AMES, Iowa - They can't wait to do computational chemistry
at a quadrillion calculations per second.
But it's not all that computing power that's driving
three Iowa State University and Ames Laboratory researchers as
they develop computational chemistry at the petascale. Driving
their project is the ability to run complex calculations and do
better science.
"Petascale power is required for accuracy," said Monica Lamm, an Iowa State assistant professor of chemical and biological engineering and associate scientist at the U.S. Department of Energy's Ames Laboratory who studies complex molecular binding. "Now we have to use methods that are less accurate and less reliable."
Theresa Windus, an Iowa State professor of chemistry and an associate
of the Ames Laboratory, said higher computing power will make a
big difference in her studies of atmospheric particles:
"This allows us to get results we've never had
before."
The source of the new and improved computing power is Blue Waters, a
supercomputer that's being developed as a joint effort of
the University of Illinois at
Urbana-Champaign, its National Center for
Supercomputing Applications, IBM, and the Great Lakes
Consortium for Petascale Computation, which includes Iowa
State.
Blue Waters is expected to be the most powerful supercomputer
in the world for open scientific research when it comes online
in 2011. It will be the first system of its kind to sustain one
petaflop performance - one quadrillion calculations per second
- on a range of science and engineering applications.
Blue Waters is supported by the National Science Foundation and the
University of Illinois.
Iowa State researchers Lamm, Windus and Mark Gordon,
Distinguished Professor and Frances M. Craig Chair in
chemistry, Ames Laboratory senior chemist and director of the
lab's Applied
Mathematics and Computational Sciences Program, are leading
Iowa State's work to develop computational chemistry
software that can be scaled up to petascale computing systems.
The research team also includes Masha Sosonkina, an adjunct
associate professor of computer science, of
electrical and computer engineering and an Ames Laboratory
scientist; and Brett Bode, the software development manager for
the Blue Waters project at the National Center for
Supercomputing Applications.
The researchers' work is supported by grants of more than
$1.6 million from the National Science Foundation.
The Iowa State researchers are working to scale up two
computational chemistry software codes for use on Blue Waters
and its thousands of parallel processors and high-speed
connections. ("You don't just put a CD into the
computer and hit install," Windus said.) One of the codes
is called GAMESS and was developed by Gordon's research
group at Ames Laboratory and Iowa State; the other is NWChem,
for which Windus was the lead developer when she was at the
U.S. Department of Energy's Pacific Northwest National Laboratory
in Richland, Wash. The computing power of Blue Waters is
expected to help the software deliver better, more accurate
answers to three specific research problems that have been too
computationally demanding to do full-scale calculations with
current research tools.
Lamm is studying how dendrimers (large polymers with many
branches) bind to ligands (smaller molecules that bind with
other molecules to form larger complexes). A better
understanding of the binding could have applications in health
technologies such as drug delivery and water treatment.
Windus is studying aerosols in the atmosphere and how the tiny particles grow at the molecular level. She said a better understanding of aerosols is important to understanding the chemistry of the atmosphere. She's using NWChem for the research.
Gordon is studying the molecular dynamics of water because many
aspects of its behavior aren't very well understood. To do
his studies, he's using a computational method that allows
researchers to look at a large molecular system by splitting it
into fragments. That allows researchers to make quicker
calculations while maintaining accurate results. The method is
only available on the GAMESS computational chemistry tool
developed by Gordon and his research group.
Lamm said she's hoping the Blue Waters project will help
the Iowa State researchers move their projects ahead.
"A problem of computational chemistry has been asking what
computing power is available and how can we simplify the
science for the computer," she said. "Now we have a
chance to do our problems the right way."