Natural Product Chemistry, Applied Mathematics and Aerodynamics Research Get Performance Leaps from Shared-Memory Architecture
MOUNTAIN VIEW, Calif., Aug. 22 /PRNewswire-FirstCall/ -- To safely develop
new drugs from organic compounds and to develop more stable aircraft and
satellites by harnessing the compute power of shared-memory architecture from
Silicon Graphics (NYSE: SGI), the Office of Information Technology and the
Office of Research as well as the College of Science and the Mathematics
Department at Virginia Tech, in Blacksburg, VA, recently selected SGI(R)
compute and visualization technology. The SGI systems will be used as
centralized resources available to all faculty and researchers, and to easily
port a host of scientific codes to the open systems Linux(R) OS.
A new SGI(R) Altix(R) high-performance computing system, purchased in
April, is up and running and almost 100 percent booked by faculty researchers
and graduate students, primarily in applied mathematics, high-altitude
aerospace and mechanical engineering, and quantum chemistry, which is aiding
drug discovery. The University has already placed limits on the users to
enforce fairness and plans to implement a queueing system in the future that
would keep the machine at 100 percent utilization while allowing researchers
access to as many CPUs as they need for their program. The Silicon Graphics
Prism(TM) visualization system will be configured as part of an immersive
visualization theater environment for a variety of scientific research.
One of the most important things the University's Research Division
required was the ability to port a variety of codes developed by faculty
members, in addition to community-based codes developed through a consortium
of researchers around the world, as well as publicly available domain codes.
"What shocked us is the ease with which the researchers were able to get
applications to execute in the Altix system's large, shared-memory
environment," said Erv Blythe, vice president of information technology,
Virginia Tech. "Researchers value their time probably as much as anything, and
in terms of setting up their code, they care about good utility, getting good
returns for that investment in time, and reliable and stable computing.
Researchers who are used to working on clusters are seeing a stark difference
in terms of reliability and stability with Altix. From my perspective, this
looks like one of the best investments we've made in research computing in the
last several years."
irginia Tech, which consistently ranks among the top research
institutions in the U.S., had purchased a 16-processor SGI Altix system a year
ago. Researchers loved it; almost immediately, the system was over-booked by
400 percent or more. In April 2005, Virginia Tech, purchased a SGI Altix
high-performance system with 64 Intel(R) Itanium(R) 2 processors and 256GB of
memory through SGI's Higher Education and Research VAR James River Technical,
Inc. The University also purchased, in the same month, a Silicon Graphics
Prism(TM) visualization system with four Intel Itanium 2 processors, 4GB of
memory and two ATI(R) graphics processors, to jump-start a scientific
visualization initiative. Both systems run the true 64-bit Linux environment.
"There are two main advantages of SGI Altix," said Kevin Shinpaugh,
director of research and cluster computing, Virginia Tech. The first is the
high-performance 64-bit processors. We went from a system that was over five
years old to the Altix. Essentially, one of the Itanium 2 processors that we
are using now is equivalent to all 16 of the processors in the older system,
in terms of performance. The second advantage Altix offers is the wide variety
of scientific and engineering programs that is available-or can be made
available-for the system because of Linux. There are so many different
programs that different departments need, and the Altix was really the only
system that had the capability to run these programs and run them very fast."
Quantum Chemistry To Develop New Chiral Drugs
In the drug research area known as natural product chemistry, samples of
organic compounds from around the world are collected and scientists are
frequently able to develop new drugs based on these compounds. One such drug
is the anti-cancer agent paclitaxel (patented as Taxol), which is actually
derived from the bark of a Pacific yew tree. More specifically, it is derived
from one "hand" of a chiral molecule taken from yew tree bark, and then
synthesized in a laboratory. It is critical to precisely match the "hands."
Using the wrong hand of a chiral molecule, or using the entire molecule, can
be tragic. It was discovered that infant deformities resulting from
Thalidomide use in the late 1950s/early 1960s came from distributing the
drug's entire chiral collection. Today, most drugs we take are a single chiral
Dr. T. Daniel Crawford, associate professor, chemistry, at Virginia Tech,
was one of the first professors to leap at the chance to study chiral
molecules on the new SGI Altix system. "In quantum chemistry we carry out
fairly large scale modeling of individual molecules using the principles of
quantum mechanics," said Dr. Crawford. "These kinds of calculations tend to be
pretty intense, and they really stress almost all parts of the computer. We
require systems to be very fast, with very large system memory, and very large
disk with fast I/O. The SGI Altix system has all of these features. The very
large memory is especially appealing because the complicating factor in chiral
molecules is that you may actually have not just two possible hands, but a
thousand possible hands. The Altix will allow us to do much larger
calculations than we've ever been able to do, so far."
Applied Mathematics for Aircraft and Space Systems
The Interdisciplinary Center for Applied Mathematics at Virginia Tech
brings faculty from various disciplines together to work on research projects.
Terry L. Herdman, director of the Center, and also director of research
computing, works with a group that is using partial differential equations to
build accurate mathematical models that are firmly grounded in physics and
engineering principles, which, in turn, lead to analysis and simulations of
aircraft and space systems. Most noted for its study of flutter of aircraft
wings, researchers developed rigorous mathematical models for the unsteady
aerodynamic loads and proposed feedback laws to control flutter.
"Our current project, which is a joint effort with DARPA, NASA Langley and
the Air Force Research Labs, is to develop accurate mathematical models for
large space systems," said Herdman. "In particular, we're looking at building
a large space antenna, being able to deploy it in either low- or mid-Earth
orbit and then being able to control it, point it, etc. If there are any
vibrations in it, we will be able to mathematically model those parts and
determine how and where we can control them. The SGI Altix is a tool to enable
us to provide approximations for solutions to these space systems, and also
give us simulations. Altix also makes it easy to use third-party software.
Simply put, it is a system that's reliable, very easy to get on to, to run, to
get successful runs and to be able to look at results in a timely manner."
"The research community in higher education is a key driver in leveraging
the power of today's science and technology and the sharing of ideas to create
the scientific and technological breakthroughs of tomorrow," said Dave Parry,
senior vice president and general manager, Server and Platform Group, SGI.
"The performance of SGI's NUMAflex architecture, coupled with the portability
and ease of use inherent in its open-standards Linux operating environment,
are important factors in enabling these breakthroughs. We at SGI look forward
to seeing the fertile minds at Virginia Tech use their new Silicon Graphics Prism and Altix systems to produce advances that benefit society and