A Small Company Builds a Big Supercomputer

By Richard L. Brandt

January 30, 2013

Atipa Technologies may not be on everyone’s radar. It’s a small Kansas company, a division of Microtech Computers, which makes everything from $700 desktop computers to Linux clusters for Atipa’s HPC systems.

It may end up on the radar soon. Atipa just got a big deal. It’s building a $17 million computer for a Department of Energy laboratory. That’s not bad for a Linux cluster company that survived a big shakeout in the Linux cluster business five years ago.

The Atipa computer is destined for the Environmental Molecular Sciences Laboratory (ESML) at the Department of Energy’s Pacific Northwest National Laboratory (PNNL) in Richland, Washington. It should go live by October. It replaces the Chinook, a 163 teraflops system that cost the lab $21.4 million five years ago. Moore’s Law marches on.

“We’re very excited,” says Dana Chang, vice president of technology at Atipa. “It’s a very important sale for us.”

The new computer is a 1,440-node system packed into 42 racks, with a theoretical peak processing speed of 3.4 petaflops and 2.7 petabytes of usable storage. That puts it just ahead of the 2.9 petaflops SuperMUC, built by IBM for the Leibniz Supercomputing Centre in Germany – number six on the November 2012 TOP500 list.

ESML has some specialized computing requirements. It is used by hundreds of researchers around the world to employ molecular-level theory for climate studies, genomics, biological analysis, chemical catalysis, and solid-state physics. It’s computationally-intense work and requires a lot of storage capability. On the Chinook, climate scientists and quantum chemists were using one core and using up all the memory they could get.

To provide that power, the Atipa computer relies heavily on Intel’s Xeon Phi MIC accelerators. Each of its 1,440 compute nodes use x86 processors and the Xeon Phi accelerators, plus 128 GB memory per node. Its 2.7 petabyte storage is a shared parallel filesystem with 60 GB per second read/write.

Atipa was able to create a system to meet the lab’s needs at a great price. “All the bids we received were very similar, not much differentiation [in specs,]” says William Shelton, Associate Director of EMSL. “Atipa had the lowest price. Price became the main selling point.”

DOE can drive very hard bargains, notes Chris Willard, chief research officer at Intersect360 Research. Although not a major supplier, Atipa has proved to be a survivor. “That PNNL would buy a system from a company like this is not surprising,” he says. “PNNL will often go with a smaller company, often because they provide more specialized bids” with tighter margins. Nevertheless, he thinks the price was a good one for the size of the system, and probably allows Atipa to realize a profit.

The computer is also another validation of Intel’s Xeon Phi accelerators – and accelerators in general. Intersect360’s Willard believes that the fact that a computer of this size is dependent on Xeon Phi takes the interest in accelerators in general up a notch. While there’s been a growing interest in accelerators over the past few years, many companies have still just been testing their capabilities. “Accelerators are moving from a technology that people are checking out to one that people are interested in buying in production systems,” he says.

Chang agrees. She says that the Xeon Phi was key to providing the necessary price/performance. “It absolutely reduced the cost per FLOPS,” she says. “It was the Intel Phi being more affordable while increasing the performance. And it will become more and more affordable in 2013. Customers are now showing a strong interest in getting an Intel Phi card.” Atipa has a long-standing relationship with both Intel and AMD as suppliers.

According to Chang and Dan Mantyla, HPC programmer at Atipa, there’s an advantage of being a smaller company rather than a giant public corporation with an eye on quarterly profits. “We’re such a small company, not tiny but not a big corporation, and we build every cluster on a per-customer basis,” says Mantyla. Chang adds that the company’s Midwest roots help. “People feel comfortable talking to us because we don’t have a big company attitude,” she says. “We’re from Kansas.”

This may not be the last interesting deal from the folks from Kansas. Chang confirms that Atipa has interest from other potential customers as well. “We have a few opportunities we’re working on,” she says. “We won’t know much until the next month or so.”

Whether or not those pan out, parent company Microtech computers can already make an interesting boast. It can say its computer selection includes everything from a $700 PC to a $17 million supercomputer.

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