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!

Penguin Computing Brings Cascade Lake-AP to OCP Form Factor

July 7, 2020

Penguin Computing, a subsidiary of SMART Global Holdings, Inc., is announcing a new Tundra server, Tundra AP, that is the first to implement the Intel Xeon Scalable 9200 series processors (codenamed Cascade Lake-AP) in t Read more…

By Tiffany Trader

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 t Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

HPCwire: Let's start with HLRS and work our way up to the European scale. HLRS has stood out in the HPC world for its support of both scientific and industrial research. Can you discuss key developments in recent years? Read more…

By Steve Conway, Hyperion

The Barcelona Supercomputing Center Offers a Virtual Tour of Its MareNostrum Supercomputer

July 6, 2020

With the COVID-19 pandemic continuing to threaten the world and disrupt normal operations, facility tours remain a little difficult to operate, with many supercomputing centers having shuttered facility tours for visitor Read more…

By Oliver Peckham

What’s New in Computing vs. COVID-19: Fugaku, Congress, De Novo Design & More

July 2, 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

AWS Solution Channel

Maxar Builds HPC on AWS to Deliver Forecasts 58% Faster Than Weather Supercomputer

When weather threatens drilling rigs, refineries, and other energy facilities, oil and gas companies want to move fast to protect personnel and equipment. And for firms that trade commodity shares in oil, precious metals, crops, and livestock, the weather can significantly impact their buy-sell decisions. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time last year, IBM announced open sourcing its Power instructio Read more…

By John Russell

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 fam Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

HPCwire: Let's start with HLRS and work our way up to the European scale. HLRS has stood out in the HPC world for its support of both scientific and industrial Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

ISC 2020 Keynote: Hope for the Future, Praise for Fugaku and HPC’s Pandemic Response

June 24, 2020

In stark contrast to past years Thomas Sterling’s ISC20 keynote today struck a more somber note with the COVID-19 pandemic as the central character in Sterling’s annual review of worldwide trends in HPC. Better known for his engaging manner and occasional willingness to poke prickly egos, Sterling instead strode through the numbing statistics associated... Read more…

By John Russell

ISC 2020’s Student Cluster Competition Winners Announced

June 24, 2020

Normally, the Student Cluster Competition involves teams of students building real computing clusters on the show floors of major supercomputer conferences and Read more…

By Oliver Peckham

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

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

Leading Solution Providers


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

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

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

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

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