• Overview
• Conference Logistics
• Session Schedule
• Session Materials
• Session Program
• Poster Session
• Booth Presentations
• Student Competition
SC08 Education Program Poster Session
The Education Program Poster Reception will be Saturday, November 15, 7:00 pm – 9:00 pm in the Oaks Room at the Omni Southpark Hotel. Hors d'oeuvres will be served.
View the room layout of the poster session
Poster Abstracts
P01 - SC09 Education Program
Join us in Portland, OR next year for the SC09 Education program (November 13-17, 2009). The SC09 Education program goals are to
- provide continuity and broader, sustained impact in education
- increase participation of larger, more diverse communities in the SC Conference
- and integrate HPC into undergraduate science, technology, engineering and mathematics classrooms
The on-site SC09 Education program begins Saturday, November 13th, and includes educational workshops, an expanded student program, student team competitions, and presentations of prestigious awards for students, undergraduate faculty, and K-12 educators.
P02 - SC Education Award Opportunities
The SC Education Program is pleased to announce that three categories of awards will be presented at the SC Education Conferences.
- The Dr. Mary Ellen Verona Computational Science Teacher Leader Award is open to those who demonstrate computational science leadership and education, either in a formal classroom setting or in an after school program.
- The Dr. Robert M. Panoff Student Award for Explorations in Science Through Computation is open to high school, undergraduate, and graduate students exploring science made possible through computation.
- The Undergraduate Computational Engineering and Sciences (UCES) Award, hosted by the Krell Institute, is open for undergraduate faculty who have developed computational science curricula.
P03 - A Survey of Computational Physics
Introductory Computational
Science
Rubin H Landau
Oregon State University
Princeton University Press has published two new textbooks in the last three years based on courses that are part of the Computational Physics curriculum at Oregon State University. Together they form a bridge through an undergraduate curriculum in computational science, with only the more advanced parts specialized to physics. The paper text is accompanied by video lectures, codes in Java, Fortran90, C and VPython, visualizations, animations, and tutorials.
P04 - Grid Computing at UHD
Hong Lin
University of Houston
In the trend of moving from traditional parallel computing to multi-disciplinary scientific computing, grid computing has provided a framework for more efficient use of computing resources and therefore served as a platform for inter-disciplinary collaboration for solving large-scale computation-intense problems. To position UHD in an active role in this trend, we started to establish a grid computing lab, which supports high performance computing with computing clusters. This poster will present a historic review of the work we have done and show applications that have been developed on the clusters and therefore demonstrate the support that the grid computing can bring to the research and education in various fields.
P05 - Dense Linear System Solver Templates for Distributed Memory Architectures Using MPI
S.V. Providence
Hampton University
Dense linear system solvers are important in many applications, such as: fluid flow around dynamic and static objects, solid body diffusion into a liquid, and noise reduction. When migrating from a sharedmemory system to more available scalable distributed memory systems, alternatives for scalable parallel software libraries include: traditional function libraries, to protect legacy code; reactive servers on a network, that can respond to users special computational needs; general interactive environments, such as Mathematica; domain specific problem solving environments; or reusable templates, a description of a general algorithm rather than executable object code that offers whatever degree of customization the user may require. This paper explains how our O(n log3 n) algorithms based on an algebra of scaling and displacement generators which describe dense general matrices, will be used with the message passing interface through templates to perform dense linear system solver computations.
P06 - Graphics Processor Based Implementation of Bioinformatics Codes
Andrew Bellenir , Christian Trefftz, and Greg Wolffe
Grand
Valley State University
We created a powerful computing platform based on video cards
with the goal of accelerating the performance of bioinformatics codes. To
satisfy the demands of the video gaming industry, modern graphics processing
units (GPUs) have become very advanced computational devices, using a large set
of stream processors to render multiple pixels in parallel. Recently, computer
scientists have taken interest in a GPU's ability to execute a single
instruction on multiple data (SIMD computation) for general applications, as
opposed to graphics processing only. This is known as general purpose
computation on a graphics processing unit, or GPGPU.
Our project was
comprised of three stages. First, we researched and constructed a computer
containing GPGPU capable hardware including two high-end graphics cards. Second,
we explored the hardware and software characteristics of the GPU cards to fully
understand both how they function and how to program them. Third, we developed
and wrote bioinformatics software; specifically a massively parallelized version
of the Smith-Waterman algorithm, which is used for performing DNA or protein
sequence alignment. We are currently in the final optimization and performance
analysis stage of development.
P07 - PS: A Portable Secure Peer-To-Peer Protocol for Wireless Sensor Networks
Graciela Perera
Youngstown State University
Unstructured Peer-to-Peer (P2P) networks for content
distribution are decentralized and robust. Searching for content in the network
is based on the Gnutella protocol which does not provide security. As more
wireless and mobile communication devices are used to share information
anywhere, anytime on any device, there is a need for secure and robust
decentralized P2P protocols that enable users to search and distribute content.
For example, soldiers can use wireless sensor networks for battlefield
surveillance and enemy tracking.
We propose to investigate a likely
secure P2P protocol based on the Diffie-Hellman key agreement protocol (DH) over
a wireless sensor network. The challenge is how to deploy DH in a decentralized
manner over a wireless sensor network with limited processing, energy, and
memory capabilities? DH is a simple solution to establish a shared session key
that can provide confidentiality and integrity. The computation of the shared
session key requires considerable processing capability that can drain the
energy available in a wireless sensor node. Thus, we propose to experimentally
evaluate a new power efficient DH protocol called PDH (Portable Diffie-Hellman).
In PDH each sensor node uses a set of previously calculated primes to compute
the shared session key that expires. Experimental results show that although
replicated shared session key are more than likely because shared session key
expire and are recalculated, it is improbable that an intruder for a given
moment of time determine the shared session key of a sensor node.
P08 - Microwulf: Personal, Portable, High-Performance Computing
Joel C. Adams and Timothy H. Brom
Calvin College
Microwulf is a 4-node 8-core Beowulf cluster whose measured
performance is 26.25 Gflops (Rmax, measured via HP Linpack). It cost less than
$2500 to build in 2007, giving it a cost-efficiency of $94/Gflop, making it the
first cluster to break the $100/Gflop barrier. Today it can be built for less
than $1000, improving its cost-efficiency to $38/Gflop.
Microwulf’s
theoretical maximum performance (Rpeak) is 32 Gflops, giving it a computational
efficiency (Rmax / Rpeak) of 82%.
Microwulf measures just 11” x 12” x
17”, making it small enough to sit on one’s desk or fit into a checkedluggage
suitcase. It plugs into a normal 120V wall outlet, runs at room temperature, and
draws just 450W under load, giving it a power efficiency of just 17W/Gflop.
P09 - Material Point Method Investigations of Trauma to Fluids and Elastic Solids Due to Finite Barriers
J.L. Dean
Iowa State University
M.W. Roth and Paul A.
Gray
University of Northern Iowa
A Material Point Method (MPM) algorithm is developed and utilized to investigate how the dynamics of (Langrangian) Navier-Stokes fluids as well as that of elastic solids are affected by trauma due to finite barriers. For fluid simulations, material point particles are placed in a two dimensional pipe with various initial and boundary conditions and stationary perturbations to fluid flow. Results show that eddy currents are present not only in the wake of the perturbing object but are also responsible for disruption of laminar flow upstream from the barrier. However, unphysical simulated conditions arise due to failures for the fluid medium to enclose the region. An unfortunately relevant application for sudden finite trauma to an elastic solid involves simulations of an aircraft striking a large building under varying system conditions. The work presented here is introductory in nature; the ramification and importance of continued study is discussed and emphasized.
P10 - The North Polk CSD Computational Science Curriculum and Outreach Program
Bruce Bennett, Rosalie Eimers, and Steve Latimer
North Polk
Jr-Sr High School, Alleman, IA
Marian Houseman, Carol Peterson, and Jennifer
Raes
St Pius X Middle School, Des Moines, IA
Computational Science is offered as an introductory class in our
computer science program. In addition to learning beginning Fortran90, students
in this class learn to use SketchUp, a 3-D program that uses visualization and
modeling. Students design structures such as dream homes, schools, and sports
stadiums and then compete in a spring regional technology
fair.
Computational science is introduced to our middle school students
in an exploratory technology class. Students in this class learn to use Jaroo -
a free program that stimulates problem solving and experimentation and engages
the students with story telling and animation.
During the 2007-08 school
year, plans were made to extend the use of computational science into other
curricular areas (TAG, science, math, social studies and vocational classes)
within our district and to develop an outreach program with a small private
school in the area. Those plans will be solidified and developed during the
2008-09 school year.
P11 - Virginia STEM initiative: STEM summit, student projects and Teacher Professional Development
Bonnie Bracey Sutton, Mano Talaiver, and Bill Wilson
In this poster session, we will share details on our STEM initiatives with the participants.
- STEM summit: We conducted a two-day STEM summit for rural teachers and guidance counselors. Academic experts from Pittsburgh Supercomputing Center, Longwood University, George Mason University, the College of William & Mary, and Shodor Foundation addressed the need for developing 21st century skills to prepare STEM work force. Speakers from Technology and Utility companies addressed the STEM work force needs
- Student project: As part of the NSF grant: Developing interactive game design and programming skills, our activities included workshop on climate changes and robotics.
- Expanding STEM Career and Technical Education (ESTEMCaTE): As result of our networking in SC 07, Talaiver developed a professional development program for teams of math, science, and CTE teachers.
- STEM Learning for ALL (summit planned for January 2009)
P12 - Integrating Computational Chemistry into the Undergraduate Chemistry Curriculum
Roxanna Delgado, Nicole Massanet, Yashira Negrón, Camila Ramírez
and Carlos M. Torres Díaz
University of Puerto Rico, Río Piedras Campus, San
Juan, PR
The objective of this project is to integrate Computational Chemistry as a formal area along the Chemistry Curriculum at University of Puerto Rico in Río Piedras. Last year we already installed WebMO facilities integrating through this graphic inter-phase the programs Gaussian, MOPAC, Tinker and Gamess. Hosted by SC08 the Workshop of Computational Chemistry for Chemistry Educators was offered in our campus. Of the 28 participants, 10 professors and 4 undergraduate students come from our campus. Since August 2008 we are offering a special topic course of Computational Chemistry with an enrollment of 22 undergraduate students, most of them in their second year of bachelor. Topics in Computational Chemistry are introduced in the General Chemistry and Physical Chemistry courses. Looking for new learning activities in this field, an educational research is being developed beginning with learning-research activities as interstellar chemistry modeling of several organic compounds found in comets, photophysics of the nucleic acid bases and the study of the boron-nitrogen bond in aromatic compounds. In these works ab-initio and semi-empirical calculations are being performed to calculate: ionization energies in aqueous solutions and in vacuum of the nucleic acid bases, modeling different addition reactions that leads to simple molecules observed in comets and the strength of the B-N bond in aromatic rings upon changing their bonded H for other substituent.
P13 - On the Integration of High Performance Computing into 4-year CS Curriculum
Weidong Liao
Shepherd University
With the emergence of cluster and grid computing, High Performance Computing has become a more and more important subject to undergraduate students in the 4-year CS programs. Nevertheless, several challenges exist for 4 year colleges to offer high performance computing in their curriculum. Among these challenges are lacking of lab resource, motivation and interest from students, and qualified faculty members. Herein we describe several attempts we have made to integrate high performance computing in our CS courses.
P14 - Theoretical Studies of Some Donor-π-Donor Heterocyclic Systems for Molecular Electronics
Courtney E. Dula and Edmund Moses N. Ndip
Hampton
University
It is well known that organic molecular systems with large
multi-photon absorption, MPA, in particular, 2PA cross sections have a broad
spectrum of technological applications (optical power limiting, frequency up
converted lasing, three dimensional optical data storage, three dimensional
microfabrication, three dimensional fluorescence imaging, and photodynamic
therapy, etc.). The ease with which organic molecules can be modified
(tunability) coupled with molecular-level optimization of various nonlinear
optical properties (NLO) has resulted in a large number of both experimental and
theoretical studies aimed at broadening the pool of materials with large MPA
cross sections. Factors that influence the MPA cross section include: strength
of the donor/acceptor, the extent of conjugation (π-conjugation length),
molecular polarization, molecular dimensionality, and aggregation.
The
present study focuses on the design and computational characterization of a
series of D-π-D / A heterocyclic systems. The linear absorption spectra, energy
gaps, intensities and / or oscillator strengths, dipole moments, and other
molecular properties have been computed for these systems at both the semi
empirical and ab initio levels of theory. Optimized geometries, linear
absorption (uv-vis) spectra, and HOMO-LUMO energies have been determined at the
DFT/B3LYP level with 6-31G (d,p) basis set using Titan and Spartan06 programs.
The ZINDO-CI method in Arguslab was used to calculate the uv-vis spectra, the
corresponding oscillator strengths, and the groundexcited transition dipole
moments.
Optimized geometries, the HOMOs, the LUMOs, and uv-vis spectra
were visualized with Arguslab, Jamberoo, ORCA, and Spartan06.
P15 - Evolution of Earth Science Education
Kathleen Affholter1, Peggy Bertrand2,
Marie Westfall3, Audrey Williams1
1. Pellissippi State
Technical Community College
2. Oak Ridge High School
3. Oak Ridge
Institute for Science and Education
From giving 200 question pencil and paper exams and one and one half hour lectures, to developing a mashup of the Smoky Mountains, plotting real-time wave data from the National Data Buoy center, and participation in S'COOL (a NASA cloud project), earth science education for pre-service teachers at a community college has changed. Exposure to CSERD (Computational Science Education Reference Desk), mashup instruction, TeraGrid resources, and visualization has inspired educators to rethink teaching methods. The new methods inspire students to be creative, develop teamwork and make earth science a more personal experience.
P16 - Development of a Multiagent System Platform for the Study of Social Cognition
Alvaro de la Ossa and Andrés Segura
National Collaboratory
for Advanced Computing
National Center for Advanced Technology Studies
San
José, Costa Rica
We are currently developing a multiagent platform to study
social interaction. First, we extend current multiagent system (MAS)
architectures with Theory-of- Mind, or ToM features in the agent's model.
Second, we incorporate data mining (DM) methods to support the analysis of
social interactions within an instance of the MAS. Both components together
provide a unique tool for cognitive scientists and social psychologists to study
cognitive aspects of social interaction and the emergence of social
cognition.
Adding the above mentioned ToM features, however, poses some
interesting computational problems related to the size complexity of the agent's
model and the time complexity of the decision making task during social
interaction. Complexity arises from the possible number of ToM features within
an agent's model and the distributed nature of social memory.
We are
currently evaluating various MAS platforms to pick one for the proposed
extensions. Simultaneously, a set of mining methods is being developed that will
comprise the social interaction analysis component.
Next steps include
the development of the interaction protocol language extensions to the selected
MAS architecture and the design of the underlying knowledge representation
language and the structure of the agent's and shared memories, and putting the
resulting environment to test with a pilot sample social group.
P17 - Using MATLAB and Simulink in Introductory Computational Science
Robert J. Olsen
Richard Stockton College of New Jersey
A high priority of the Computational Science program at Stockton is that graduating students have a thorough working knowledge of MATLAB. MATLAB is not widely used in mathematics and other science courses at Stockton as yet, so its use in the Computational Science curriculum must be pervasive if we are to reach our goal. It is therefore essential that students begin using MATLAB as early as possible. I report on the incorporation of MATLAB and Simulink in CPLS 2110 (Introduction to Computational Science) this semester primarily through presentation of student projects modeling dynamics of competing populations, meteor trajectories, rocket flight, and star formation in Simulink.
P18 - Center for Computational Biology at the University of California, Merced
Mike Colvin, Arnold Kim, and Masa Watanabe
School of Natural
Science
University of California at Merced
Since its establishment in fall, 2004, UC Merced Center for
Computational Biology (UCM-CCB) has been a crucial part of this university by
creating its academic and research programs for building towards its longterm
goal of life sciences researchers who possess advanced knowledge in mathematics
and computational sciences.
The center’s educational contribution to the
university’s academic program is also indisputable: its involvement is
exemplified by 1) creation of courseware bridge between biology and computer
application and 2) establishment of the undergraduate summer research internship
program. This has a sixweek intense program to experience and learn
computational biology and its practical applications. The center is also
facilitating the development and dissemination of undergraduate and graduate
course materials based on the latest research in computational biology. This
project is a multi-institutional collaboration including the new University of
California campus at Merced, Rice University, Rensselaer Polytechnic Institute,
and Lawrence Livermore National Laboratory, as well as individual collaborators
at other sites.
All course materials are being released under an open
public license. The electronic, modular course materials produced by the UCM-CCB
are also facilitating linkages to feeder schools at the state university,
community college, and high school levels.
P19 - An Inexpensive Self-Contained Field-Deployable Water Parameter Measuring Device
Nhlanhla Maduna, Mikio Takizawa, Dylan Parkhurst, Bryan Purcell,
and Charlie Peck
Earlham College
Richmond, IN
Typical field-deployable water parameter measurement devices
with the capability to store and transmit readings via the public switched
telephone network are very expensive and almost always use proprietary software.
Here we present a simple, inexpensive design based on commodity off-the-shelf
hardware, open source software, and an industry standard water
sonde.
Each unit is powered by a small solar panel which charges a
battery which is housed in a waterproof case with a single board computer and
charge controller. The unit communicates data via an embedded cell phone. All of
this makes it possible to deploy the unit in remote locations without power or
wireline/wireless data service.
The units measure, record, and transmit
the water's temperature, conductivity, oxidation-reduction potential, salinity,
total dissolved solids, dissolved oxygen, and pH. To analyze the reported
parameters we built a simple mashup with Google Earth which visualizes the
data.
P20 - LittleFe + BCCD + CSERD = Acme; Computational Science Education on the Move
Paul Gray1, Kevin Hunter2, David
Joiner3, Alex Lemann2, Tom Murphy4, Skylar
Thompson5, Charlie Peck5, and Kristina
Wanous1
1. University of Northern Iowa
2. CAKTUS
3. Kean
University
4. Contra Costa College
5. Earlham College
The overwhelming majority of the High Performance Computing (HPC) resources currently deployed are dedicated to research rather than education -- yet the nation faces a shortage of HPC expertise, due largely to the lack of faculty trained in HPC pedagogy. To address a part of this situation our group designs and implements hardware, software, and curriculum to support teaching parallel and distributed computing, computational science, and Grid technologies to a range of 9-16 STEM students and faculty. Acme is the sum of LittleFe, a complete multi-node Beowulf-style portable computational cluster, the Bootable Cluster CD (BCCD), a complete Linux distribution designed for HPC and computational science education, and the Computational Science Education Reference Desk (CSERD), a source of verified and validated curriculum modules.
P21 - Institute for Chemistry Literacy through Computational Science (ICLC)
Edee Norman Wiziecki and Thom Dunning
The National Center for
Supercomputing Applications
University of Illinois at Urbana-Champaign
The Institute for Chemistry Literacy Through Computational
Science (ICLCS) is a National Science Foundation-funded 5-year program to
increase the chemistry literacy and chemistry-related pedagogical skills of
rural Illinois high school teachers. We will immerse these “ICLCS Fellows” and
their students in new models of instruction, especially focusing on computers
and their instructional uses, that will improve student achievement and prepare
students for 21st Century careers through an intensive, multi-year Summer
Institute for teachers built upon existing, successful curricula and methods,
enhanced with stateof- the-art science research data and applications. The use
of computational tools for 21st Century science will be the context for the
delivery of the curriculum that includes particular focuses on medicinal
chemistry (biomedicine), materials science, including nanotechnology,
agricultural chemistry and the computational aspects of molecular-level
chemistry. The Institute is designed to build teachers' competence and
confidence in teaching chemistry, to use computational tools and methods in
their curriculum, and to create a community of practice among research faculty
and high school teachers working together as colleagues to improve student
achievement.
One goal of the program is to increase teachers' use of, and
comfort with, computational and visualization tools.
The Summer
Institutes, key to the professional development program, are two-week, intensive
residential experiences that build in content-level each year over three years.
Additional real and virtual presentations over the course of the year provide
340 hours of continuous professional development, mentoring, and support to
ICLCS participants.
P22 - Supporting High Performance Computing Research: DOE Computational Science Graduate Fellowship Program
Mary Ann Leung
The Krell Institute
This poster will provide an overview of the Department of Energy Computational Science Graduate Fellowship (DOE CSGF) program, its benefits, requirements, and unique approach to supporting Ph.D. students. This program provides a stipend renewal for up to four years, full tuition reimbursement, an academic allowance, an annual conference, and other benefits to students pursuing full-time study towards a Ph.D. in a variety of computational science and engineering disciplines. We will also be available to share information about current fellows, alumni, and the application process.
P23 - TeraGrid Campus Champions
Scott A. Lathrop
Blue Waters Technical Program Manager for
Education
TeraGrid Area Director for Education
The Campus Champions program supports campus representatives as
the local source of knowledge about high-performance computing opportunities and
resources. This knowledge and assistance will empower campus researchers,
educators, and students to advance scientific discovery. Your campus will
benefit by having direct access to the TeraGrid and input to its staff, resource
allocations awarded for their use, and assistance in using those
resources.
The Campus Champion Program will serve as a:
- Source of local, regional and national highperformance computing and cyberinfrastructure information on your campus,
- Source of information regarding TeraGrid resources and services that will benefit research and education on your campus,
- Source of start-up accounts on your campus to quickly get researchers and educators using their allocations of time on TeraGrid resources, and
- Conduit for the campus high-performance computing needs, requirements and challenges, with direct access to TeraGrid staff.
http://www.teragrid.org/eot/campuschamps.html
P24 - Impact of the Copyright Limitation for Sensory Disabilities on Assistive Technology
Raja Kushalnagar
University of Houston
The copyright act grants authors exclusive rights to display,
distribute, or prepare derivative works. However, people with sensory
disabilities cannot fully access and enjoy multimedia works. Assistive
technology solutions such as speech production and recognition transfer
information carried in the nonfunctioning sense to the functioning sense,
therefore creating a derivative work. Under the copyright act, derivative works
may not be reproduced or distributed without the author's consent, absent a
limitation. A limitation to the copyright statutes, section 121, permits
derivative works to be reproduced or distributed in Braille, audio or digital
text only, along with specified added disclaimers for the blind. There is no
limitation on copyright for works partially or wholly inaccessible to the
deaf.
The copyright limitation boundary is examined for the various
assistive technology reader approaches for sensory disabilities in commerce and
research labs. Research and development guidelines on avoidance of breaching the
copyright limitation privileges for assistive devices for sensory disabilities
are discussed.
P25 - Computer Modules in Science Teaching (CMIST) - a program of the National Resource for Biomedical Supercomputing (NRBSC) at Pittsburgh Supercomputing Center (PSC)
Karen Runtich
Pittsburgh Supercomputing Center
Being a part of CMIST, I was able to incorporate these modules
into virtual lab experiences that paralled concept discussions from my students.
Here they were able to apply critical analysis of a variety of sophisticated
visualizations of molecular transport illustrating many science concepts that
are difficult to convey with only textbook photos and discussion.
The
goal of CMIST is to bring innovative science tutorials to secondary classrooms,
focusing on the integration of computational science skills to various branch
science courses. These lessons will inspire and improve student learning and
understanding of a variety of topics. Ultimately, this encourages application of
critical thinking analysis to prepare our students for cutting edge career paths
and the opportunities of tomorrow.
Careers in the Biosciences
Karen Runtich
Pittsburgh Supercomputing Center
Being a part of the Better Educators of Science for Tomorrow
(BEST) High School Teachers (2007 – 2008), I was exposed to the undergraduate
Bioinformatics curriculum and shown integrative techniques to incorporate these
concepts across the various disciplines. We developed and aligned to state
standards a semester draft for a high school bioinformatics curriculum.
I plan to present at SC08 one of the lessons developed that my Advanced
Chemistry students just completed as a research topic which had introduced this
new unit module. More lessons will continue to follow in my class. The
presentation will include some of my students brochures on "Careers in the
Biosciences" . Today, the multidisciplinary nature of the Human Genome Project
(HGP) impacts many different career fields such as: engineering, computer
science, math, law, agriculture, education, pharmaceuticals, instrumentation,
medicine, forensics, biofuels and journalism. My students were overwhelmed and
excited to learn through this project how these future programs would be so
influenced by the HGP to be dubbed the "biology century" since it is implemented
in biological research, practice of medicine and also agriculture. This project
has opened many doors and windows of opportunity that await them in the world of
science for tomorrow.