The Perlan 2's flight, from an airstrip in the western US state of Nevada, took place two hours after the planned 1:45 (local time) start time due to heavy rain.
It lasted just a few minutes -- instead of 30 minutes to two hours as scheduled -- because the aircraft is considered more efficient in dry weather, according to chief pilot Jim Payne.
"It was short," said chief executive Tom Enders, who served as co-pilot, said after exiting the plane. "Because of the clouds, we couldn't see any more otherwise we would still be up there."
Airbus, supporting the Mission Perlan 2 group that launched the ambitious project, aims to test every aspect of the unpowered aircraft, flying it at various speeds and altitudes and subjecting it to different scenarios of stress and vibration.
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Its designers hope to show that the lightweight aircraft, with its extremely long, thin wings, is strong enough to resist intense stresses that could destroy a less solid plane.
"The airplane is very stable. We got what we called dead beat response, so the way we like it," said Payne.
Designers, drawing on computerised simulations, plan to induce high-frequency vibrations to the wings to see if the glider itself can contain those vibrations at safe levels.
Ed Warnock, chief executive of the Perlan group, said his team wants to test whether it is possible for the crew to breathe only the air inside the craft without condensation damaging instruments or causing windows to fog up. "We have to control it," he said.
The glider, with a wing span of 90 feet and a weight of only 815 kilogrammes, is designed to ride updrafts to an altitude of up to 90,000 feet, even though air density at that height is only two percent what it is at sea level.
Perlan 2 also aims to collect atmospheric data useful in fighting climate change as it travels to the edge of space.