Numerical Model, Now Tracking Pollutant Emissions in
Up to 35 Atmosphere Levels Around the World, Runs 3-to-4
Times Faster On SGI Altix 350
DIEGO, Booth 90, Jan. 10 /PRNewswire-FirstCall/ --
Silicon Graphics (NYSE:SGI) today at the 85th American
Meteorological Society Annual Meeting announced that
SGI(R) Altix(R) systems and SGI(R) InfiniteStorage
solutions are assisting two cutting-edge assistant
professors in two very diverse fields of research
in the Physics and Atmospheric Science Department
at Dalhousie University, Halifax, Nova Scotia. Both
researchers are immersed in solving intense computational
problems requiring the speed and expandability of
SGI(R) high performance compute (HPC) power and storage,
and both agree SGI Altix computers turned out to be
the best choice for the large data sets they run.
Randall Martin is currently conducting global pollution
studies -- including how pollutants react in the atmosphere
and how pollution spreads across the globe -- as well
as developing tools to monitor emissions for international
agreements, such as the Kyoto Protocol, on two SGI
Altix systems with heavy duty SGI storage support.
Dr. Jordan Kyriakidis is researching theoretical quantum
nano-electronics, with a long-term goal to develop
quantum materials as replacements for transistors
in computers and other electronics, using another
pair of SGI Altix systems linked to SGI RAID storage
via fiber optics.
Global Pollution Studies
No stranger to the power of SGI high performance computers,
Dr. Martin, a Research Associate at the Harvard-Smithsonian
Center for Astrophysics in addition to his role at
Dalhousie, previously assisted in the design of a
global numerical model at Harvard, GEOS-CHEM, which
is now used at a number of universities. A UNIX(R)
OS-based application originally developed on an SGI(R)
Origin(R) family system running SGI(R) IRIX(R) OS,
GEOS-CHEM uses simulated meteorological fields from
NASA and other models to divide the atmosphere into
a grid and solve for chemical composition. The application
was already in the process of being ported to a variety
of other platforms including 32-bit Linux(R) operating
system when Dr. Martin considered the Linux OS-based
SGI Altix for his work at Dalhousie. SGI technicians
easily ported GEOS-CHEM to the 64-bit Altix system.
Dr. Martin reported the SGI Altix system runs his
global atmospheric data sets at 3 to 4 times the speed
of computers he used at Harvard University a little
over two years ago.
To track global emissions, Dr. Martin receives satellite
data from NASA and the European Space Agency (ESA),
as well as data from aircraft and other sources. During
the summer of 2004, Dr. Martin completed his first
satellite retrieval using the two SGI(R) Altix(R)
350 systems, each with 16 Intel(R) Itanium(R) 2 processors,
linked via gigabit Ethernet to an SGI(R) InfiniteStorage
TP9100 with 3TB of RAID storage. Taking raw spectra
data of the earth's atmosphere and of the sun, he
assessed pollutant concentrations around the globe
and is now providing that data to NASA for analysis
as part of an integrated satellite aircraft campaign.
The campaign, called ICARTT, is designed to investigate
the outflow of pollution from North America into the
global atmosphere. The aircraft take samples of a
whole range of atmospheric constituents, including
aerosols and trace gasses -- some of which are toxic,
some greenhouse gasses.
"SGI Altix is much, much faster than anything
I've ever used before," said Dr. Martin, "probably
three to four times faster, which is just phenomenal.
Altix also enables us to run our simulations at higher
resolutions and therefore provide a more accurate
picture of the atmosphere, and it enables to us examine
results more quickly: in my work, time is of the essence.
It's important to have a fast computer; otherwise
we'd have to restrict what we could do, the type of
sensitivity studies we could perform, the resolution
at which features can be examined, and the number
of pollutants that we can put into our model."
Resolution currently runs at two degrees by two and
a half degrees (approximately several hundred kilometers)
on Dr. Martin's SGI Altix system running GEOS-CHEM
software. GEOS-CHEM divides the atmosphere up into
about a million boxes -- and within those boxes there
are roughly 30 to 35 layers in the atmosphere -- and
solves for all of those attributes, simultaneously,
every three hours.
"Thanks to the SGI Altix systems, we're contemplating
the possibility of running at one by one degree globally,
which is something we never would have even considered
beforehand, but I believe we can do it with the SGI
system," added Dr. Martin. "Understand:
one by one increases the number of 'boxes' by a factor
of five and in each of those boxes we have maybe 45
different pollutants that we advected (transported
from one box to the other, either vertically or horizontally)
around between boxes, so all of these numbers all
multiply and you can get a very large array of data
Not only can SGI Altix handle the one by one degree
calculations, said Dr, Martin, but, "Most importantly,
SGI InfiniteStorage TP9100 with 3 TB of RAID can expand
to support one by one resolution."
By using satellites to observe the abundance of pollutants
in the atmosphere, and combining the satellite data
and the models, Dr. Martin said he could infer what
the emissions from various countries had to have been.
He is expecting to develop techniques towards enforcing
protocols, such as the Kyoto Protocol, to monitor
emissions from various countries from space using
the SGI Altix 350 system running the GEOS-CHEM model.
Dr. Martin will also be investigating the use of the
GEM-AQ model, currently being developed in Canada,
to similarly examine surface air quality and climate
"SGI Altix offered the best price/performance
of any vendor," concluded Dr. Martin. "We
looked at IBM, Sun, and HP, but SGI had a much better
price/performance, and by price/performance I mean
relating to the number of computations it can do within
a shared memory framework and the RAM that could be
provided as well. Plus I'd had a lot of good experience
with SGI beforehand, on their Origin platform. SGI
has a strong history of shared memory systems and
that was important as well."
More information on Dr. Randall Martin's work can
be found on the Web at http://fizz.phys.dal.ca/~atmos/.
Exploring Quantum Nano-Electronics Theory on SGI Altix
Dr. Jordan Kyriakidis' work is taking him into uncharted
territory; as he points out, he is "a theorist,
not an experimentalist." His work revolves around
a simple fact: the world has relied on transistors
(which replaced vacuum tubes) for more than 40 years,
and while electronic devices grow ever smaller, there
has been no essential change in the original transistor.
Many scientists, especially in nanotechnology, feel
a replacement -- a new technology -- will soon be
needed. Dr. Kyriakidis uses his two 16-processor SGI
Altix 350 systems, with 54GB RAM and SGI Infinite
Storage TP9100, with one TB of storage, to work with
quantum dots -- "think of them as artificial
atoms" -- which can be designed and engineered
to have properties a scientist wants them to have,
i.e. artificial hydrogen, artificial helium, etc.
"Nanotechnology is a gigantic field and, within
that, the small piece that we're looking at is called
quantum nano-electronics," explained Dr. Kyriakidis.
"This field is relatively new but it's moving
very rapidly. The bottleneck in all of nanotechnology
is that we don't have any good way to control the
systems. We know we can do things -- place atoms one
at a time -- but we can't do it very well or very
quickly. And part of the issue that needs to be resolved
before the field can progress is, we have to find
new and innovative techniques that will enable us
to control these systems far beyond the current levels.
What I do is look at what kinds of controls we can
have on these systems, and how fine a level of control
can we have. We have a theory of how these artificial
atoms should behave and we use the SGI Altix systems
to do quantum simulations -- calculations to figure
out if they do actually have the properties that we
think they should have."
This is the first time Dr. Kyriakidis has done serious
research on SGI computers, and a high performance
Linux OS-based system was exactly what he was looking
for. "I've had lots of experience with Linux,"
he added. "We write a lot of our own software
because there is no generally accepted software: everything
is very bleeding edge. The fact that SGI has these
64-bit Altix machines, which are Linux OS with such
huge processing power in a very professional, high
performance grade of machine, was very attractive
to us because it meant we could start being productive
right away. We didn't have to spend time writing software
again on some specialized operating system."
In addition to 64-bit performance on SGI Altix, powerful
storage is essential for quantum simulations. "We
have a huge database that we need to store somewhere,"
explained Dr. Kyriakidis. "In a sense, we can't
handle the data that our software produces all in
one shot, so we have to store it somewhere and then
we have to go back and look through the data and see
what it's trying to tell us. The storage is an integral
part. We have a SGI TP9100 -- a big storage array
-- and it's connected via fiber optics to one of our
two Altix systems. With fiber optics from the processor,
we can really, very quickly write the data to the
hard drive, which is a collection of about 10 or 15
hard drives, and then read the data back again."
Dr. Kyriakidis chose SGI as a company, and Altix in
particular, because, "It represented the best
value in pure processing power, operating system and
storage requirements and price," he concluded.
"Combine all those things together and SGI Altix
far and away became the best option for us. And so
far, we've been bang-on in our decision; we're quite,
quite happy with it. Because we now have SGI Altix,
I'm able to do things that just were not possible
before. SGI Altix systems will clearly enable us to
move the science forward -- more forward than we've
ever been able to do before."
More information on Dr. Jordan Kyriakidis' work can
be found on the Web at http://soliton.phys.dal.ca/
Collaboration Key To Best SGI Solution
Both Dr. Martin and Dr. Kyriakidis applied for Canada
Foundation for Innovation (CFI) funding, through a
program called the New Opportunities Grant, for the
monies to acquire super-fast computers and storage
to further their research. Both received their funding
grants and -- in an unusual collaboration -- decided
to pool their money to get more together than they
would have individually.
"Dalhousie is Nova Scotia's leading research
university and our researchers and graduate students
have used SGI high-performance computer and visualization
systems for many years," said Dr. Carl Breckenridge,
vice-president of research at Dalhousie University.
"We're very pleased with this collaborative initiative
by these new researchers, which led to this acquisition
of state-of-the-art SGI Altix systems under the CFI
grant. We encourage our researchers to consider the
benefits of pooling funding when approaching companies
like SGI. It can give researchers great strategic
advantages. We look forward to the results of their
"SGI's cost-effective 64-bit Altix systems continue
to be of huge importance to atmosphere, weather, and
physics researchers around the world as the migration
to Linux continues among many disciplines in the scientific
community," said Martin Pinard, president of
SGI Canada. "Dalhousie University experienced
first-hand how easy it is to port code written in
SGI IRIX over to what is simply the highest performance
Linux OS-based computer system in the world: SGI Altix,
backed by the most solid and reliable storage in the
world, the SGI InfiniteStorage family."
Installed in early July 2004, the Dalhousie University
installation included four SGI Altix 350 systems with
16 processors in each system and two SGI InfiniteStorage
TP9100 systems -- one with 3 TB of storage, the other
with 1 TB storage -- plus assorted networking hardware
enabling a gigabit Ethernet connection in one department
and fiber optic connectivity in the other.
About Dalhousie University
Located in Halifax, Nova Scotia, Canada since 1818,
Dalhousie is one of Canada's leading universities.
It attracts more than $93 million dollars in research
awards and grants yearly. In 2003, The Scientist magazine
named Dalhousie the best place in the world to work,
outside the United States, as a scientific researcher.
For more information, please visit www.dal.ca.
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