The Navy’s newest warship is powered by Linux

Perhaps it's appropriate that the first commanding officer of the Zumwalt will be Captain James Kirk (yes, that's actually his name).
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The design of the Zumwalt solves that problem by using off-the-shelf hardware—mostly IBM blade servers running Red Hat Linux—and putting it in a ruggedized server room. Those ruggedized server rooms are called Electronic Modular Enclosures (EMEs), sixteen self-contained, mini data centers built by Raytheon.

Measuring 35 feet long, 8 feet high, and 12 feet wide, the 16 EMEs have more than 235 equipment cabinets (racks) in total.
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Each EME has its own shock and vibration damping, power protection, water cooling systems, and electromagnetic shielding to prevent interference from the ship's radar and other big radio frequency emitters.

The EMEs tap into the Total Ship Computing Environment, the Zumwalt's shipboard Internet. Running multiple partitioned networks over a mix of fiber and copper, TSCE's redundantly switched network system connects all of the ship's systems—internal and external communications, weapons, engineering, sensors, etc.—over Internet protocols, including TCP and UDP. Almost all of the ship's internal communications are based on Voice Over IP (with the exception of a few old-school, sound-powered phones for emergency use).
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There's no "radio room" on the Zumwalt; all the communications are managed from the operations center. The ship's guns are fully automated and operated by an operations center watch stander instead of a gunner's mate in the mount. Theoretically, the ship could even be steered from the ops center—the ship is piloted by computer, not a helmsman. And all of these tasks are performed from the same type of console.

It communicates with the operations center over the ship's network.
Called the Common Display System, or CDS (pronounced as "keds" by those who work with it), the three-screen workstations in the operations center are powered by a collection of quad-processor Intel motherboards in an armored case
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Each CDS system can run multiple Linux virtual machines atop LynuxWorx's LynxSecure, a separation kernel tthat has been implemented in CDS as a hypervisor. This allows the workstation to connect to various networks partitioned by security level and purpose. "Every watch stander station runs out of the same box," Raytheon's DDG-1000 developer lead Robert Froncillo told me. "So they can sit at any CDS and bring up their station." This may not seem like a big deal to most people. But on past ships, workstations tended to be purpose-built for a specific weapons system or sensor. That meant every system had a different configuration and interface, and you couldn't have a watch stander handle multiple tasks without having to switch seats. The CDS workstation uses common USB interfaces for its peripheral devices
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The Zumwalt may not have sailed yet, but its software has already shipped six times. When Release 5 was completed, Raytheon brought in more sailors to test the system, tethering it to the company's Total Ship System Simulator to run through a number of combat scenarios. "We did antisubmarine warfare, air, and land attack missions," Froncillo said. The lessons learned were incorporated into release 6, and 7 will be installed on the ship before the ship's "shakedown" cruise. Another upgrade will be installed post-delivery, and continual improvements will be made as the software is deployed to the other two ships in the class.