November 30, 2017

Students discover the power of scientific supercomputing to advance their research

Laurel Marsh with simulation of wind turbine on computer screen using Hyak

UW doctoral students Laurel Marsh and Whitney Thomas are discovering the advantage that a supercomputer like Hyak can bring to their research.

They are among 13 students enrolled in Pramod Gupta’s scientific supercomputing course, Astronomy 598, designed to introduce graduate students to Hyak, the UW’s on-site shared cluster supercomputer, supported by UW Information Technology (UW-IT).

Colorful cryo-electron microscopy image of human infecting coronavirus

Hyak was used by Lexi Walls, a PhD candidate in the Department of Biochemistry, to determine the structure of the spike protein of a human coronavirus pictured here. Photo: Lexi Walls and Melody Campbell.

“While supercomputing was once reserved for a few branches of science such as physics and astronomy, that is no longer the case,” said Gupta, a research scientist with the UW Department of Astronomy. “It’s common everywhere.”

Gupta has taught the course for the past three years, and he recently presented a talk on the course at the international Supercomputing 2017 conference held in Denver in November.

Students in his course come from a variety of backgrounds, ranging from fields in the College of Arts and Sciences, the College of Engineering, the College of the Environment and the School of Medicine.

Laurel Marsh, a PhD student the Department of Mechanical Engineering, is using Hyak to investigate the speed of the water flow in front of and behind a submerged turbine, the kind that could be used to capture tidal energy in the ocean or rivers for renewal energy. Only, to take advantage of this source of energy, researchers need to understand the fluid mechanics of the water flow.

Laurel Marsh with simulation of water flow on Hyak

Laurel Marsh, PhD student, Department of Mechanical Engineering

She depends on Hyak to build and validate a computer model of water flow around the turbine. The model is a three-dimensional mesh grid made up of six million cells. Hyak runs through thousands of iterations as the model simulates a rotating turbine and how the turbine extracts energy from the water flow. Hyak speeds through these calculations, attaining a level of precision that would otherwise be impossible said Marsh.

Whitney Thomas, a PhD student in the Department of Aeronautics and Astronautics, is studying the potential for plasma – a gaseous state of matter composed of charged particles that interact strongly with electromagnetic fields – to harness microwaves for a variety of uses, including wireless communication and radar cloaking. She is using Hyak to simulate the behavior of a plasma photonic crystal application that can control microwave frequencies. Hyak runs computer algorithms developed in the UW’s Computational Plasma Dynamics Lab, which does not have an individual allocation on Hyak. Because these computationally intense algorithms depend on parallel supercomputers, Thomas gets access to Hyak through the student-led High Performance Computing Club.

Whitney Thomas with computer model on Hyak

Whitney Thomas, PhD student, Department of Aeronautics and Astronautics

Any student — undergraduate or graduate — can gain access to the Hyak supercomputer by joining the High Performance Computing Club. The Student Technology Fee has awarded nearly $800,000 in funding to the club for access to Hyak and storage space on lolo, a shared central file system for research archives.

“Using a supercomputer for scientific computing is very different from using a desktop or laptop,” said Gupta, “and there is a learning curve for using Hyak.”

“There are a lot of Harry Potter-like spells that you need to know so that you can tell the supercomputer what to do,” he said.

Students in the course learn how to use the supercomputer effectively. They learn how to request nodes through the scheduler, and how to do parallel computing by dividing their scientific computation so that all of the supercomputer’s processors are used.

“After the course, the students can use Hyak to enable and speed up their research and make new discoveries while they are at UW,” Gupta said. “Moreover, since Hyak is very similar to the largest supercomputers in the world, the students can also use these skills after they graduate from UW.”