Rick Stevens: Connecting Computing to Science

By Michael Feldman

March 9, 2007

Perhaps the two most important technologies of the 21st century will be information technology and biotechnology. Certainly they have become the most rapidly expanding domains of our era. The advancements in devices such as microarray biochips, medical imaging, and mass spectrometers have created a wealth of biological data to be analyzed. The result is that, increasingly, biological problems now require large scale computing. In a sense, life science has become a sub-domain of information science.

Expressions such as bioinformatics, computational biology and systems biology are being used to describe this new integration. And research organizations are actively exploring problems within the intersection of biology and computer science.

At the Department of Energy's (DOE) Argonne National Laboratory, the Computing and Life Sciences (CLS) directorate is attempting to synergize these two technologies to fulfill the department's mission. At Argonne, the integration of computational science with systems biology is designed to help build basic scientific knowledge, solve environmental problems related to energy production, and develop and manage new energy sources.

Heading the CLS directorate is Rick Stevens, a man who seems perfectly suited for the type of interdisciplinary work that the organization is doing. There, he is able to indulge his deep interests in algorithms, math and science, especially biological science.

As a scientist, Stevens is hard to categorize. In fact, he himself is not a great believer in distinct scientific disciplines. According to him, calling yourself a biologist, a chemist or a computer science is a just way people self-identify with a community. But these disciplines have become a rather artificial way to view the world. There are just people and problems, he says.

“I've always been interested in trying to connect computing to science,” says Stevens. “But I'm not that interested in computing for computing's sake.”

As a kid, Stevens was very much attracted to computing as it was portrayed on Star Trek. In the 23rd century, computers were things you used to do exciting things, like computing wormhole trajectories. In the 21st century, we'll have to be satisfied with sub-warp applications. But that still leaves plenty to do.

According to Stevens, putting biology and computing under the same lab directorate is a kind of experiment. By forging these cross-cultural relationships, they want to see if the sum is greater than the parts. Since Stevens is personally aligned with this intersection of computing and biology, to him the challenges are not only some of the most interesting problems in the world, but also are just great fun.

As one might imagine, the life of the head of an DOE lab directorate can be rather intense. It's not unusual for Stevens to be up at 5:00 AM.  At that ungodly hour, he tries to pound out a little code, which he mostly writes in C, Perl, Python or Mathematica. He says he's also learning a little UPC.

“If I spend a couple of hours in the morning writing code, I'm a much more cheerful person the rest of the day,” notes Stevens.

He spends the remainder of the day managing the lab: cheerleading the staff, working with the funding agencies, and planning the direction of the lab work. He tries to reserve some time for himself to reflect on the big picture and think about the future.

But when things get onerous at the lab, Stevens retreats to his other job — as a professor of computer science at the University of Chicago. There you'll find him working with his five PhD students. With one exception they are all working on projects in computational biology.

Stevens seems to get the most out of both his roles. He says Argonne is a great place to get things done. It's a very high energy, very focused environment, and the people are extremely supportive. “We think of it as a cross between a university and a start-up company,” he says. On the other hand, he also enjoys the teaching culture and more free-wheeling atmosphere of the university. There, he's able to wander off and follow his interests, wherever they take him.

But one of the big advantages of working for the DOE is the access to big iron. As one of the department's leadership computing centers, Argonne is on a select list to receive the latest cutting-edge supercomputers. It is expected to get a 100 teraflop IBM Blue Gene machine sometime this year. In 2008, the lab is looking to deploy a 500 teraflop system. Stevens says the lab is on a trajectory to get a sustained petaflop and even beyond.

High-end capability supercomputing systems for life sciences have traditionally focused on biochemical modeling at the level of atoms and molecules. But, according to Stevens, that misses the complexity of the organism and interactions of the ecosystem. Lately, he has become interested in applying petascale power to systems biology problems. For example, modeling microbial soil habitats is a vast computational undertaking, but promises to help us understand one of the most complex and important ecosystems on the planet.

Another promising use of petascale systems involves building models of cells that incorporate genetic information. This will allow scientists to predict a cell's response to different environment and substrates, and perform computational what-if questions to understand design tradeoffs in natural or man-made biological systems. For example, this type of application could be used to model highly efficient ethanol-producing microorganisms for different nutritional substrates.

“To understand the dynamics of how something works, you have to execute a simulation on a computer,” explains Stevens. “There's no other way to do it. So in many ways, doing theory in biology is going to be equivalent to doing these complex simulations. That's an insight that is just starting to hit lots of people.”

The computing power required to pursue some of these problems already exists today. As teraflop systems become available to more people, the opportunity for scientists to do interesting systems biology is exploding. While the hardware continues to become more accessible, building the models is the hard part.

“We don't have enough people with a background in computing and mathematics and, at the same time, with a background in biology, to actually wire these two things together,” he says. “Most bioinformatics programs are too superficial. Because of that we have a lack of models.”

The lack of expertise in computational biology may be holding back the field, but futurist and inventor Ray Kurzweil probably considers that problem just background noise. If there's anyone more bullish than Rick Stevens on the potential of computer science and biology, it's Kurzweil. His notion of “Singularity” is the predicted outcome of merging immense computational power with human beings, precipitating “a technological change so rapid and profound it represents a rupture in the fabric of human history.” Not surprisingly, Kurzweil's prediction of a transhumanist world draws its share of controversy.

“Ray has a hugely optimistic vision of where humanity could go,” says Stevens “What he's try to say is that the future could be so unbelievably cool that we should all want to get there. He's thinking in terms of exponentials and trying to understand the effects of extrapolation. The question is: How good are we at predicting the outcome of complex questions where there are underlying exponential drivers, like Moore's Law?”

“Is there merit to this view of the world?” continues Stevens. “Well, probably. It's been well understood that people have a hard time thinking in exponentials. This is a classical futurist viewpoint, whether it is understanding population increases, global warming, pollution or whatever. People are very bad at making predictions. They tend to over estimate in the near term and under estimate in the long term. What this means is that Ray could very well be correct that in 10 to 20 years, the convergence of these underlying technologies will enable many, many things to be different. Now, if he just simply said that, I don't think anyone would disagree.”

The fact is, Kurzweil is making a more precise prediction: achieving Singularity in 2045. According to Stevens, that's where he gets sort of quasi-theological. What Kurzweil is essentially arguing is that the technological juggernaut will take us to this brave new world regardless of the specific technologies in play. In other words, it's not a function of Moore's Law, network bandwidth, storage capacity, bioimaging technology, microarray chips or any number of rapidly growing technologies; it's the exponential rate of technology itself.

Stevens sums it up as follows: “To solve problems you need three things — time, money and ideas. If you have two, you can compensate for the other one. Kurzweil collapses time and money because of exponential processes. What's left are the ideas.”

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

D-Wave Delivers 5000-qubit System; Targets Quantum Advantage

September 29, 2020

D-Wave today launched its newest and largest quantum annealing computer, a 5000-qubit goliath named Advantage that features 15-way qubit interconnectivity. It also introduced the D-Wave Launch program intended to jump st Read more…

By John Russell

What’s New in Computing vs. COVID-19: AMD, Remdesivir, Fab Spending & More

September 29, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

Global QC Market Projected to Grow to More Than $800 million by 2024

September 28, 2020

The Quantum Economic Development Consortium (QED-C) and Hyperion Research are projecting that the global quantum computing (QC) market - worth an estimated $320 million in 2020 - will grow at an anticipated 27% CAGR betw Read more…

By Staff Reports

DoE’s ASCAC Backs AI for Science Program that Emulates the Exascale Initiative

September 28, 2020

Roughly a year after beginning formal efforts to explore an AI for Science initiative the Department of Energy’s Advanced Scientific Computing Advisory Committee last week accepted a subcommittee report calling for a t Read more…

By John Russell

Supercomputer Research Aims to Supercharge COVID-19 Antiviral Remdesivir

September 25, 2020

Remdesivir is one of a handful of therapeutic antiviral drugs that have been proven to improve outcomes for COVID-19 patients, and as such, is a crucial weapon in the fight against the pandemic – especially in the abse Read more…

By Oliver Peckham

AWS Solution Channel

The Water Institute of the Gulf runs compute-heavy storm surge and wave simulations on AWS

The Water Institute of the Gulf (Water Institute) runs its storm surge and wave analysis models on Amazon Web Services (AWS)—a task that sometimes requires large bursts of compute power. Read more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

NOAA Announces Major Upgrade to Ensemble Forecast Model, Extends Range to 35 Days

September 23, 2020

A bit over a year ago, the United States’ Global Forecast System (GFS) received a major upgrade: a new dynamical core – its first in 40 years – called the finite-volume cubed-sphere, or FV3. Now, the National Oceanic and Atmospheric Administration (NOAA) is bringing the FV3 dynamical core to... Read more…

By Oliver Peckham

D-Wave Delivers 5000-qubit System; Targets Quantum Advantage

September 29, 2020

D-Wave today launched its newest and largest quantum annealing computer, a 5000-qubit goliath named Advantage that features 15-way qubit interconnectivity. It a Read more…

By John Russell

DoE’s ASCAC Backs AI for Science Program that Emulates the Exascale Initiative

September 28, 2020

Roughly a year after beginning formal efforts to explore an AI for Science initiative the Department of Energy’s Advanced Scientific Computing Advisory Commit Read more…

By John Russell

NOAA Announces Major Upgrade to Ensemble Forecast Model, Extends Range to 35 Days

September 23, 2020

A bit over a year ago, the United States’ Global Forecast System (GFS) received a major upgrade: a new dynamical core – its first in 40 years – called the finite-volume cubed-sphere, or FV3. Now, the National Oceanic and Atmospheric Administration (NOAA) is bringing the FV3 dynamical core to... Read more…

By Oliver Peckham

Arm Targets HPC with New Neoverse Platforms

September 22, 2020

UK-based semiconductor design company Arm today teased details of its Neoverse roadmap, introducing V1 (codenamed Zeus) and N2 (codenamed Perseus), Arm’s second generation N-series platform. The chip IP vendor said the new platforms will deliver 50 percent and 40 percent more... Read more…

By Tiffany Trader

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availabilit Read more…

By John Russell

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

Future of Fintech on Display at HPC + AI Wall Street

September 17, 2020

Those who tuned in for Tuesday's HPC + AI Wall Street event got a peak at the future of fintech and lively discussion of topics like blockchain, AI for risk man Read more…

By Alex Woodie, Tiffany Trader and Todd R. Weiss

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Leading Solution Providers

Contributors

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Japan’s Fugaku Tops Global Supercomputing Rankings

June 22, 2020

A new Top500 champ was unveiled today. Supercomputer Fugaku, the pride of Japan and the namesake of Mount Fuji, vaulted to the top of the 55th edition of the To Read more…

By Tiffany Trader

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

Intel Speeds NAMD by 1.8x: Saves Xeon Processor Users Millions of Compute Hours

August 12, 2020

Potentially saving datacenters millions of CPU node hours, Intel and the University of Illinois at Urbana–Champaign (UIUC) have collaborated to develop AVX-512 optimizations for the NAMD scalable molecular dynamics code. These optimizations will be incorporated into release 2.15 with patches available for earlier versions. Read more…

By Rob Farber

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This