Creating a holistic geoscientific model is complicated enough. So when scientists have to debug their computer code, they turn to Allinea DDT, a tool easy enough for undergraduates to use. “People were impressed with the results Christine achieved using Allinea DDT and assumed she was a highly educated computer science technician; whereas, at the time, I think she might have taken just one ‘intro to computer science’ course.” – Dr. Shawn Matott, computational scientist, University at Buffalo’s Center for Computational Research. Read more at http://www.allinea.com/case-studies/

1. Case Study: Allinea DDT Helps Drive the
Evolution of Geoscientific Model Development
Snapshot
Client: The University
at Buffalo’s Center for
Computational Research (CCR)
is one of the leading academic
supercomputing sites in the U.S.
Challenge: To gain a more
holistic view of the planet,
environmental scientists and
engineers are linking their
models together and bringing in
more data. The size, complexity
and distributed nature of their
projects make the traditional
methods of debugging
ineffective. Time and budget
constraints make the problem
seem insurmountable.
Solution: Allinea DDT – the
leading graphical debugging
tool – makes it easy to debug a
complex, multi-tiered project.
Results: A new framework for
debugging geosciences projects
was created with the help of an
undergraduate math major, who
had such a positive experience
with Allinea DDT she is switching
her discipline to computer
science.
Summary quote: “People
were impressed with the results
Christine achieved using Allinea
DDT and assumed she was
a highly educated computer
science technician; whereas, at
the time, I think she might have
taken just one ‘intro to computer
science’ course.” – Dr. Shawn
Matott, computational scientist,
University at Buffalo’s Center for
Computational Research.
Creating a holistic geoscientific model is
complicated enough. So when scientists
have to debug their computer code, they
turn to Allinea DDT, a tool easy enough for
undergraduates to use.
When it comes to modeling the
Earth, we aren’t in the Garden of
Eden anymore.
The days are gone when a
scientist could run a single
model that works for a collected
dataset and then publish
the results. Today’s teams of
geoscientists, hydrologists,
and engineers are using
supercomputers to link their
models together and create
experiments that are ever-more
complex.
“You want to get a large-scale
holistic picture,” says Dr. Shawn
Matott, computational scientist
at the Center for Computational
Research (CCR). “So, you want
the best-trained person making
the model for groundwater,
and you also want to see what
is happening with the fish
population, human cancer rates,
and so on. You’ve got to be able
to link these different disciplines
as represented by the computer
models.”
CCR has 8,000 cores capable
of more than 100 teraflops.
The center’s system is
heterogeneous: 384 cores have
access to GPUs while others can
access large memory stores.
As scientific models become
more sophisticated, so must
the tools for finding and solving
errors. To this end, CCR uses
Allinea DDT, the most advanced
debugging tool available for
scalar, multi-threaded and
large-scale parallel applications.
Allinea DDT is designed to
make solving even the most
complex multi-process, software
problems straightforward.
“You might have a model that
runs in parallel on a CUDAenabled GPU, and then the
optimizer runs in parallel using
MPI,” says Matott. “You need
tools that can manage that kind
of complexity.”
Christine Baxter,
undergraduate
student
Dr. Shawn Matott,
computational
scientist
University at
Buffalo’s Center
for Computational
Research
University at
Buffalo’s Center
for Computational
Research

2. Case Study: Allinea DDT Helps Drive the
Evolution of Geoscientific Model Development
Overcoming
Time and Budget
Constraints
Compute program, funded by
the National Science Foundation.
Students work 15 hours a week
on a research project alongside
their regular courses.
Time and budget constraints
add even more challenges.
Organizations like CCR need
a debugging tool that is both
robust and easy to use.
Matott had four undergraduate
math students, two from the
University at Buffalo and two
from Buffalo State College. He
met with the group once a week
to talk about their progress and
answer questions.
“You really can’t afford to stick
a PhD or Master’s student on
something like debugging code,
because their expertise lies more
in the science side of bringing
these models together, building
a better optimizer or better
algorithms,” says Matott.
He often finds assistants through
the Undergraduate Research
Group Experience, or URGE to
The group tested five different
optimizing algorithms on
15 different test functions,
generating 200,000 simulations.
Not all of the experiments ran
successfully. Matott trained
undergraduate Christine Baxter
to write Bash scripts to isolate
roughly 1,000 simulations that
failed and then let her loose on
Allinea DDT to debug several
thousand lines of code. She
discovered the bug in the sort
function of one algorithm.
“She had two weeks of training
on Bash scripting, and basically
no training on Allinea DDT. I
just told her how to launch the
software and, working through
the GUI, she was able to figure it
out,” says Matott. “I think if she’d
had to use one of the commandline debuggers, it would have
meant another two weeks of
training to get her up to speed.”
Once Baxter completed the
debugging, she and Matott
constructed the idea of a
framework, which generalized
her process so other
computational scientists could
benefit from it.
Center for Computational Research Machine Room in the NYS Center
of Excellence in Bioinformatics and Life Sciences

3. Case Study: Allinea DDT Helps Drive the
Evolution of Geoscientific Model Development
Positive Experience
with Allinea
DDT Inspires
Undergraduate
It was a heady experience for
an undergraduate to contribute
to the evolution of geoscientific
model development.
Baxter took the debugging
framework to the fall meeting of
the American Geophysical Union
with 25,000 attendees, where
she displayed and defended her
results in a poster session.
“Here were these
undergraduates standing sideby-side with professors, PhD
students, and post-docs. People
were impressed with the results
Christine achieved using Allinea
DDT and assumed she was
a highly educated computer
science technician; whereas, at
the time, I think she might have
taken just one ‘intro to computer
science’ course,” says Matott.
Baxter had such a positive
experience using Allinea DDT
and developing the debugging
framework, she decided to
switch majors from math to
computer science.
Center for Computational Research’s Computer Visualization Laboratory
Ease-of-Use
Makes Scientists
More Independent
As for the future of the
debugging framework, Matott
says he is considering publishing
a paper along with a case study
of Baxter’s experience. He may
even write a software package to
help geoscientists implement the
debugging framework.
In the meantime, he’s looking
forward to trying out Allinea MAP
,
a performance analysis tool
that uses the same interface as
Allinea DDT.
Matott says he could benefit
from MAP’s problems-at-aglance approach. He’s also keen
on the tool because part of his
job is to help other researchers
run their experiments on the
supercomputing cluster.
“Right now I have a lot of
meetings with the users. If they
are in a different discipline, they
often need to train me about their
area of study before I can help
them,” says Matott. “It would be
nice if I could turn them loose
on a product as user-friendly
as Allinea DDT. They could
independently find out where in
the code they’re spending all
their time and we could take it
from there.”
Allinea DDT and Allinea MAP
combine robust capability with
unmatched ease-of-use so that
scientists like Shawn Matott
can focus on grand challenges
like pushing the evolution of
geosciences modeling so we
can make better decisions about
managing planet Earth.

4. the
environment
Allinea Software Inc.
2033 Gateway Pl Ste. 500, San Jose,
CA. 95110 USA
Tel: +1 (408) 884 0282
www.allinea.com • info@allinea.com
Allinea Software Ltd.
The Innovation Centre, Warwick Technology Park,
Gallows Hill, Warwick CV34 6UW UK
Tel: +44 (0)1926 623 231 Fax: +44 (0)1926 623 232
For more information about
the Allinea environment, visit
www.allinea.com