Jim McGregor, an analyst at In-Stat, warned that despite the benefits of the technology for some commercial applications, such implementations could be rocky early on.

"It can be an IT nightmare," he said. "This isn't [yet] something for the general enterprise. This is for highly specialized applications, no matter how you look at it. You've got to be willing to pay."

One big engineering challenge, said John Morrison, high-performance computing division leader at Los Alamos, is tweaking the software so it can run on hybrid machines.

To take advantage of an accelerator, programmers have to rewrite existing applications so they send appropriate data to the accelerator. The developers must also add code to the accelerator that tells it what to do with the data.

Vendors such as Nvidia, AMD and IBM are selling specialized tools designed to help make this reprogramming challenge a bit easier, but it's still a daunting task.

"It takes some innovation and understanding of what the algorithms are and how the data flow is going," said Morrison, who noted that of everyone on his IT team, the programmers are doing the heaviest lifting in the effort to bring the hybrid Roadrunner online.

"You have to restructure your code to do this. Each application has its own strategy for what work will be handed off to the [accelerator]. A portion of each application has to be rewritten," Morrison explained. "It's more of a challenge for our programmers than [for] our IT people."