Discovering at Thayer School
Marvin Doyley
Thayer School of Engineering
Marvin Doyley, Research Assistant Professor at Thayer School of Engineering,
is part of Keith Paulson’s alternative breast imaging team that is working on
techniques that may one day allow earlier detection and classification of
breast tumors. Early discovery and classification of these tumors will improve
treatment options and also help avoid the many unnecessary biopsies now
required to determine tumor type. Doyley uses an emerging technique called
magnetic resonance elastography (MRE) in which a small amount of motion is
applied to tissue. Since a tumor is many times stiffer than normal tissue, it
deforms less than the surrounding tissue. The Thayer School research group has
developed a technique where they use a computationally intensive numerical
method to visualize the stiffness distribution within the breast, which allows
them to differentiate between diseased and normal breast tissues. They make an
initial guess of the stiffness distribution within the breast, calculate the
motion of the tissue, and compare the calculated results to magnetic resonance
imaging (MRI) results. They then use an iterative process, refining their last
guess and repeating the calculation until the computed results match the MRI
results.
Utilizing the resources of the Discovery cluster has allowed Doyley to
reduce job runtimes from one week down to four hours. Utilizing 48 of
Discovery’s 300 CPUs has sped up the research process, reports Doyley, and has
allowed the team to work on more complex problems than in the past. In
assessing the impact that more computational resources has had on his research,
Doyley is quite clear about the impact the of Discovery: “Discovery gives us a
lead. It allows us to be more competitive.”
More at CREATE: Computing,
Research and Teaching
About Discovery
Discovery is a collection of 101 computers, or nodes, with a total of 342
CPUs, 11 Terabytes of disk space, and 600 Gigabytes of memory. The combined
power of these interconnected nodes allows for fast processing of programs. In
addition, some Discovery nodes have special infiniband hardware that allows
them to communicate up to five times faster than the normal Gigabit
connections. The Discovery cluster was conceived and funded by Dr. Jason H.
Moore, Director of Bioinformatics at DMS, to become a campus-wide coop cluster
designed to serve the needs of Dartmouth researchers and students.
With this faster interconnect, users running parallel programs that run on
multiple nodes are able to run their programs faster and more efficiently on
large numbers of processors. For example, a physics application that uses
message passing (MPI) was able to run about 35% faster on Infiniband.
Here are some benefits of using the Discovery cluster:
- Access to a 340 CPU cluster.
- Full system administration support, including backups.
- Services including programming, debugging, parallelization, and
optimization support.
- Full suite of standard compilers and research applications.
- Access to inactive nodes.
- High-speed connections between some nodes.
For more about Discovery, including information about courses, see Getting Started with Discovery or
contact John Wallace.
- Pete Schmitt (646-8109), Systems Administrator
- Susan Schwarz (646-1458), Training and Application Development
- John Wallace (646-1412), Outreach and Consulting
Research Computing Study
Research is integral to Dartmouth’s mission, and computing is a key
resource. The Research Computing Oversight Subcouncil (RCOS), with faculty,
graduate student, and staff representatives, is reviewing Dartmouth’s research
computing environment. In 2006, RCOS conducted a survey and interviews to learn
about current and anticipated use of tools and resources, including hardware,
software, and support.
RCOS is now preparing a set of recommendations for the Vice President for
Information Technology and the Provost. Its members are seeking input from
campus researchers. Contact Joseph BelBruno, Malcolm Brown, Edmond Cooley,
Richard Granger, Michael Herron, Stephen McAllister, Jason Moore (chair),
Stanley Pyc, Scout Sinclair, Ellen Waite-Franzen, and Martin Wybourne with
suggestions for future directions in research computing support.
Academic Computing Highlights
A 16-processor sun server, Andes, is now available to all campus
researchers. Users can run SAS, parallel Matlab, Mathematica, and other
standard applications, as well as their own programs (including parallel
programs). Contact John Wallace (646-1412) or Susan Schwarz (646-1458).
Blackboard now has improved versions of its popular blog and wiki tools,
which allow students or groups of students to build Web sites within
Blackboard. Also, we are seeking volunteers for spring term to beta-test the
next version of Blackboard. Contact blackboard.support@dartmouth.edu.
The Cook Auditorium renovation is complete. Along with numerous cosmetic and
access enhancements, Cook now has the same smart classroom technology that
faculty are familiar with in other campus classrooms. Contact Andrew Faunce
(646-3614).
 
Media Production Group prepared videos for the opening
of several campus facilities.
Contact Academic Computing
Academic Computing assists faculty in the use of information technology for
research, in the curriculum and the classroom, and with video production
services.
- Malcolm Brown, Director, malcolm.brown@dartmouth.edu, 603
646-1349, Room 179e, Berry Library
- Research Computing, research.computing@dartmouth.edu
- Curricular Computing, curricular.computing@dartmouth.edu
- Classroom Technology Services, classroom.technology.services@dartmouth.edu
- Media Production Group, robert.m.murray@dartmouth.edu
- Blackboard Support, blackboard.support@dartmouth.edu
- Academic
Computing on the Web
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