The University of Hawaii has filed a protest with the U.S. Government Accountability Office after losing the university’s biggest contract to run a supercomputer center on Maui for the Department of Defense.

Since October 2001, UH has had the contract to run the Maui High Performance Computing Center — one of six supercomputer centers in the country for the Department of Defense — worth an estimated $181 million over 10 years.

But the Air Force told UH officials on Aug. 1 that it awarded the "follow-on" contract for the Maui center to SAIC, a major mainland defense contractor, UH officials said.

Science Applications International Corp., or SAIC, was one of UH’s two major subcontractors, along with Boeing Rocketdyne Technical Services, when the university won the contract in 2001.

The Maui site, at the time, represented the second most powerful supercomputer center in the Department of Defense, UH officials said.

UH continues to operate the supercomputer while a formal legal proceeding over its protest is under way, UH officials said Wednesday.

Hawaii News Now first reported the loss of the contract on Tuesday.

UH officials said their proposal to extend the contract would cover "our direct and indirect costs. … UH did not include ‘profit’ for UH in our proposal" for the new contract, which has an initial 4-year term, with options for two, 3-year extensions, UH officials said.

UH officials said they did not immediately know how many military and civilian employees work at the supercomputer, which is based in Kihei.

The new contractor will determine how many people will operate the facility, UH officials said.

To bid on the follow-on contract, UH had formed a partnership with Lockheed Martin, which manages four Department of Defense supercomputing centers, and Maui-based Pacific Defense Solutions and Honolulu-based Referentia Systems Inc.