Rice researcher Cindy Farach-Carson is working to understand why slow-growing prostate cancer turns aggressive after spreading to bone. She has identified over 220,000 genetic sequences that may play a role but needs more computing resources to analyze the large amount of data. Rice has significantly increased its shared supercomputing capacity in recent years through new grants and donations, totaling almost $13 million, in order to support researchers like Farach-Carson and remain competitive. An IBM donation will more than double Rice's computing capacity and also provide collaborators to help researchers solve complex problems.

1. Bumping
Up the
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B Y J A D E B OY D
Rice biologist Cindy Farach-Carson has a mystery on her hands. She
wants to know why slow-growing prostate cancer turns into a fast-grow-
ing killer after it moves into bone. It’s a genetic whodunit, and there’s no
shortage of suspects.
“We have 220,000 genetic sequences that we’ve identified as potential- member had to go it alone — winning grants to buy and maintain
ly playing a role, but we don’t know how they work or what they do,” their own computers.
said Farach-Carson, associate vice provost for research and professor Jan Odegard ’96, K2I executive director, said he meets with a
of biochemistry, cell biology and bioengineering. “We often joke that half-dozen prospective faculty candidates each year to discuss Rice’s
each of these is a thesis project for a graduate student, but I don’t shared research computing resources. “We never had these kinds of
have 220,000 graduate students. The reality is that I need computing meetings 10 years ago,” he said, “but today’s faculty candidates don’t
resources and trained people who can help develop algorithms that want to manage their own systems. The resources we have to offer
can mine this data and find new hypotheses.” can be the deciding factor in whether they come here or not.”
Farach-Carson is not alone. Researchers in laboratories the world By all measures, 2010 was a banner year for research computing
over are relying more than ever on high-performance computers. It’s at Rice. Faculty won two major federal awards for new supercomputers,
a trend that crosses scientific disciplines and presents challenges for and IBM donated a machine that doubled capacity in one fell swoop.
universities in hard economic times. But the seeds for that success date to 2002, when Rice landed a $1.2
Rice has more than 40 times the shared supercomputing capacity million federal grant for the Rice Terascale Cluster (RTC). When it came
it had just six years ago. And it is set to more than double that capac- online in early 2003, RTC made headlines as the fastest academic su-
ity in 2011 thanks to new grants and gifts totaling almost $13 million. percomputer in the state. But more importantly, RTC was the first su-
“These machines are expensive, but this is the way science percomputer that would be shared by researchers all over the campus.
is done today,” said Moshe Vardi, Rice’s Karen Ostrum George Two years later, when Kamran Khan arrived at Rice as vice pro-
Professor in Computational Engineering, professor of computer vost for information technology, RTC was pushing Rice’s on-campus
science and director of the Ken Kennedy Institute for Information data center to its limits. With a brand new federal grant for an even
Technology (K2I). “For example, let’s say you want to understand larger system in hand, something had to be done.
what happens when two galaxies collide. What experiment are you “One of Rice’s missions in the Vision for the Second Century is
going to do? You don’t have galaxies that you can collide. You use raising our research profile, and research computing is crucial for
computational experiments.” that,” Khan said. “For Rice to remain competitive, we needed a place
Even in instances where physical experiments are possible, they to house these computers, and we needed people to run them. It was
often are expensive and time-consuming. With increasingly realistic absolutely vital for the V2C, and with the support of the administration
simulation environments, researchers find it more efficient to run and the board of trustees, we obtained the necessary resources.”
thousands of virtual experiments on a computer, if only to narrow By mid-2007, Rice had completed the single largest technology
down the range of possibilities that must be explored by hand. upgrade in the university’s history. Virtually every building on cam-
While scientific computing has been around for decades, its pus was rewired for high-speed data networking, and Khan’s team
scope has changed dramatically in recent years. As recently as 2003, opened a new $16 million data center — with an enormous room
there were no shared supercomputing resources at Rice. Each faculty called Pod B that is dedicated solely to supercomputers.
38 www.rice.edu/ricemagazine Rice Magazine • No. 9 • 2011 39

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“For Rice to remain 000100111101100101001001110100100010001110011110001110001
competitive, we needed
a place to house these Heart of the Recipes for Complex Solving Multifold Not Enough Matter in
computers, and we Matter Problems Problems the Universe to Write
needed people to run Matteo Pasquali is no detective, Robotics and biology may sound Proteins self-assemble in a frac-
It Out
them. It was absolutely but he’s stalking America’s big- about as similar as oil and water, tion of the blink of an eye, but sim- When it comes to complicated
vital for the V2C, and gest killer. More than 5 million but it all depends on what you’re ulating even a simplified version puzzles, Rice chemist Gustavo
11101000101010001100110 with the support of the Americans have failing hearts,
and of the 30,000 that need trans-
trying to cook. of the process with a computer
can take weeks.
Scuseria has the mother of all
examples.
110000111100100011101000101010001100110 administration and the plants each year, only about 2,000 “An algorithm is like a recipe. It tells
01001100110000111100100011101000101010001100110
01000101010001100110 board of trustees, we receive them. you all the steps you have to take in
order to solve a problem,” said Lydia
“Protein folding is regarded as one of
the biggest unsolved problems in bio-
Put 216 hydrogen atoms in a cube,
squeeze them together with the force
obtained the necessary Pasquali, professor of chemical and Kavraki, the Noah Harding Professor physics,” said Jianpeng Ma, Rice pro- that exists inside a star and then solve
resources.” biomolecular engineering and of chem-
istry, is working with Professor Marek
of Computer Science and professor
of bioengineering. “The underlying
fessor of bioengineering and Lodwick
T. Bolin Professor in Biochemistry at
the equations for the quantum mechan-
ical “wave function” that will reveal the
Left to right: Kim Andrews, Jan Odegard, —Kamran Khan
algorithms that we use to solve prob- Baylor College of Medicine. “This is fate of their electrons.
Richard Talbot, Kamran Khan Behr from RWTH Aachen University in
lems in computational biology and a technically challenging task. Many “If you want to calculate the
Aachen, Germany, surgeons at the Texas
robotics are very similar.” groups around the world have compet- wave function, the equations exist
Heart Institute and Houston-based
For Kavraki’s group, the common ed for years to make the process faster — they’ve been known for 80 years,”
MicroMed Cardiovascular, Inc., to de-
factor is analysis of shape and mo- and more accurate.” said Scuseria, Rice’s Robert A. Welch
velop a new pump for an artificial heart.
tion. In biology, her team attempts Ma and Rice graduate student Professor of Chemistry and professor of
When legendary surgeon Michael
to decipher molecular function by Cheng Zhang pioneered a new method physics and astronomy, “but the num-
DeBakey asked Rice engineering re-
studying how molecules bend and for accurately simulating protein fold- ber of possible configurations is greater
searchers to help him design the world’s
flex. In robotics, the group plans the ing. In publishing their findings last year, than the number of neutrons, protons
first artificial heart 45 years ago, every-
moves a robot should make to com- they showed the method could deliver and electrons in the entire universe.
one envisioned a device that would beat
plete a task, which can range from unprecedented accuracy and speed in Even though the equation tells me I
like a natural heart. But Pasquali said ro-
removing a heavy jet engine from a simulating the folding of three relatively can compute the answer, there is not
tary pumps, which move blood continu-
tight space inside an airplane to exe- short but well-understood proteins. enough matter in the universe to write
ously, are simpler, cheaper and smaller.
cuting a common household chore. In Protein folding is a mystery that it out.”
“The flow is very complex, and
both robotics and biology, a key con- reaches to the heart of life science That’s the sort of conundrum that
the shape of the pump is complicated,”
sideration is the “state space” — the because proteins are the workhorses quantum chemists like Scuseria face
Pasquali said. “We have to resolve tiny
“We use more bandwidth in Pod B than the entire campus com- specifically interested in accelerating the delivery of enhanced treat- full range of shapes or positions that of biology. They’re the enzymes that daily. In theory, they have the tools to
features, and we have to follow the
bined times two,” said Kim Andrews ’92, manager of Rice’s research ment options and cures for complex disease processes.” a robot or molecule might take. The metabolize food, the building blocks of precisely describe how matter will be-
movements of the blood cells in very
computing group. Andrews and his team of five specialists not only Talbot said IBM has found that collaborative groups of clinicians, group’s specialty is creating novel bone and tissue, the signals transmit- have; in practice, they can investigate
small increments of time.”
keep Rice supercomputers running, they manage workflow to maxi- scientists and engineers are best suited for solving the sort of prob- search algorithms that can probe the ted between cells, and more. And when only simple examples.
For example, the rotors have to spin
mize usage and act as code consultants to streamline and optimize lem that Farach-Carson has with her bone cancer data. He said one “state space” to find motions that are they misfold, they become key players Since joining Rice in 1989,
at about 10,000 rpm, and the rotor blades
jobs. They even are working on a social media platform that Rice of IBM’s goals with Blue BioU is to help create the interdisciplinary feasible for a particular task or sat- in diseases like Alzheimer’s, cystic fi- Scuseria and his students have repeat-
don’t quite touch the sides of the pump.
graduate students can use to help share information about tackling teams that can solve those problems. isfy a set of biological conditions. brosis, emphysema and some cancers. edly pushed the envelope to bring ever
“In this small space between the edge of
tough research challenges. “Rice is getting more than just equipment,” Khan said of Blue For example, the group might Ma said that the previous state of larger and more complex molecules
the blade and the pump wall,” Pasquali
“I was a supercomputing user for many years before I ever got BioU. “Another of our V2C goals is fostering collaboration, and IBM create an algorithm that narrows the art was to run multiple copies of within reach of computational chem-
said, “the shear forces are capable of
into the administration side, so there’s a lot of empathy for the user,” has committed staff scientists and application engineers to helping us down the possible function of a a simulation in parallel on many com- istry. They’ve developed mathematical
damaging blood cells and platelets.”
Andrews said. “We always are looking for ways to make it easier for build collaborations within the TMC.” protein molecule, or they may cre- puters — an intensive and expensive tools and methods that have been in-
The researchers also need to make
people to do their research.” Khan said IBM’s decision to partner with Rice was partly due to ate one that finds the best way to approach. So he and Zhang created corporated into software that’s used in
certain the pump doesn’t jostle red
From 2004 to 2009, K2I helped Rice faculty win a stream of Rice’s proven success in research computing in recent years. inspect a building with one or more a single-copy approach that uses one hundreds of labs worldwide. Scuseria’s
blood cells so badly that they loose
robots. Like a chef refining a recipe, simulation to find the native folded efforts have attracted a number of in-
grants that paid for a new supercomputer every 20 months. These “Rice faculty members are second to none,” Khan said, “and Kim their grip on oxygen-carrying hemo-
the team employs supercomputers state of a protein. ternational honors, including the 2010
are shared by more than 400 researchers across campus, and thanks Andrews and his research computing support group have a level of globin molecules — a process called
to refine its algorithms. And with the Zhang and Ma first tested their Feynman Prize in theoretical nano-
to outstanding funding wins in 2010, Pod B is in the midst of a expertise that most institutions would envy.” hemolysis. Another even more complex
advent of shared computing at Rice, new approach on a Rice supercomputer technology — one of most prestigious
spring building boom. For example, most supercomputers run the Linux operating sys- problem to model is clot formation.
they’ve been able to tackle increas- called the Shared University Grid, or honors in nanotechnology.
The federal stimulus aided Rice faculty in winning a total of tem, and the highest certification a Linux systems administrator can re- Pasquali said the team’s early com-
ingly complex problems over the past SUG@R, and they are continuing the A prominent example of his nano-
$3.5 million from the National Science Foundation and the National ceive is the “architect” designation from Linux vendor Red Hat. “There puter models helped solve problems re-
seven years. work and simulating the folding of lon- technology research is a 2006 study
Institutes of Health for two new computing systems that are com- are only 250 certified Red Hat architects in the world,” Andrews said, lated to hemolysis, but Rice supercom-
“The training of our students has ger protein sequences on Rice’s new of graphene in which Scuseria’s team
ing online this spring. In addition, Khan and Vivek Sarkar, the E.D. “and we have three of them here at Rice.” puters are now powerful enough that
improved greatly because of what’s Blue BioU supercomputer. predicted the exact size and shape of
Butcher Chair in Engineering and professor of computer science, Like the BioScience Research Collaborative, the Blue BioU com- the team is ready to take on questions
available today,” Kavraki said. “Their “I can’t overstate the significance graphene nanoribbons that would be
spearheaded an effort to secure an IBM donation for Blue BioU, the puting platform is another tangible sign of Rice’s strengthening ties about clotting, which can be simulated
experience using shared systems at of state-of-the-art computing facili- needed for particular types of semicon-
most powerful supercomputer on campus. Valued at $9.4 million, Blue with the TMC. only with very large sets of equations.
Rice is easily translatable to other sys- ties,” Ma said. “These supercomputer ductor applications. The predications
BioU came online in spring 2010 and is notable in two respects: It was “When we go over to the medical center and talk to people about But this is just the beginning.
tems, including even larger machines resources continue to make Rice one proved correct and helped spur interest
the first computer system in the world to use IBM’s much-anticipated what they are most interested in at Rice, computational strength and “Right now we have to run each
at national laboratories. This is a great of the leading institutions in the field in graphene, which made the leap to
POWER7™ microprocessors, and it was designed to be used by re- computational research always top the list,” said Jim Coleman, vice model and infer how to improve the
value to our students.” of protein folding and computational worldwide prominence when its dis-
searchers throughout the Texas Medical Center (TMC). provost for research. “It’s almost impossible for medical institutions design,” Pasquali said. “If the computer
“Life sciences research is the major focus of this program,” said to build the kind of programs Rice has in engineering and computer could automatically change and evolve —Jade Boyd biophysics.” covery attracted the 2010 Nobel Prize
Richard Talbot ’79, IBM’s program director for Blue BioU. “We are science. They all would love to leverage that.” the shape on the fly, that would be a —Mike Williams in physics.
great tool.” —Jade Boyd
—Jade Boyd
40 www.rice.edu/ricemagazine Rice Magazine • No. 9 • 2011 41