A new IBM supercomputer opened at Brown University’s Center for Computation and Visualization in Providence, RI, today is 50 times faster than Brown’s next best machine and is the most powerful computer in Rhode Island, according to an announcement from IBM (NYSE: IBM). Researchers at Brown and other institutions intend to use the 1,440-processor machine to model subjects such as the genomes of ocean-going microbes, the mechanics of human and animal movement, and the topography of other planets. Brown ordered the multimillion-dollar supercomputer in June; its exact cost hasn’t been disclosed, but IBM and Brown are calling it “a shared investment.”

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Well, we can’t all be Amazon. While the Seattle-based e-commerce giant (NASDAQ: AMZN) raked in a $199 million profit for the third quarter of 2009—a 68 percent increase in net income over the same period last year—Microsoft (NASDAQ: MSFT) posted an 18 percent decline in its profits (still $3.57 billion, better than analysts expected).

But beyond these giants of the global tech scene, Seattle has some mid-market public tech companies that we’ve been paying closer attention to lately. That’s because they provide a much more complete picture of what’s going on in the public markets, as well as the mood across different industries like digital media, data storage, and high-performance computing.

Of these local bellwethers, two companies announced modest quarterly profits this week, and two others posted losses but are on the long-term comeback trail. It’s clearly still tough times out there, but here are the highlights:

—RealNetworks (NASDAQ: RNWK), the Seattle digital media and entertainment company, managed to post a surprising profit of $1.5 million for the third quarter of 2009, its first profitable quarter since the first three months of 2008. That’s despite posting quarterly revenue of $140.3 million, a decrease of 8 percent from $152 million in the same period last year (when the company posted a net loss of $4.5 million). RealNetworks reduced its operating costs and formed partnerships with Facebook and Apple over the past few months.

—Cray (NASDAQ: CRAY), the Seattle-based supercomputing company, reported a net loss of $2.1 million for the third quarter. But its revenue was $58.6 million, a 7 percent increase over the same period in 2008. In the second quarter of this year, Cray posted a surprise profit of $3.4 million on the strength of large government contracts and a broader customer base.

—InfoSpace (NASDAQ: INSP), the meta-search company based in Bellevue, WA, posted a profit for the second straight quarter (following three consecutive quarterly losses). Its net income for the third quarter was $1.8 million, based on revenue of $54.4 million, an increase of 38 percent over its revenue from the same period a year ago.

—Isilon Systems (NASDAQ: ISLN), the Seattle-based data storage firm, reported a net loss of $4.9 million for the quarter. The company’s quarterly revenue was $30.5 million, up 1 percent over the same period a year ago, but its net loss increased from $3.7 million in the previous quarter this year. I wrote about nine-year-old Isilon’s efforts to bounce back from some tough times in a profile last week.

On October’s last trading day, the stock market plunged. As Scott E. Marcouiller, a senior equity market strategist at Wells Fargo Advisors in St. Louis, told the New York Times today, “The market is focusing on the glass is half empty…We just needed to let some of the air out of the balloon.”

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How do you go about summarizing a company’s culture in one word? I haven’t a clue, but whenever I ask CEOs, they always come up with something interesting—and often surprising. In the past couple of months, I’ve been asking top executives at Northwest tech startups to talk about their company culture and why it’s unique. So far, none has refused to play the “one word” game.

I’ve received a fascinating array of responses that speak to the companies’ management styles, the kinds of talent they’re looking for, and their overall strategy—what they think sets them apart from their competition. From Bellevue, WA-based Apptio’s “paranoid” to Seattle-based Picnik’s “easy,” you can see a lot of a company’s mindset through the keyhole of just one word. And last month, Bob did a comparison of Boston vs. Seattle one-word cultures—and found that the New England startups were a little more New-Agey in their responses than companies here in the Northwest. (No idea what this means, but it’s always fun to go up against the East Coast.) And Bruce followed that up by checking in with five San Diego firms.

Now I’m extending the exercise to Seattle’s public tech companies. I wondered whether their responses would show any glaring differences from the startups—more conventional, say, or boring. After checking with a few of them (each has been around for six years or longer), my scientific answer is “not really.”

Our initial short list of public companies spans the fields of supercomputing, data storage, and online advertising. Be warned, Mr. Ballmer, Mr. Bezos, and Mr. Glaser—I’m coming for you too.

Cray (NASDAQ: CRAY)
CEO: Peter Ungaro
Culture: “Next”
Comments: Ungaro says, “Never satisfied with the status quo, our employees are committed to providing our customers with the next-generation of Cray supercomputers. Collectively as a company, our passion is setting new boundaries of what supercomputers are capable of and providing those resources to the world’s researchers and engineers.” He adds, “We celebrate achievements and acknowledge milestones, but we are focused on what’s next and what we all have to do to get there.”

Isilon Systems (NASDAQ: ISLN)
CEO: Sujal Patel
Culture: “Driven”
Comments: Patel says, “We have been through a million different things that show how driven we are. We survived…we grew, we built, we went public, we ran into some nasty roadblocks, we recovered from that.” He adds, “We only get through that stuff because we are driven as an organization—and that’s not about me, it’s about the people in this building.”

Marchex (NASDAQ: MCHX)
COO: Peter Christothoulou
Culture: “Innovative”
Comments: Christothoulou says, “Being innovative is at the core of everything we do; from delivering the most innovative products and technology, to hiring and employing innovative, collaborative people to provide our customers with the best experience possible.”

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When California Gov. Gray Davis created the California Institute for Telecommunications and Information Technology in 2000, it was part of a broad state initiative that spawned four new centers for science and innovation with a shared mission “to invent the future.” The specific mission for the institute known as Calit2 (Cal IT²), which is based at UC San Diego and UC Irvine, was to “radically expand the capacities of communications and information infrastructures.”

In the nine years that he has served as Calit2’s director, Larry Smarr has done all that and more. He describes the institute as a “collaboration framework” that enables researchers throughout the University of California to take a multi-disciplinary and systems-based approach to complex problems. As a result, Smarr says Calit2 has engaged hundreds of UC researchers, formed affiliations with over 300 federal agencies, and worked with more than 200 industry partners. “I have to say we’re pleased with the progress we’ve made,” he says. (Smarr talks about the origins of the Internet in Part 1 of my story here.)

But Smarr also is looking at the path forward. He tells me he’s spent the past six months “on a vision quest” to identify the large societal challenges that he anticipates the next decade will bring. And if there is a thread that runs through his vision, it is to harness the power of Calit2’s expanding resources—“to build across the successes that we’ve had”—to tackle four over-arching problems of the next decade. These are Smarr’s big ideas for what he calls the digital transformation of healthcare, energy, the environment, and of our culture itself:

—Healthcare. Smarr sees healthcare moving increasingly to “a prevention and wellness model” that relies on innovations in the emerging field of “wireless health” technologies and the digital transformation of medical care. In our conversation, Smarr compares the way it will work to an automobile maintenance schedule:

“I just bought a new car, a hybrid,” Smarr says. “It has 30 computers in it. It probably has another 60 or 70 sensors, actuators, and memory chips. So my car will easily run …Next Page »

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Seattle-based Cray, the supercomputing company, announced today it has signed a multi-year contract with the Korea Meteorological Administration worth more than $40 million. Cray (NASDAQ: CRAY) will deliver a next-generation supercomputer (capable of more than 600 trillion calculations per second), as well as service and support, to the Seoul-based weather forecasting and climate research organization. Delivery and acceptance of the supercomputer are expected in 2010.

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Seattle-based Cray (NASDAQ: CRAY), the supercomputing company, announced late last week it has acquired the PathScale Compiler Suite assets from Maynard, MA-based SiCortex. Financial details were not released. SiCortex shut down in May. The purchase could help Cray improve its own compiler technology, as well as give PathScale customers a way to move forward on Cray supercomputers.

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In the past week, companies have been releasing their financial results for the second quarter. There’s a mix of good and bad news from Seattle’s public tech companies weathering the economic storm, with surprisingly positive news from some quarters.

—Bellevue, WA-based metasearch developer InfoSpace announced its revenue was $43.8 million for the quarter, up 14 percent from the same period last year. InfoSpace (NASDAQ: INSP) now has $208.3 million in cash and securities. This was better than analysts had expected from InfoSpace, which has undergone some significant growth recently, including a new charity search website Xconomy previously wrote about.

—Good news was also reported by Seattle-based supercomputer manufacturer Cray (NASDAQ: CRAY), which turned a profit with $62.7 million in revenue last quarter, up 34 percent from the same period last year. Cray’s success has a lot to do with recent, lucrative contracts the company has landed. Xconomy recently profiled Cray here.

—Things were less positive for Seattle-based digital media company RealNetworks (NASDAQ: RNWK), which reported $135.7 million in second-quarter revenue, an 11 percent decrease from last year. For this quarter, RealNetworks had a net loss of $188.3 million. The company said it hopes to show some improvement for the second half of the year.

—Online diamond retailer Blue Nile (NASDAQ: NILE) also reported a slight decrease in revenue. The Seattle-based company posted net sales of $69.9 million, a decrease of 5.2 percent from the same period last year, although sales are continuing to increase slightly from year-to-year for the company.

—Slightly more cheerful news was posted by embedded device software developer Bsquare (NASDAQ: BSQR). The Bellevue, WA-based company earned $16.1 million in revenue, up 5 percent from the second quarter of 2008. The company announced last month it will start working with Coca-Cola to create the Coca-Cola Freestyle software-driven fountain dispenser.

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Seattle-based supercomputing company Cray (NASDAQ: CRAY) surprised analysts this morning by turning a modest profit in the second quarter, and was rewarded with a 12 percent bump in its stock price today.

Cray said today its revenues for the quarter ($62.7 million) increased by 34 percent compared with the same period last year ($46.7 million). That sales performance was enough to lift Cray to a profit of $3.4 million, compared with a $6.4 million loss it reported in the same period a year ago. This translated to a 10 cent per share profit in the quarter, which handily beat the consensus expectation of analysts, who forecasted a break-even quarter, according to First Call.

It has been a long road back for Cray, as I reported last week in an in-depth profile of the company. CEO Peter Ungaro told me Cray has become debt-free as of this spring (it had been saddled with $80 million of liabilities), and has been boosting its revenues through an aggressive three-pronged business strategy: selling high-end supercomputers to national laboratories, performing custom engineering and services, and selling lower-end machines to corporate customers through partnerships with companies like Microsoft and Intel. This strategy has been paying off handsomely, as the company announced several new contracts as part of its quarterly report—and this puts the company on sound enough footing to be profitable for the full year in 2009 and beyond.

Last month, Cray was awarded a multi-year contract with the Department of Energy’s National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory. The contract, worth more than $50 million, includes the delivery of a Cray XT5 supercomputer, which will be upgraded to a future-generation Cray machine. And just this week, Cray received a contract to upgrade its “Jaguar” machine at Oak Ridge National Laboratory. Jaguar, which runs scientific applications at a rate of more than one petaflop (quadrillion mathematical calculations per second), will be upgraded to exceed two petaflops, which would make it the world’s most powerful supercomputer. The upgrade is expected to be installed by the end of this year.

“We’ve made tremendous progress on some of our new initiatives, expanding our product and service offerings to further solidify our leadership position in the industry,” Ungaro said in a statement. He added that Cray is delivering its supercomputing technology to a “broader set of customers,” and cited “over $70 million in new wins in just the last week.”

Cray has about 850 employees, 160 in the Seattle office. The company also has large facilities in Minnesota and Wisconsin, its original birthplace. (Cray Research was founded in 1972 by the renowned engineer Seymour Cray.) Its main competitors in supercomputing include IBM, Hewlett-Packard, Silicon Graphics, Hitachi, and NEC.

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Where I grew up in the Midwest in the 1970s and early 80s, Cray was synonymous with supercomputing. Back then, a supercomputer was a top-flight machine that could perform a few hundred million floating point operations per second (”flops”). That was good enough to help scientists do intensive calculations in areas like weather forecasting, climate modeling, and nuclear weapons simulations. Cray’s first supercomputer, the famed Cray-1, was bought by Los Alamos National Laboratory for $8.8 million in 1976; eventually, some 80 of the machines were sold, for $5 million to $8 million a pop.

Today, your average desktop computer is far more powerful than a Cray-1, and so the definition of “supercomputer” keeps changing to keep up with the times. But one thing has not changed. Cray (NASDAQ: CRAY) is still a major player in the space, despite a long history of ups and downs. The company, which began in 1972 as Cray Research in Chippewa Falls, WI, was bought by Silicon Graphics in 1996 for $767 million, and then was reborn in Seattle in 2000 following a $50 million merger with Tera Computer (which was renamed Cray). Since then, it has been a long uphill climb to get back near the top of the supercomputing heap against heavyweight competitors like IBM and Hewlett-Packard.

Nobody better to tell that story than Peter Ungaro, the chief executive of Cray. I recently had a chance to speak with Ungaro by phone at his Spokane, WA, office about his company’s strategy and recent history, the technical challenges involved in modern supercomputing, and innovative ways of gaining new customers (how do you sell someone a $10 million machine?). What impressed me was his ability to lay out the financial concerns of his company while also diving deep into the technological aspects of supercomputers—how they will interact with cloud computing, how computational records will continue to be broken, and when computers might exceed all processing capabilities of the human brain.

First off, I wanted to know how Ungaro (left) defines a “supercomputer” these days. Some would say it should be one of the 500 fastest machines in the world. Others would say it’s a machine used for scientific and technical problems that costs more than a certain amount. Ungaro’s definition is simple and focuses on the bottom line. “We like to think of supercomputers as costing more than a million dollars,” he says.

Ungaro, a Washington State University alum, joined Cray in 2003 to run sales and marketing as senior vice president. He had been at IBM for 13 years, most recently running its high performance computing group, a $2 billion business inside Big Blue. Why did he make the jump to Cray? “I really loved the supercomputing space,” Ungaro says. “Customers are doing really interesting things. I really wanted to try and see what a smaller company was like. Even at $2 billion, you’re only 2 percent of IBM’s revenues.” In short, like many entrepreneurs, he wanted to have more impact. “There was no better place to go than Cray. It was a natural move.”

But Cray had its share of problems. The company had struggled to get its next-generation supercomputer product ready, and 2004 was “really rough,” Ungaro says. Cray was losing money and …Next Page »

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Civic leaders, economic visionaries, and passionate residents often claim that their city is the next to rebound. I say with confidence that my city is next in line for metamorphosis. Some find their new meaning through the arts and other organic movements, but in most recent accounts, it seems, a few deserving cities are staged for a comeback with the help of high-tech industry. Holyoke, Massachusetts, is one of these cities.

Last week, it was announced that the Massachusetts Institute of Technology, University of Massachusetts, and Boston University would be collaborating with Fortune 500 technology giants Cisco Systems and EMC and the Commonwealth of Massachusetts to build a high-performance computing center (HPCC) in the city of Holyoke.

I got involved in the early stages of this effort back in October of 2008, when I was invited to a Technology Roundtable at MIT. It was surreal finding myself, a young web entrepreneur, talking with and having breakfast at the same table as Governor Patrick, MIT president Dr. Susan Hockfield, Cisco’s John Chambers, and various other leaders and innovators in the world of business and technology. Major topics included the future of the tech industry in Massachusetts, its impact on the state economy, and support of entrepreneurship. When the conversation moved in my direction, I was encouraged to share my thoughts and suggest various underutilized opportunities I saw as a young entrepreneur living and working in the western part of the state. I made what I hoped were persuasive statements for my city, advocating that it would be the premier location for sustainable, cost-effective, large-scale data centers. By the look on everyone’s faces, it was clear that Holyoke had been on their radar for such a project.

Western Massachusetts has many valuable resources that would make it an appealing and economically advantageous destination for the tech industry. But what firmly stands out in this region is the small city of Holyoke and its abundance of power—specifically, cheap, renewable hydro-electric power. The city receives approximately three-quarters of its energy from its hydro-electric sources, which include an expansive dam and turbines located along canals powered by water diverted from the Connecticut River. The municipality-owned utility company also announced recently that it would be acquiring hundreds of acres of land on a nearby mountain range to develop a high-capacity wind farm. In regards to technology, Holyoke already has an extensive high-speed fiber optic network throughout its downtown and is located along the Mass Information Turnpike backbone.

It is likely that Holyoke’s new computing and data center will be modeled after Google’s “Project 02″ in The Dalles, OR, and its data-center in Baudour, Belgium. Water from the river or industrial canals will be used to cool the servers and ensure that the hardware runs efficiently.

When it was founded in the mid-19th century, Holyoke was one of the first cities planned for industry—and it promoted its plentiful supply of inexpensive energy and labor to lure manufacturing businesses and investors. It became the center of the global paper industry and spurred tremendous amounts of wealth, laying claim to being the richest city per-capita in the United States by the 1920s. At the city’s prime, Holyoke’s cultural offerings were compared to those of New York City and Paris. After the Great Depression and general de-industrialization that struck the Northeast, Holyoke slowly began to lose its prosperity, businesses, jobs, population, and reputation. For as long as I can remember in my 21 years of existence, the city has been in rough shape. People often blame the city’s reputation as what’s repelling business—but real innovators, entrepreneurs, and “urbanists” see past that image and recognize this diamond in the rough. The raw, undisputed assets stare you straight in the face—and, finally, the right people are staring back. This new computing collaboration will be an anchor, attracting entrepreneurs and young minds eager for involvement in something of great magnitude.

As this high-profile project moves forward, I’d expect many eyes from the technology sector to be fixated on Holyoke. There is still over two-million square feet of vacant building space, consisting mostly of red-brick factory structures ready to be reclaimed by the high-tech community at bargain prices. Is there a chance that a company like Google might look at Holyoke for its next data-center in the Northeast? I believe it’s very likely.

I’m optimistic about what the future holds for the city of Holyoke. High tech offers the much-needed flow of capital, job creation, and stimulus that post-industrial cities like Holyoke desperately thirst for. With the escalating focus on green industry, sustainability, and long-term cost factors, Holyoke is a premier location for the Northeast IT sector. The beloved Queen of Industrial Cities as it was called at turn of the century, fell off her throne many decades ago, but is now back with a new purpose. Thanks to the forward-thinking powers at hand, Holyoke will be given a new identity as a coveted destination for high tech.

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Updated with additional detail June 9, 8:10 pm; further update and a correction added June 10, 7:15 am—see below

A university, industry, and Massachusetts government coalition is set to announce a major initiative in high performance computing later this week, Xconomy has learned. Official sources are guarded, and specifics were hard to come by tonight. But a new center for high performance computing is apparently being planned for Holyoke, MA. A public event is planned for Thursday, with representatives of the state of Massachusetts, MIT, EMC, and a variety of others due to be on hand, according to our sources.

This paragraph added, June 9, 8:10 pm: The presidents of the University of Massachusetts and MIT, as well as leading executives of Cisco, are also involved with the effort, we have learned. And a centerpiece of the announcement is the creation of a data center that will bring jobs to Holyoke, an economically depressed region, our sources say.

Kofi Jones, director of Communications and External Affairs for the state Executive Office of Housing and Economic Development, confirmed that an announcement on high performance computing was scheduled for Thursday at Mt. Holyoke, but did not provide further details by the time of this post. We could not determine whether federal funding is part of the arrangement.

The new computing center is also intended to blaze trails in so-called “green” computing, according to our sources. This usually refers to getting more performance per kilowatt of electricity from computing systems. High performance computing systems are notorious energy hogs.

This section added, June 9, 8:10 pm: “It’s a big data center. What they’re trying to do is bring to Massachusetts companies like Google and Microsoft,” said a source, whom we promised not to identify. The source referenced the large data center operated by Google along the Columbia River in Oregon. “They’re trying to replicate this, I think, in Holyoke.” Holyoke is built on the banks of the Connecticut River.

A vigorous job training program is also part of the effort, our source said.

Update, June 10: An article this morning in the Boston Globe, which had apparently arranged with state officials to have an exclusive on this story before our article came out, confirms the basics of our report, but adds more details. It says the effort is expected to cost roughly $100 million, that it will seek federal stimulus funding, and that it will be managed by a collaborative led by MIT and the University of Massachusetts, with participation from EMC and Cisco. “At this stage, the partners have only agreed to participate in an intensive 120-day planning project that’s intended to work out details such as siting, organization, and funding,” the Globe says. “But the backers say the computer center will create an important resource for the state’s high-tech industry and academic institutions.”

Correction: A reference to Mt. Holyoke College in our original post was deleted as it became clear the center is being planned for the city of Holyoke and not the college as one source had seemed to indicate.

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SiCortex, a six-year-old startup building energy-efficient supercomputers in Maynard, MA, has shut its doors. The company ran out of working capital and was unable to raise more from its venture investors, according to a report that surfaced yesterday in HPC Wire, a trade publication in the high-performance computing industry.

Xconomy obtained confirmation of the shutdown news from John Mucci, the founding CEO of SiCortex, who was replaced 10 months ago by current CEO Christopher Stone. Stone himself was not immediately available for comment.

“It is a sad day for all… less competition, unemployed seventy some workers…” Mucci said in an e-mail.

SiCortex had raised $42 million in venture capital, including a $21 million Series A round in 2004 contributed by lead investor Polaris Venture Partners and syndicate members Flagship Ventures, JK&B Capital, and Prism Venture Partners. All of those investors returned for the company’s $21 million Series B round in 2006, with the addition of new lead investor Chevron Technology Ventures. Bob Metcalfe, a Polaris partner frequently quoted about SiCortex in the past, said this morning he had no comment about the shutdown.

According to the HPC Wire report, which was based on information from an anonymous source close to the company, most of the company’s employees have been let go, and a sale of the company’s assets is underway.

SiCortex had been in the process of raising additional working capital; according to documents filed with the Securities and Exchange Commission on May 13, it planned to sell $1.1 million in subordinated convertible promissory notes. It’s not known whether that debt fundraising was completed.

SiCortex had developed a line of large, multiprocessor, parallel computers that saved electricity by using somewhat slower processors, but made up the speed difference using an advanced internal communications network for shuttling data between processors. The company targeted customers doing technical computing work in areas such as geological exploration, climate simulation, and intelligence. Sales were apparently brisk; the company had announced record growth in the first quarter of 2009. The Royal Military College of Canada was one recently announced customer.

SiCortex had also been emerging as a leader in the field of “green” high-performance computing. Last November it introduced the “Green Computing Index,” a list that ranked the world’s largest supercomputers not according to their sheer speed but according to their power efficiency (expressed in billions of floating point operations per second per kilowatt consumed).

We expect to obtain further details about the shutdown later today.

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The most powerful computer in Washington state goes by the name of Chinook, and stands along the banks of the Columbia River. It is being used for thorny computing tasks like modeling ways to more efficiently store hydrogen for fuel cells, and how to safely sequester carbon dioxide residue underground.

This morning, I heard an overview of what this machine does from Moe Khaleel of the Pacific Northwest National Laboratory in Richland, WA, as part of the Technology Alliance’s monthly Discovery Series talks. The lab is known for studying nuclear contamination at the nearby Hanford site from the Manhattan Project, but today it likes to tell stories about all the non-military things it’s working on. The lab has 4,200 employees and an $850 million annual budget, so there’s certainly a lot of potential to get things done.

The Chinook machine was built by Hewlett Packard, with design help from the national lab, Khaleel said. It’s not the world’s most powerful machine—that title belongs to the roughly 1,000-teraflop RoadRunner at Los Alamos National Laboratory in New Mexico, while Chinook weighs in at about 160 teraflops, Khaleel says. But Chinook could achieve bigger things if pooled with resources just a few hours down the road at Washington State University in Pullman, and at the University of Washington in Seattle, he said.

Khaleel didn’t get too specific in his talk about what this machine is really being used for, other than national security, cybersecurity, and biology. One interesting part of the talk was the challenge in managing such a demanding piece of equipment. The thing draws enough juice to run up a $1 million a year electricity bill, with about one-third of that needed to keep it cool and the rest going to actual computing power, he said. Like most supercomputers, it’s quite inefficient, too, with 40 percent of the energy lost through conversion from AC current to DC current, he said.

“People tend to worry a lot about the upfront cost, but they forget about the operational cost,” he said.

These days the lab is trying to think of ways to make this system more “green,” Khaleel said. Scientists there are thinking of how best to capture the heat thrown off from the machine to help keep the rest of the building warm in winter. However, he said, “If it’s a cold winter, and the machine’s not running, folks could be in trouble.”

Not everyone in the audience was enamored with the idea of investing gobs more taxpayer money in supercomputers. Linden Rhoads, the University of Washington’s vice provost for technology transfer, asked Khaleel whether it might be a better idea to make an appeal to citizens to let scientists tap into the power of their millions of desktops around the country during off-peak hours. Khaleel pooh-poohed the idea, saying it would take too long to get the calculations done because improvements need to be made in virtualization technology to organize the data. (When I asked Rhoads afterwards if she bought that answer, she shook her head, saying maybe the country should then invest more in virtualization to tap into all those desktop computing resources.)

“If you asked people to contribute their computers to do this, they’d do it,” Rhoads said.

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There’s a small company in downtown Seattle called 3Tier Group that has a goal of no less than “Remapping the World” for alternative energy. T. Boone Pickens, the billionaire Texas oilman, is such a big fan, he used 3Tier’s maps to draw a bold conclusion-that the United States has the potential to be “the Saudi Arabia of Wind.”

3Tier might sound a little New-Agey in its goals, maybe a little pie-in-the-sky in a world where Exxon Mobil has enough money in the bank ($36.7 billion on Sept. 30) to bury all U.S. cleantech startups. So I decided to check it out personally, meeting with Kenneth Westrick, the founder and CEO, at his 21st floor offices in the Westin Building in downtown Seattle. Westrick, an atmospheric scientist with a master’s from the University of Washington, greeted me with a boisterous handshake. He was wearing a long brown leather jacket like the one worn by Jimmy McNulty, the protagonist of HBO’s “The Wire.” (One of my all-time favorite shows.)

When we sat down in a conference room looking out over South Lake Union, I asked what he really meant with his “Remapping the World” initiative. It’s about using high-powered computers to crunch data that helps developers, financiers, and governments decide where the best places are to put a wind farm, solar panels, or hydropower turbines. This isn’t nearly as easy as it sounds, because wind ebbs and flows at different times of day, different seasons of the year. Some years are El Nino, some La Nina. Measurement instruments at Sea-Tac airport don’t always capture wind speed at the corner of 1st Avenue and Pike Street. Same goes for solar, and hydro.

That’s a lot of variables to account for, especially if you’re General Electric and looking to invest $300 million in a wind farm that’s supposed to pay off over two or three decades. So 3Tier inhales huge amounts of climate data into its computers, and analyzes it in models to come up with an accurate forecast of what kind of power a particular wind farm is going to produce over time. It can also take measurements at a site over a year’s time, and crunch numbers that may spot a better site a few miles away from one the developer originally scoped out, Westrick says.

“The greatest risk is in the availability of fuel,” Westrick says. “We can create a map of where the wind blows. We can ask where is it abundant? Will it be abundant when we need it?” He added later, “Only a couple of companies can do this.”

Westrick started this company in 1999 in his bedroom. It has grown to about 70 employees. About one-third were trained in earth sciences, one-third are software programmers, and the rest in are in administration, support and business development, he says. 3Tier doesn’t disclose its financials as a private company, but he says the company has boosted sales growth by more than …Next Page »

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There’s no such thing as a free flop.

A “flop,” or floating-point operation, is a calculation involving a decimal number; engineers often measure the performance of computers in terms of the number of “gigaflop/s” (billions of floating-point operations per second) they can sustain. In the supercomputing community, it’s a longstanding ritual to compare various machines’ maximum gigaflop/s as they tackle standardized math problems called benchmarks. The world’s fastest computer—a 122,400-processor IBM machine at the Los Alamos National Laboratory called Roadrunner—can run at just over a million gigaflop/s, or 1.026 petaflop/s, according to Top500, the most prominent list of top supercomputing sites.

But as a general rule, the faster a computer runs, the more power it consumes—and the more waste heat it generates, and the more additional power is needed to run cooling systems. If current trends continue, according to McKinsey & Company, then by 2020 the electric plants needed to power the world’s data centers will be churning out more greenhouse gases than the entire airline industry. The problem is getting so serious that some organizations are having to scale back plans to upgrade their data centers with faster machines—not because they can’t afford them, but because local utilities can’t supply any more electricity.

Maynard, MA-based SiCortex serves the high-performance computing market, so it’s naturally obsessed with the gigaflops game—but with a twist. The six-year-old startup builds massively parallel computers with thousands of processors. The processors themselves aren’t very fast. They run at around 700 Megahertz, slower than the chips inside most desktop and laptop PCs, which saves a lot of electricity. But they’re wired together in a way that makes SiCortex’s computers extremely zippy nonetheless. And today SiCortex is proposing an overhaul in the way the performance of high-end computers is measured and ranked, one that would take a machine’s power consumption into account and reward machines that use it sparingly.

The company calls its new measuring system the Green Computing Performance Index, and it’s urging managers of government and academic supercomputing centers and corporate data centers to use it to evaluate the full benefits and costs of owning high-performance computing systems from companies like Cray, SGI, Hewlett-Packard, IBM, and of course, SiCortex itself.

When evaluating the full cost of owning a high-performance computer, SiCortex argues, organizations should divide its performance in gigaflop/s by its power consumption in kilowatts. When you do that, a number of machines that are nominally faster than SiCortex’s machines—such Cray Inc.’s XT3 and XT4, IBM’s Blue Gene, and SGI’s Altix 8200EX—come out looking like power hogs. When running the standard Linpack benchmark, for example, an 1,100-processr Cray XT3 machine at the Swiss National Supercomputing Centre gets just 17 gigaflop/s to the kilowatt, while a 1,458-processor SiCortex machine gets a comparatively huge 253 gigaflop/s to the kilowatt.

“If you look at the high-performance computing benchmarks that Top500 produces, it’s great stuff, but it doesn’t give you a measure of the actual energy efficiency of the computers themselves,” says Christopher Stone, SiCortex’s CEO. “Everyone in the high-performance computing business is running around talking about being green or wanting to be green, so we thought why not …Next Page »

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The Assabet River these days rushes through Maynard, MA, without lending any of its liquid muscle to local industry. But for more than a century, the river supplied power to the Assabet Woolen Mill, a vast brick complex that, in its heyday, was the largest source of wool for U.S. military uniforms. I went to the mill two weeks ago to visit computer maker SiCortex, which is just one of numerous high-tech startups, including Monster.com and 38 Studios, that have taken over the complex, now known Clock Tower Place. And when I saw how swiftly the Assabet flows past the old mill buildings, I was reminded that for some companies—including, increasingly, computing companies—rivers are still a prime source of power. Google, for example, spends so much money on electricity that the search giant decided to build its newest data centers near hydroelectric dams in Washington state, where electricity is cheaper.

As it turns out, SiCortex’s whole mission is to help organizations do lots of computing without having to worry so much about energy costs. The company makes massively parallel computers that contain thousands of individual processors, wired together in a way that lets them exchange data very quickly—so quickly that the processors themselves don’t have to be very fast in order for the machine as a whole to carry out trillions of operations per second. And because the processors in SiCortex’s machines run at a relatively pokey 700 Megahertz, they don’t consume nearly as much power (or give off as much waste heat) as the multi-Gigahertz processors hawked by the Intels of the world.

If you take power and cooling expenses into account, according to SiCortex, its machines are only one-third as costly to own and operate as equally fast Intel-based clusters. In fact, a SiCortex machine uses so little electricity that it can be powered by a small team of cyclists. The company organized just such a stunt at MIT last December, when 10 members of the MIT cyclocross team hooked stationary bikes up to generators and pumped out enough juice to run a fusion simulation. Of course, “That’s not a great way to power your computer system,” admits Matt Reilly, SiCortex’s co-founder and chief engineer. “The first thing we found out was that you have to cool the people pedaling the bikes. A really good bicyclist can sustain something like 300 watts, but normally they’re moving through the air while they do that. These guys were sweating like pigs.”

Reilly and co-founders Jud Leonard (now CTO) and John Mucci (a board member and the longtime CEO) came up with the basic idea for SiCortex’s fast but energy-efficient hardware back in 2002. The time needed to finish a computation, Reilly explained to me, is usually determined by three factors: the time required to do arithmetic in the CPU, the time required to move data around in memory, and the time required for input/output operations (that is, getting data into and out of the CPU). For parallel computers—which most of today’s high-performance computers are—there’s also a fourth factor: the communications time, or the time needed to move data between processors.

Semiconductor manufacturers have done an amazing job of speeding up both CPUs and memory chips over the last three decades (but at a high energy cost, as already mentioned). I/O operations are a still a bottleneck, though a variety of tricks exist for speeding them up. But Reilly, Leonard, and Mucci—all veterans of the famed Boston minicomputer company Digital Equipment Corporation—noted that nobody was really working on the fourth problem: reducing the travel time between processors in parallel machines. “That created an opportunity for a very small company to do very large things,” says Reilly.

In a machine with thousands of processors, you can’t simply string an Ethernet cable from each processor to every neighbor that it might need to communicate with. (Imagine how many phone lines would be coming out of your house if you needed a dedicated line to connect with every home or office you might want to dial.) To keep the number of wires manageable, a parallel machine’s “backplane” or communications mesh has to take the form of a …Next Page »

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Proving that the blogosphere isn’t all about Paris Hilton or even Perez Hilton, Waltham, MA-based Interactive Supercomputing this week launched a new multi-author blog on high-performance computing called Parallel Lounge. With contributors including MIT computer scientist Alan Edelman and Cray Research veteran Steve Reinhardt, Interactive Supercomputing’s vice president of joint research, it’s the only Boston blog where you are likely to find such gems as:

Compare element-wise multiplication in a for-loop

for idx=1:n
y(idx) = 2*x(idx);
end

to a vectorized multiplication

y = 2*x;

In the for-loop, a command is sent from client to server in each iteration. This totals 1000 client-server calls, slowing down the code. Not only is the vectorized code simpler, but it requires only one client-server call.

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As the red, white, and black uniforms of the MIT Cycling Team bobbed up and down before me early this afternoon, I couldn’t help thinking: human abacus. Okay, the logic might be twisted (most folks here at Xconomy figure that’s a given when I start writing), but there is method to my madness. The cyclists, 10 of them, had gathered in the lobby of MIT’s Stata Center specifically to do some human-powered computing. Their bikes were hooked up to generators, and as the team members pedaled, they produced direct current energy. The generators, in turn, were connected to a converter that transformed that energy to alternating current, which was used to power a couple of small SiCortex supercomputers, which were running an application that simulated a fusion reaction.

It was all about human power, cheap and clean energy, a Google prize, a Guinness Book of Records record, and low-powered computers—a kind of combination energy awareness statement and publicity stunt rolled up into one. Or, rather, two—because although the basic setup described above remained the same, there were actually two parts to what went on today.

Let’s start with Google. At stake here was the Innovate or Die contest sponsored by the search giant and Specialized Bicycle Components of Morgan Hill, CA. The basic idea is to use pedal power to invent something cool—”zero-emission inventions,” as the website says. Entrants have to film their submission and post it on YouTube. The deadline is Friday, so five members of the MIT team (the most the contest allows) used their pedal power to run a software simulation of a fusion-type reaction inside a Tokamak reactor.

The cycling team, by the way, won last year’s National Collegiate Athletic Association Division 2 cyclocross championship. Cyclocross is a combination of dirt biking and traditional road racing, across lots of different types of terrain—”like a steeplechase on bikes,” says team member Ilana Brito, a graduate student in biology. The team will be defending its title this Sunday in Kansas City. Brito thinks it has a chance both to repeat as national champs and to win the Google contest, which includes a Specialized bike for each team member and a single check for $5,000. But she also seemed to think the whole idea was cool. “Using bicycle power to do something novel and something that will hopefully lead to maybe solutions for alternative energy, something like that.”

The afternoon was about setting a Guinness record for human-powered computing. This time the team used 10 riders. As in the morning run, the bikes were used to power machines made by SiCortex, of Maynard, MA, a venture-funded startup (investors include Flagship Ventures, Polaris Venture Partners, and Prism VentureWorks, along with Chevron and JK&B Capital) that specializes in low-powered supercomputers. To give you an idea of how low-powered, CEO John Mucci says the chip in his supercomputer, with six processors, uses about eight watts of power. The single-processor chip in my laptop, he told me, takes almost 100 watts. Ouch.

It turns out Guinness doesn’t actually have a category for human-powered computing (which will probably be measured by how many floating point operations are performed as a result of all that pedal power). No worries. “We will be submitting a new category,” Mucci says. His marketing manager, James Bailey, also says the team, which pedaled for about 15 minutes, is a slam-dunk to set the standard. In that time, he says, the computer will perform “more arithmetic computations than were done on the whole planet up until about 1960.” All I can say is that’s a lot of abacuses.

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