to NAS scientists for guidance on how to best measure

grid efficiency and user-friendliness.

With a background rich in experience following the success

of the NAS Parallel Benchmarks (NPB) for high-performance

computers, NAS scientists Michael Frumkin and Rob Van Der

Wijngaart have just received GGF approval of their charter

to establish a formal research group on grid benchmarks.

Official approval means the scientists can hold regular sessions at GGF workshops and continue their work developing

grid benchmarks in collaboration with other organizations

interested in developing global grid standards.

“Benchmarking is a long-standing trade at NASA,” explains

Van Der Wijngaart. “Computational grids are really at the

same stage as parallel computers were about 10 or 15 years

ago. So we thought, ‘let’s take these NAS Parallel Benchmarks, which are highly respected, and use them as building blocks to construct more complicated distributed tasks

that need to share information with each other on computational grids.’”

Although many grids already exist, including NASA’s Information Power Grid, the European DataGrid, UNICORE,

Seti@home, and Condor, there are currently no generally

accepted tests in place to determine the efficiency of the varying standards and toolkits, like Globus and Legion.

“We need to find a common denominator to test the best

solution,” says Frumkin. “All these grid communities embrace the idea of benchmarking because it gives them the

opportunity to show that their products work well.”

So far, NAS scientists have defined four different model grid

applications, derived from common NASA operations, such

as flow visualizations and parameter studies. For each of these

applications, they have provided exact specifications, resulting in the NAS Grid Benchmarks (NGB). For ease and convenience, they have also developed some reference implementations of the NGB, using grid tools developed using

Java and Globus.

Frumkin and Van Der Wijngaart first presented an implementation of their suite of benchmarks at GGF3 in Rome

last year, and although the presentation was late in the afternoon and unannounced, the meeting room was packed. This

large show of interest led to a “birds of a feather” session in

Toronto this past February, and contact with other groups

interested in collaboration.

Allan Snavely, the Performance Modeling and Characterization Laboratory leader at the San Diego Supercomputing

Center, says that several months ago his group also recognized that the lack of ways to measure grid performance

posed a real problem for grid developers. “We have a window of opportunity to develop grid metrics and influence

the design of grid systems in a very

positive way,” says Snavely. “We can’t

leave it aside – it just won’t be as interesting or compelling in a year’s time.”

Snavely’s team is taking a different

approach to develop benchmarks

that can measure performance and

compare configurations. By talking

and working with groups of application developers, they hope to

develop a skeleton suite of applications that will represent the ways

applications exercise and stretch grid

systems. Snavely sees this approach as complementary to

NAS’s, and will co-chair the GGF research group with Van

Der Wijngaart.

The next step for NAS, says Van Der Wijngaart, is to generate new problem sizes for each family of benchmarks so that

tasks can be scaled up. For the NAS research group as a whole,

Van Der Wijngaart believes that some hard and disciplined

thinking now needs to take place, especially focusing on areas

not yet covered by the NGB, like data-intensive applications.

But Frumkin is optimistic that ultimately the grid benchmarks will generate useful results and guide tool developers

to write more efficient code. “When the NAS parallel benchmarks were released, everyone tried to show that their

machine was better because it took less time to successfully

execute the benchmarks. We are expecting the same thing to

happen with the grid benchmarks.”

— Julie Jervis

Setting the Standard for Grid Benchmarking

Artist’s conception of the Information Power Grid in action. (IPG/NAS Division)
6 Gridpoints

Visualizing Uncertainty in Earth

Observing System Satellite Data

While scientists continue to explore the mysteries

of the Earth’s biosphere, innovative technology

from the NASA Advanced Supercomputing

(NAS) Division is helping researchers unravel the complex

web of interactions between natural phenomena and human

activity on our planet.

Using visualization tools and techniques developed by the

NAS Division, scientists in NASA Ames’ Ecosystem Science

and Technology Branch are working to gain a better picture

of the Earth’s surface. The goal is to gain a better understanding of the Earth’s primary forces, its climates and ecosystems, and the effects of human activity on them. Ultimately, scientists hope to be able to predict change in the

Earth’s biosphere and its consequences for human civilization.

To achieve this monumental task, NASA scientists have been

studying land, climate, and environmental changes using

images from a variety of sensors in low-earth orbit. One of

these sensors, the Moderate Resolution Imaging SpectroNASA researchers are developing sophisticated visualization tools for displaying 

statistical summaries that will help Earth scientists interpret variations in satellite data.

Figure 1: Earth Observing System (EOS) satellite data interpreted using David Kao’s new visualization techniques: The bottom

plane shows the mean field colored from non-forest (blue) to closed forest (red). The upper plane is generated from three measurements: the surface is deformed by the standard deviation and colored by the interquartile range, and the heights of the vertical bars represent the difference between the mean and median measurements, similarly colored. Places where mean-median

is largest are not parametric, so this is where the interquartile range shows a better picture of uncertainty than standard deviation.

(Data courtesy Jennifer Dungan, Visualization by David Kao)

Mean

Surface graph: Standard Deviation

Contour color: Interquartile

Bars: | Mean – Median |
www.nas.nasa.gov/gridpoints Gridpoints 7

radiometer (MODIS), was launched on the Terra satellite in

1999. Terra and its sister satellite Aqua, due to go live this

fall, are part of the Earth Observing System (EOS), which

provides scientists with daily images of the Earth’s surface.

With resolutions of 250 by 250 meters per pixel or smaller,

the EOS creates huge challenges in charting the entire Earth’s

surface, especially monitoring changes over time. One of the

challenges is how to detect and interpret errors or uncertainties in this immense quantity of data.

Jennifer Dungan, a research scientist in NASA Ames’ Ecosystem Science and Technology Branch explains: “NASA’s

EOS satellites are producing large quantities of images that

represent reflected light within a spectral region. Measurements of the amount of light reflected have error in them,

which could be due to several factors – including sensor

error or atmospheric contamination – and that adds uncertainty. We’re interested in getting a gestalt view of this uncertainty, as well as being able to query specific variables.”

Identifying this uncertainty is not just important for mapping, adds Dungan, but could have a major impact on international policies, such as the Kyoto Protocol, a United Nations’ initiative to limit the amount of greenhouse gases emitted into the atmosphere.

NAS researcher David Kao has been working with Dungan,

Professor Alex Pang of the University of California at Santa

Cruz, and Professor Han-Wei Shen at Ohio State University

for more than a year on innovative visualization techniques

for analyzing distribution data. Jointly, they responded to a

NASA Intelligent Systems Program research announcement

with a proposal to compare and understand distributions in

EOS applications. Despite strong competition, the project

team was awarded a three-year grant under the Intelligent

Data Understanding topic led by Joseph Coughlan at NASA

Ames, and started work in March 2001. To date, research has

resulted in compelling new visualization tools that show the

distribution of data for each pixel in each grid cell of a map

in ways Earth scientists have not seen before.

“Scientists currently use common geographic information system packages that only allow them to look at one realization –

Figure 2: The bottom plane shows the median field, and the upper plane is deformed by the degree of peakedness (kurtosis) and

colored by the skewness measurement (green denotes negative and red denotes positive). Areas where skewness is large are also places

where an understanding of uncertainty is not gained through standard deviation alone.

(Data courtesy Jennifer Dungan, Visualization by David Kao)

Surface graph: Kurtosis

Contour color: Skewness

Bars: | Mean – Median |

Median
8 Gridpoints

which is a likely outcome of a map – at a time,” says Kao.

“Our tool not only allows them to associate information

among hundreds of realizations, but can display four different statistics simultaneously.”

Using distribution data derived from satellite images, Kao’s

team developed two approaches to visualize such data: pixelwise summaries and feature-wise summaries. When presented with a set of possible numbers in one pixel (a distribution), the standard approach is to compute the mean and the

standard deviation of the given data. Kao’s software computes

several statistical summaries, including the mean, median,

standard deviation, interquartile range, kurtosis, and skewness at each pixel across the realizations (see Figure 1, page 6

and Figure 2, page 7). This provides the scientist with a pixelwise summary of measurements that are color-coded onto

the whole image and can be displayed separately or simultaneously in the same viewing space. This enables the scientist

to study relationships among the measurements at each pixel.

In addition to examining uncertainty about individual pixels,

scientists are interested in understanding clumps of pixels

Figure 3: Positioning the probe (represented by the white crosshair) in a

chosen location provides a histogram of

the surrounding area. The x-axis represents the area size and the y-axis represents the frequency as a percentage,

that is, the number of realizations

found with the same class at the probe

location divided by the total number

of maps. The histogram of clump area

at current probe position shows that

the green clump’s area is likely to be

high among all of the realizations.

(Data courtesy Jennifer Dungan,

Visualization by David Kao)

Figure 4: Vertical line bars provide

visual markers for each clump. The

length of these lines indicates the

size of the area, a visual guide that,

unlike traditional color-coding, is

less likely to be fooled by complex or

circuitous shapes. 

(Data courtesy Jennifer Dungan,

Visualization by David Kao)
www.nas.nasa.gov/gridpoints Gridpoints 9

with similar values. These clumps may

be categorized into classes, such as forest, grasses, cropland, and water, depending on the resolution of the image.

Clump information, represented as a feature-wise summary, helps scientists

identify the areas and shapes of individual clumps, as well as understand the

uncertainty about the area. “When you

navigate with a highly accurate road

map, you can see when you’ll get to the

end of the road,” says Dungan. “When

you’re on the trail and using a map that’s

colored according to what is on the

Earth’s surface, you need to be able to

understand why an area that’s mapped

as grassland is actually forest. A map is

just a model of the world and we need

information about the quality of that

model to determine the plus or minus

percentage of error at each grid cell.” To

help researchers analyze clump area statistics, Kao and his team have designed

tools that allow scientists to both interactively interrogate the clump area’s statistics with a crosshair probe, and highlight the sizes and locations of clumps

(see figures 3 and 4, page 8).

Dungan and Kao discussed their work

at the July 2002 NASA-sponsored

MODIS Vegetation Workshop. Hosted

by the University of Montana in Missoula, the MODIS Land Science shared

step-by-step details of the processing,

distribution, analysis and interpretation

of the MODIS vegetation variables to

the Earth science community (see figure 5). In addition, Kao’s team continues to translate visualization ideas and

techniques into methods and algorithms for understanding distribution

data. The next stage, Kao says, is to

investigate ways to describe both visually and numerically the differences in

the distribution of data between pixels

and features.

— Julie Jervis

Figure 5: MODIS Enhanced Vegetation Index observations from January to June

2001 for the United States show the cycle of vegetation from winter’s nadir to the new

growth of spring. Vegetation ranges from 0, indicating no vegetation, to nearly 1, indicating densest vegetation. (Courtesy of NASA-Goddard/University of Arizona)

For more information, see: David Kao,

Jennifer Dungan, and Alex Pang,

"Visualizing 2D Probability Distributions from EOS Satellite ImageDerived Data Sets: A Case Study," in

Proceedings of IEEE Visualization '01,

pages 457-460.
10 Gridpoints

Computational Models to Predict

Outcome of Vascular Surgery

Scientists at NASA’s Center for Turbulence Research and Stanford University are using

magnetic resonance imaging data to create numerical flow simulations of blood flow

through vessels of patients with cardiovascular disease.

Ranking number one on America’s “top ten list” of

killers, heart disease claims the lives of nearly one

million Americans each year. At this very moment,

61.8 million Americans are battling with a cardiovascular

disease – one of these people dies every 33 seconds. Surgeons

perform vascular surgery on seven million patients every year,

with no way to predict, with certainty, the effectiveness of a

particular treatment. 

Charles A. Taylor, assistant professor of surgery and mechanical engineering at Stanford University, Valerie Favier, a Stanford post-doctoral student funded

by the Center for Turbulence Research (CTR), which is co-managed

by the NASA Advanced Supercomputing (NAS) Division, and

colleagues at Stanford University

are working to cut the guesswork

out of cardiovascular surgery. The

group is creating computational

models of the circulatory system in

patients with cardiovascular diseases (outlining aspects such as vorticity, recirculation areas, and flow

stagnation) to assist doctors with

planning future surgical procedures. “This is something that will

really impact vascular and cardiovascular surgery – it is a better way

of planning treatments for patients,” says Taylor.

When creating these computational

models, one of the group’s primary

focuses is on the connection between

the way blood flows through the circulatory system and how

disease forms in the body. Using computational methods,

Taylor and his group have been studying blood flow patterns

in disease-prone areas of the bloodstream for the past eight

years. “How blood flows through the circulatory system

doesn’t just affect where we get disease, but how well treatments work,” says Taylor. One of these unfortunate locations

is the carotid bifurcation, a branch point in the artery going

up to the brain. Plaque deposits form more readily at this

location, because its unique geometry causes backflow of the

blood. When plaque ruptures, it blocks blood flow to the

Figure 1: Sectioned view of a pig’s thoracic aorta bypass showing the internal fluid dynamics. Red depicts high blood flow velocity. Blue shades represent low pressure areas along the

artery wall where plaque is most likely to form, leading to blockages.

(Courtesy Charles Taylor, Stanford University)
www.nas.nasa.gov/gridpoints Gridpoints 11

brain, causing a stroke. Similar observations of blood flow

patterns in the coronary arteries indicate a connection to

heart attack: clots break off and travel downstream, closing

off major vessels, leading to a heart attack. 

While every patient’s condition is unique, several generalizations can be made about blood flow patterns and how they

are related to the formation of disease: Areas in the circulatory system with recirculation, low wall shear stress (low surface forces), and irregular blood flow are areas where plaque

is most likely to form on artery walls. 

Blood flow velocity is boosted significantly with an increase

in physical activity. When sitting, there is a five-fold reduction in the demand for blood flow to the lower extremities.

This interruption in blood flow causes irregular flow patterns

and slows the movement of blood in some locations along

the artery walls. Under this sedentary state, the chance of

fatty deposits attaching to artery walls increases significantly.

Once formed, these deposits have the potential to break away

into the blood stream, causing blockages, which can lead to

stroke or heart attack. Conversely, when a person maintains

a physically active lifestyle, the blood flow velocity in all areas

of the circulatory system increases, boosting shear stress on

the artery walls, reducing the opportunity for lipids to attach

themselves to the artery walls.

Converting Data to Computational Models

In the late 1960s, computers evolved to a point where the

aerospace industry could use computational methods to

model fluid flow over aircraft configurations to improve their

design. The medical community reached this same conclusion in 1976, creating one of the first computational simulations modeling Newtonian behavior of blood. Computational methods enable Taylor and his group to visualize

blood flow very effectively and efficiently.

Before the use of computational methods, rigid, hand-blown

glass heart models were used to collect data about fluid flow.

Making any changes to the configuration of the glass model

was a time-consuming, costly, and laborious process. “With

computer models, conditions can be altered very quickly,

and there is an opportunity to do things that are both subject- and patient-specific,” explains Taylor. “NASA/CTR has

played an important role in the development of numerical

algorithms for this project.” Previous computational work

was conducted on a NAS Division-supported IBM SP2, in

1995. Now, Stanford University has its own supercomputing

facility that houses a 128-processsor SGI Origin 3800 supercomputer, dedicated to bio-computations.

To build a computational model of blood flow through the

circulatory system, the group begins with MRI (magnetic

resonance imaging) data gleaned from select cardiovascular

disease patients at Stanford Hospital. From the MRI data,

the team uses Stanford-developed software, known as

Geodesic, to identify and “trace out” patterns that the blood

vessels follow. Once the boundaries of the blood vessels are

defined, a series of 2-D slices are taken at various locations

along the vessel, and using the Level-Set method, the team is

able to reconstruct an anatomic model of the blood vessel

(see Preoperative Model Creation Process, page 12). “When we

first started constructing models, it would take months to go

from MRI data to a prototype. Now, we can acquire data and

have a preoperative model constructed in about an hour’s

time,” says Taylor.

Figure 2: Looking at the options presented by the ASPIRE

System, doctors can see which treatments will produce acceptable

pressure drops in patients, guiding their decision for treatment

type. The pressure map offers a quick way to evaluate pressure

losses associated with each treatment. Here, two treatment

options are provided; the pressure distribution (generated using

finite element methods) is captured during peak systole for a preoperative case of ilio-occlusive disease, or complete closure of the

air passage. The gray bands represent a complete blockage of the

artery due to plaque formation. Graft implant: end-to-end

aorto-iliac bypass. 

(Courtesy Charles Taylor, Stanford University)
12 Gridpoints

Once a simulation model is created, a doctor can implant a bypass graft in

various locations along the blood vessel to see how it will affect blood flow

(see Figure 3). Taylor and his group have worked closely with vascular surgeons on this process to ensure that the capabilities of the models will be

something that will meet their needs.

Gathering Results

One very important phase in the engineering design cycle is the creation of

a prototype. At this stage, researchers have the opportunity to make changes

to their model to avoid design failure in the real world. In the medical field,

however, doctors and scientists do not have the same freedom to test their

theories on patients. In order to validate their simulation models, the group

must have experimental results for comparison. Joy Ku, a doctorial candidate in Electrical Engineering at Stanford University and one of Dr. Taylor's

students, is gathering experimental results from 15 different swine. “We

decided to use pigs as our experimental animal, because the aorta of a pig is

similar in size to that of a human. In addition, the blood clotting (thrombus) process in pigs is similar to humans,” explains Favier. The team

implants grafts in each subject and takes velocity, flow rate, and pressure

measurements before and after each procedure to gather data for the computational models (see Figure 1, page 10).

Selecting the Right Treatment

How well a surgical procedure works depends on blood flow conditions as

well as a number of other factors. “Medicine is really a build and test

approach in the sense that we acquire diagnostic data that tells us what the

problem is, and then surgeons have to rely on pencil and paper sketches

thinking, ‘Okay, this is what I’m going to do – this is what worked for me

Preoperative Model

Creation Process

To create anatomic models of the vessels in cardiovascular patients, Charles

A. Taylor and his team must work carefully

through several steps. The process for preparing a simulation takes only two days – an

acceptable timeframe for preoperative planning of bypass graft procedures. Beginning

with a surgical procedure, the team gathers

experimental results with which to compare their computational results. To construct the models, the team uses Magnetic

Resonance Image (MRI) data gathered at

Stanford. From the MRI data, the paths of

vessels are traced out and their boundaries

defined, in order to build the geometric

models. To complete the model creation

process, the team develops numerical flow

simulations, which include both velocity

and pressure components.

While the anatomic data for a patient is very

important to understand when selecting the

proper surgical treatment, it only tells a part

of the story – physiological data is also

important. “If you're going to do blood

flow simulations, you have to know how

much flow is coming in, and what all of

the conditions are,” explains Taylor. The

team also uses Magnetic Resonance Imaging

to acquire blood flow velocity data in

given planes. This image data is used to

prescribe velocity conditions for the computational models, making them both

anatomic and physiologic.

Step I. Surgery

A vascular bypass graft made with a polyester fabric is implanted during surgery.

The top and end of the graft are connected

to the thoracic aorta, creating two anastomoses. Then, the thoracic aorta is pinched

with polyester umbilical tape midway

between the two anatomoses. The last step

simulates the presence of a stenosis with an

occlusion of approximately 80 percent.

Step II. Magnetic Resonance Imaging

a. Measurements are taken using Magnetic

Resonance Angiography (MRA) – about

100 slices, each with a thickness of 2.6 millimeters, are used to construct the 3-D

Figure 3: Computational simulation of a pig aorta with an implanted bypass

graft, during the acceleration phase (systole) of the cardiac cycle. The curved

model represents a 2-D slice of the velocity magnitude, plus an iso-surface for a

given value of the velocity magnitude. Red defines the outside of the artery wall,

while green denotes high blood flow velocity. (Visualization by Valerie Favier)

Continued on page 14
anatomy. Even the smallest vessels are

visible using this technique.

b. Cine-phase contrast Magnetic Resonance Imaging (MRI) techniques are

used to measure the three components

of blood velocity at select locations.

Twenty-four frames in the cardiac cycle

are obtained, and the 2-D images are

segmented using the Level-Set method.

The flow rate over the cardiac cycle is

extracted from the velocity across the

area of the vessel. Step IIIa. Creation of Geometric Models

A path is created through points along

the vessels of interest. Normal to this

path, 2-D slices are used and segmented

using the Level-Set method to extract

the closed boundaries of the lumen. A

surface is lofted through these curves,

and a solid model is constructed using

the Parasolid geometry kernel (Unigraphics Solutions, St. Louis, Missouri).

The model is then meshed using an

automatic mesh generator, developed

byMeshSim, Simmetrix, Inc., New

York. Typical mesh sizes are one million

element meshes. Step IIIb. Processing Flow Data for Inlet Boundary Conditions For numerical simulation, a velocity profile is imposed as a boundary condition at

the inlet. The physiologic pulsatile velocity is extracted during this step. Step IV. Numerical Flow Simulations

A finite element code, PHASTA, developed by Kenneth Jansen, an associate

professor at Rensselaer Polytechnic Institute (RPI), Troy, New York, and former NASA CTR fellow, is used to solve

the incompressible Navier-Stokes equations. The velocity and pressure are computed in this realistic anatomic model,

with a physiologic velocity profile. For

the purpose of these simulations, the

walls are rigid, and blood is behaving as

a Newtonian fluid. Note: In addition to working closely

with Stanford’s Departments of Surgery, and Radiology, the team is also

collaborating with Rensselaer Polytechnic Institute on the numerical aspects of

this research.

Courtesy Joy Ku, Stanford University

Gridpoints 13
14 Gridpoints

before in similar patients.’ There is a certain amount of guesswork involved,” says Taylor. 

Although there are still many uncertainties, some things are

known with confidence – the effects of maximizing volume

flow, for example. If a surgeon implants a bypass graft, he or

she wants to make sure there is enough blood flowing

through it, in order to avoid blood flow re-circulation, which

leads to clot formation or bypass failure (see Figure 2, page

11). “The purpose of implementing a bypass graft is to

improve blood flow – modeling will help determine before a

procedure is done, if it will do just that.” To determine if a

treatment will work, Taylor and his team look at factors such

as a drop in pressure, which helps identify any restrictions

in the artery.

Currently, medicine is largely diagnostic, and empirically

based. “Diagnosis tells you what’s there, but what we’re trying to do is develop tools that will help surgeons answer the

‘what ifs,’” explains Taylor. The team is working on a tool

called the ASPIRE (Advanced Surgical Planning Interactive

Research Environment) System that they hope will help surgeons answer those “what if” questions.

The ASPIRE System is a web and Java-based interface, best

described as a “surgical sketch pad” (see Figure 4). Taking a

preoperative model, surgeons can sketch out their proposed

procedure, and the program then pulls in results from a simulation. The team has recently begun to apply this tool, retrospectively, to actual patient data. “The ASPIRE System

will enable physicians to do design, using diagnostic data to

create operative plans to predict outcomes, and actually figure out what’s going to happen before they do it,” says

Taylor. “The dream is to be able to simulate the whole body

and to enable the surgeon to do whatever he or she wants to

do with the model – add a graft or stent, for example,” says

Favier. “This project is really difficult, because it’s also

research-in-progress in the experimental field – when we try

to compare the computational results with experimental results, the experimentalists want to compare their results with

the simulation results.”

—Holly A. Amundson

Figure 4: The ASPIRE System’s graphical user interface makes the tool easy for doctors to use, enabling quick feedback and preoperative planning. The visualization captured here represents one bypass possibility – a femoral to femoral artery bypass.

(Courtesy Charles Taylor, Stanford University)

Continued from page 12
When the ancient Babylonians first looked to the

night sky and named the portentous blood-red

dot Nergal, God of the Underworld, they never

dreamed that mankind’s obsession with this celestial body

would inspire centuries of religious

and scientific debate. Nor could

they have dreamed that by the end

of the 20th century, humankind

would have sent more than 30

spacecraft to the planet we now call

Mars, hoping to capture elusive

clues to the history of our solar system and possibly to the origins of

life itself.

Although several Mars-bound spacecraft failed to arrive at the planet,

the United States’ success with Mariner 9, Vikings 1 and 2, the Mars

Global Surveyor, and the Mars

Odyssey spacecraft has provided the

space research community with

unprecedented images and data.

Scientists are now using these data

to guide NASA’s next Mars exploration project, the twin Mars Exploration Rovers (MER) planned

for launch June 2003.

The MER 2003 mission’s aim is to

search for evidence of liquid water

in the planet’s past that will provide

more information about the geologic and climatic history of

Mars. The twin rovers will land in areas where conditions

may once have been favorable to life. By careful study of

orbital data, NASA scientists are currently selecting landing

www.nas.nasa.gov/gridpoints Gridpoints 15

The Marsoweb website offers researchers a one-stop shop for Mars images and data,

including tools for evaluating the best landing sites for the next Mars mission.

Marsoweb:

Analyzing the Mysteries of Mars

The Marsoweb site features resources related to landing site selection, as well as interactive global

data archives. Visit the website at:

http://marsoweb.nas.nasa.gov
16 Gridpoints

sites, specifically areas that contain minerals known to form

under wet conditions or that appear to have been formed

by water flow. To facilitate that selection process, Glenn

Deardorff, a visualization technologist in the NASA Advanced Supercomputing (NAS) Division, and Virginia

Gulick, a planetary scientist in the Space Science Division

affiliated with the Center for Mars Exploration at Ames,

have developed Marsoweb. Taken from the notion of

“Mars-on-the-Web,” Marsoweb is a NAS-hosted website

dedicated to the online analysis of Mars orbiter data and

a general repository for geological information about the

Red Planet.

“The NAS Division was initially asked to provide an interface for landing site selection processes by NASA Ames’

Center for Mars Exploration,” explains Deardorff. “Now the

site has more than 31,000 users, including scientists at

NASA, the U.S. Geological Survey office, various government laboratories, academia, and the general public.”

Working closely with Gulick, who also serves on the MER

landing site selection steering committee, Deardorff has

spent the past three years developing the website into a collaborative facility for Mars data analysis.

“The main goal of our effort has been to provide online

analysis and visualization tools so the science community can

use images of the planet taken at different resolutions and

other datasets,” explains Gulick. “We wanted to be able to

place Global Surveyor images onto Viking images, overlay

other datasets, including various engineering, topographical,

compositional and geological data, then run comparisons,

and make the data available in a user-friendly format to support the workshops on landing site selection.” 

Using a unique interactive data map viewer also developed

by Deardorff, scientists can view and query the candidate

landing sites, (which are located in the equatorial area of the

planet from 15 degrees north to 15 degrees south), or download the data maps into their own systems for further study.

Deardorff’s viewer is a Java-based graphical user interface,

which incorporates various types of maps, most of which can

be selected for further study with interactive querying tools.

The background images are from Viking, overlaid by higher

resolution images from the Mars Orbital Camera (MOC) on

board the Mars Global Surveyor (MGS), some of which

show detail at less than three meters per pixel. “In many

cases, the coordinates were off a little,” says Deardorff. “I had

to hand-place most of the thousand or so initial MOC

images, figuring out exactly how to line them up, skew,

and orient them. I developed a real eye for geographic features and shading.” Since then, more than 93,000 MOC

images have been released, and are housed at Malin Space

Systems in San Diego, Calif. All of the narrow-angle

MOC images (more than 41,000 of them) can be accessed

through Marsoweb.

Deardorff also developed a Virtual Reality Modeling Language (VRML) component in the map viewer, which provides an interactive 3-D image of Mars’ surface on the user’s

screen (see image above). VRML images change as the user

A 3-D Virtual Reality Modeling Language image of Viking terrain data is texture-mapped with a geology map in the Melas Chasma

region. This tool is a component of the Mars Explorer Rover 2003 landing site selection resources. (Dataset courtesy Tim Parker and

Matt Golombek, NASA/JPL, Visualization by Glenn Deardorff)
www.nas.nasa.gov/gridpoints Gridpoints 17

controls the mouse to simulate movement, enabling virtual 3-D exploration.

Researchers can then zoom through Mars’

canyons and valleys, or fly over its volcanoes and desert dune fields.

Deardorff says that support for this

kind of interactive data exploration tool

has been overwhelming. For the past

three years, the project has been supported by NASA’s Mars Data Analysis

Program. Last year, Deardorff submitted a proposal for “A Web-based Collaboratory for Interactive Planetary Data

Exploration” to NASA’s Office of Space

Sciences highly competitive Applied Information Systems Research Program.

The proposal was awarded a one-year

grant, which has enabled Deardorff to

extend many of the website’s interactive capabilities.

A relatively new feature allows users to

interact with data from the Mars Orbiter Laser Altimeter

(MOLA), an elevation measurement tool on board the

Global Surveyor. Users are able to create and query elevations, cross-sections, and profiles, and can select a MOLA

track to examine how the profile features correspond to the

track’s plan view. Other queriable features include data from

the MGS Thermal Emission Spectrometer (TES), which

shows measurements of thermal radiation, and digital maps

of geology units.

Although the initial focus of Marsoweb has been to provide

essential data accessing tools for landing site selection, Gulick

acknowledges that the site continues to evolve as a “one-stop

shop for Mars data and user-friendly analysis capabilities,”

offering an easy-to-access online library. Marsoweb currently

hosts a huge repository of data, including almost 400 MOC

images of candidate landing sites, global archives of over a

thousand MOC images from the first orbital phases of the

Global Surveyor, interactive archives of MOLA elevation

tracks, and other instrument and geological data. 

To keep the public up-to-date on the landing site selection

process, Deardorff has posted memoranda, presentations,

and notes from workshops. “There’s a lot of public interest in

the website,” says Deardorff. “We’ve even used voluntary

contributions from outside enthusiasts, who have spent a lot

of time making sure that every pixel on the MOC images is

enhanced as much as possible.” 

As the MER 2003 mission approaches, scientists continue to

evaluate landing sites that balance safety with scientific merit.

To aid in the search, Deardorff and Gulick are planning several enhancements to make Marsoweb even more compelling

to the Mars community. The most pressing, Deardorff says,

will be to implement an electronic notebook and a system

for sharing screen viewing for remote collaboration among

scientists, to integrate the MER 2003 landing site and global data archives, and to incorporate data from the latest

orbiter, Mars Odyssey. 

Astronomer Johannes Kepler worked out the intriguing

motions of Mars in 1609, the year before Galileo first pointed his telescope toward the stars. Almost 400 years later,

Marsoweb is bringing thousands of close-up views of the

entire martian surface to desktops around the world.

— Julie Jervis

Mars Orbiter Camera (MOC) images

for MER 2003 landing site studies can

be displayed on regional navigation

pages for closer scrutiny of the planet's

surface. This user interface is used to

select and view images in the MOC

image archive. (Glenn Deardorff)
18 Gridpoints

NASA’s Information Power Grid (IPG) team has

actively participated in the Grid Forum since its

inception in June 1999. Established to address issues

associated with grid technologies, the Grid Forum aims to

promote and develop standards and protocols to help guide

the growth and implementation of emerging grid environments. One aspect of grid computing addressed by the Grid

Forum is of particular interest to the IPG team: Grid

Monitoring Architecture (GMA), which encompasses the

identification of system parameters and data formats

required for monitoring.

Members of the Grid Forum have recently begun to agree on

GMA standards. “The current challenge is dealing with the

changing type of grid infrastructure – now everything is

XML-based, but the grid environment will be shifting to web

services, or grid services in the near future,” explains Warren

Smith, IPG development group lead. Smith has applied

some of these new standards and protocols to a grid framework called Control and Observation in Distributed Environments, or CODE. The team’s motivation for constructing CODE was very practical: The IPG environment needs a

system for observing and controlling the resources, services, and applications that make up the large production

grid. Adding resources and services

to the grid environment makes it

increasingly difficult to keep track

of everything, Smith explains.

“Our tool provides a secure framework for making observations and

performing actions on remote computer systems, directing this data

where it is needed, and analyzing

data to determine what actions

should be taken,” explains Smith.

The tool is composed of four main

components: The “observers” of the

framework perform and report

observations, the “actors” perform

actions, “managers” receive observations, and the “directory service”

maintains a database for the location of observers and actors (see

Figure 1). 

CODE provides a set of commonly

used sensors for observing a variety

of properties – monitoring hosts

and networks, and actuators for

performing various actions, such as

sending e-mail and restricting

CODE Framework Brings Structure

to Grid Computing

IPG Development team applies standards and protocols established in the Grid Forum

to a tool for monitoring and managing grid resources, even from remote locations.

Figure 1: The CODE framework is composed of four components that facilitate the control

and observation of resources, services, and applications supporting large computational grids.

The “actor” performs actions that affect local or remote resources, services, and applications.

The “observer” provides information, such as scheduling queue information and local network usage, in the form of events. The “manager” asks the observers for information, examines the information and makes decisions about it, and requests actions from actors. The

“directory service” is a searchable database used to store information about locations of

observers and actors, which enables managers to search for specific observers and actors.
www.nas.nasa.gov/gridpoints Gridpoints 19

demons. Users can easily integrate their own

components into the framework.

Structure of the Framework

At the lowest level in the CODE framework,

the distributed event service provides the user

with notifications when certain things happen, for example, when an application is

complete or when a machine goes down. All

of these notifications are transmitted through

Internet connections, using a Grid Forum

protocol based on XML. “Right now, these

notifications are being done over a socket

connection – it can be done using TCP with

no security, or it can be done using the Grid

Security Infrastructure,” says Smith.

Integrating the CODE framework into the

IPG environment has several notable benefits. “The new framework will provide

notifications – a very important paradigm for

distributed computing,” explains Smith.

CODE is also modular, allowing users to easily build a variety of “sensors” to monitor

anything within the grid environment – an

application or a piece of hardware, for example. In addition to its monitoring capabilities,

the tool allows users to manage distributed

systems or computations, and make decisions

about their operations.

Although Smith would like to see other

members of the Grid Forum community adopt CODE into

their distributed computing environments, the framework

was carefully designed to utilize the standards and protocols

set forth in the Grid Forum, making it easy to communicate

with other grids following the standards. “Even if people

don’t use the CODE framework, they can use their own tool

and interface it to CODE. It will interoperate with other

grid environments – that’s the whole point of defining protocol standards – it’s like FTP, it enables a user to talk to

someone else’s server,” explains Smith.

Working Within the Framework

Using CODE, Smith has also developed a tool called the

Grid Management System, designed for monitoring and

managing a computational grid. The management tool takes

advantage of the secure, scalable, and extensible architecture

of CODE. “The idea behind the Grid Management System

is to allow a grid administrator to keep an eye on a grid and

manage it – this tool will be tailored to the needs of system

administrators,” says Smith. 

The Grid Management System includes a clear graphical

user interface, providing system administrators with an upto-the-minute status of major grid resources, and their connecting networks (see Figure 2), all at a quick glance. Administrators can also perform administrative functions such

as adding, removing, or modifying users in the grid mapfile,

or database, on remote computer systems.

Several other systems for remote monitoring and resource

management are available, however, many of them are costly, and lack standards and compatibility with other products.

The Grid Management System, built within the CODE

framework, adheres to Grid Forum standards and is portable,

while providing the necessary functionality to use and manage grid resources. In addition, the Grid Management System supports the grid security infrastructure. 

Smith and other members of the IPG development team will

continue to integrate the latest Grid Forum standards and

protocols into CODE. In addition, they will improve and

expand the functionality of the tool based on user feedback.

Says Smith: “We hope that the CODE framework will be

one of the basic components used on the grid – it looks like

it will be deployed into the IPG within the next year.”

To learn more about the CODE framework, visit :

http://www.nas.nasa.gov/Research/Reports/Techreports/

2001/nas-01-006-abstract.html

Figure 2: This Java-developed graphical user interface allows grid administrators to

view system status, including current load of machines at three NASA centers (Ames,

Langley, and Glenn Research Centers). The color-coded system makes it easy to

determine what is happening. For example, a green line represents a successful query

of the system in the direction of the arrow, yellow means a query in that direction

failed, and red denotes two consecutive query failures. The status bars next to the

lines (light violet rectangles) represent current bandwidth usage for each resource.
NAS Technical Training Seminars

During the first half of 2002, several well-attended new

technology seminars were presented at the NASA

Advanced Supercomputing (NAS) Facility. Many of these

seminars have been videotaped, and can be borrowed by emailing the NAS Documentation Center (doc-center@nas.

nasa.gov). The seminars highlighted below are all available on

videotape. Please include the date when ordering.

Computational Electromagnetics

Pavel Bochev from the Computational Mathematics and

Algorithms Group at Sandia National Laboratories talked

about computational electromagnetics and differential complexes. Bochev noted that nearly three decades after the first

finite difference scheme for the time-domain Maxwell’s equations became a standard in computational electromagnetics,

the field abounds with discrete models of Maxwell’s equations based on finite-difference, finite-volume, and finite element paradigms. Bochev showed that successful schemes all

generate a discrete version of the De Rham complex, which

guarantees a physically correct approximation of the curl-curl

operator, and gave side-by-side comparisons of two time domain simulations of magnetic diffusion. The talk concluded

with the examination of some examples of differential complexes related to the Laplace and Stokes equations. (May 20)

Magnetic Fields

Tatyana Sharpee from the University of California San Francisco’s Sloan-Swartz Center for Theoretical Neurobiology in

the Department of Physiology discussed a semi-classical solution to tunneling decay in a magnetic field. Sharpee’s talk,

“Many-electron Tunneling in a Magnetic Field,” presented

methods that have been applied to tunneling from a strongly correlated 2-D electron system in the presence of magnetic fields parallel to the electron layer, noting that the tunneling matrix element can be used as a sensitive probe of inplane electron correlations. (April 18)

Numerical Modeling of Coating Flow

Len Schwartz from the Department of Mechanical Engineering and Mathematical Sciences at the University of Delaware discussed theoretical and numerical techniques for predicting the slow free-surface flow of liquids on solid substrates

with a variety of driving mechanisms. He presented a simulation of the three-dimensional unsteady motion of Newtonian

liquid layers and isolated droplets. Schwartz concluded with

new results relevant to biological cell division. (April 3)

Development Tools

Prakash Narayan, Ferhat Hatay, and Chansup Byun from

Sun Microsystems detailed three of Sun’s new development

tools: Forte Tools provides the user tools to create scalable,

robust, high-performance computing (HPC) applications;

Sun’s HPC ClusterTools Software enables high-performance

computing users to create, tune, and deploy scalable parallel

computing applications in an open and stable environment;

and HiMAP provides basic recommendations for compilation, debugging, and execution of message passing interface

applications on a Sun HPC environment. (March 26)

Surgical Planning

Dr. Charles Taylor, Assistant Professor of Surgery and

Mechanical Engineering at Stanford University, reviewed his

application of computational fluid dynamics to cardiovascular surgery planning. Several aspects of simulation-based

medical planning systems were described, including imagebased modeling, operative planning, and three-dimensional

and one-dimensional blood flow computational methods.

(See Computational Models to Predict Outcome of Vascular

Surgery on page 10 for additional information.) (March 21) 

Dynamic Vision

UCLA Computer Science Professor Stefano Soatto presented an overview of “Vision as a Sensor for Control and Interaction with the Physical World.” He noted that all of the

projects fall under the umbrella of “dynamic vision,” that is,

the study of a vision as a sensor for computers to interact

with physical space. Soatto discussed recent work on the estimation of three-dimensional shapes from collections of

images in the estimation of three-dimensional motion and its

application to real-time virtual insertion. In addition, Soatto

also presented preliminary results in modeling dynamics of

complex visual phenomena such as smoke, water, as well as

modeling and recognizing human gaits. (March 19)

Breast Cancer Computational Studies

Professor Suhrit Dey from Eastern Illinois University

returned to NAS to present his latest findings in breast cancer research. In this third in a series of seminars by Dey, the

focus was on computational studies on the antigen-specific

immune response to breast cancer. Dey described a new

mathematical model to fight breast cancer. The model is

three-dimensional and consists of five nonlinear reaction-diffusion type equations. They were solved computationally by

perturbed functional iterations. The results obtained so far

appear to be in agreement with those recorded in medical literature. (March 1)

Automated Systems Administration

Steve Traugott, founder of Infrastructures.Org and a former

Ames employee, discussed the practices and terminology of

automated systems administration such as concurrent versions systems; makefiles that run at boot; isconf; cfengine;

lightweight directory access protocol; kickstart; jumpstart;

and rsync. Traugott also reviewed many of the key components

of the NAS infrastructure (which he helped create) including

the division’s CVS repository, the LAN engine toolset, and the

Condor pool deployment and management tools. (Feb. 28)

20 Gridpoints
Calendar of

Events

Call for Papers: Graphics Applications for Grid

Computing

Submissions due: August 31 

The theme for a special March 2003 issue of IEEE Computer Graphics and Applications is graphics and visualization applications for grid computing. The ability to take

advantage of the disparate resources available in grid-enabled applications is both exciting and difficult. The magazine is soliciting papers that describe innovative results in

this area. For potential topics and details, visit:

www.sci.utah.edu/grids.html

15th International Conference on Parallel and

Distributed Computing Systems

Louisville, Kentucky • September 19–21

The 15th International Conference on Parallel and

Distributed Computing Systems (PDCS) provides researchers, designers, educators, and other interested parties

an opportunity to explore and exchange information about

all aspects of parallel and distributed computing systems.

Find out more at: www.isca-hq.org/confr.htm

The Grace Hopper Celebration of Women in

Computing 2002

Vancouver, B.C., Canada • October 9–12

The Grace Hopper Celebration of Women in Computing

2002 is the fourth in a series of conferences designed to

bring the research and career interests of women in computing to the forefront. Presenters are leaders in their respective fields, representing industrial, academic, and government communities. Leading researchers present their current work, while special sessions focus on the role of women

in today's technology fields. For more information, please

visit: www.gracehopper.org

10th Foresight Conference on Molecular

Nanotechnology

Bethesda, Maryland • October 11–13

Rapid advances in our ability to image, manipulate, and

probe the properties of matter at the atomic scale – together with emerging insights into structure, function and selfassembly in biological systems – is bringing to fruition the

tremendous promise of nanotechnology. The 10th Foresight

Conference on Molecular Nanotechnology covers a broad

range of topics, including: nanodevices and nanostructures,

biomolecular machinery, molecular machines, scanning

probes, self-assembly, and computational chemistry. See: 

www.foresight.org/Conferences/MNT10/index.html

Next Generation Networks (NGN) Conference

Boston, Massachusetts • October 14–18

The NGN conference focuses exclusively on future trends in

high-performance networking, looking at decisions that

vendors, service-providers, and enterprise users will have to

make two to five years down the road. Full-day and half-day

tutorials will cover: advanced internet protocols, emerging

security technologies, optical networking technologies,

trends in broadband networking, and more. Go to: 

www.bcr.com/ngn

11th Conference on Current Trends in

Computational Chemistry

Jackson, Mississippi • November 1–2 

This symposium, organized by Jackson State University,

covers all areas of computational chemistry as well as quantum chemistry. The format consists of a series of (invited)

plenary lectures and poster presentations on Friday and Saturday, covering applications as well as theory. Get details at:

http://ccmsi.jsums.edu/cctcc

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

Pressure contours behind the Shuttle Orbiter in high-supersonic flight computed using Cart3D — a grid generation tool suite

collaboratively developed by NASA Ames researchers Michael

Aftosmis and John Melton, and Marsha Berger, deputy director of the Courant Institute at New York University.

(Computations and visualization by Michael Aftosmis)

www.nas.nasa.gov/gridpoints Gridpoints 21
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Printed on recycled and recyclable paper with vegetable-based inks

Marsoweb: Analyzing the Mysteries

of Mars

The Marsoweb website offers researchers a one-stop shop for

Mars images and data, including tools for evaluating the best

landing sites for the next Mars mission. See page 15.

Visualizing Uncertainty in Earth

Observing System Satellite Data

Sophisticated scientific visualization tools help Earth scientists

interpret variations in satellite data. See page 6.

www.nas.nasa.gov/gridpoints

Median

Surface graph: Kurtosis

Contour color: Skewness

Bars: |Mean – Median |