IBM Summit supercomputer joins fight against COVID-19

Oak Ridge National Laboratory says early research on existing drug compounds via supercomputing could combat coronavirus.
Written by Asha Barbaschow, Contributor

IBM Summit, titleholder of the world's most powerful supercomputer, has joined the fight against the COVID-19 outbreak.

Housed within the United States Department of Energy's Oak Ridge National Laboratory (ORNL), after being built in IBM's Canberra Lab, IBM Summit's primary mission is to solve previously impractical or impossible tasks in fields of energy, advanced materials, human health, and artificial intelligence.

Researchers were granted emergency computation time on Summit, using it to perform simulations with what Big Blue called "unprecedented speed".

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Using the IBM POWER9-powered system, results were seen in 1-2 days, versus the months standard computing systems would have taken.

Through this work, researchers identified 77 small-molecule drug compounds that the ORNL said might warrant further study in the fight against the SARS-CoV-2 coronavirus, which is responsible for the COVID-19 disease outbreak.

The supercomputer simulated more than 8,000 compounds to screen for those that are most likely to bind to the main "spike" protein of the coronavirus, rendering it unable to infect host cells.

ORNL said the idea was born out of an interest in the coronavirus' entry point into a host cell.

University of Tennessee (UT)/ORNL CMB postdoctoral researcher Micholas Smith built a model of the coronavirus' spike protein, also called the S-protein, based on early studies of the structure.

See also: Coronavirus and COVID-19: Everything you need to know (CNET)

He used a chemical simulations code to perform molecular dynamics simulations, which analyse the movements of atoms and particles in the protein.

Smith simulated different compounds that dock to the S-protein spike of the coronavirus to determine if any of them might prevent the spike from sticking to human cells.

"Using Summit, we ranked these compounds based on a set of criteria related to how likely they were to bind to the S-protein spike," Smith said.

"Our results don't mean that we have found a cure or treatment for the Wuhan coronavirus," added Jeremy Smith, governor's chair at the University of Tennessee and director of the UT/ORNL Center for Molecular Biophysics.

"We are very hopeful, though, that our computational findings will both inform future studies and provide a framework that experimentalists will use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus."

Summit gave the researchers its massive data processing capability, enabled by its 4,608 IBM Power Systems AC922 server nodes, each equipped with two IBM POWER9 CPUs and six Nvidia Tensorcore V100 GPUs, giving it a peak performance of 200 petaflops.

Summit has also been used to help understand the origins of the universe, make sense of the opioid crisis, and show how humans would be able to land on Mars.

"We have asked IBM's technical and industry leaders to consider all options to help government and health agencies monitor and manage the outbreak," IBM CEO Ginni Rometty said.

In addition to having Summit's computational power used in the fight, Rometty said IBM's Watson Health unit is working directly with health organisations around the world to better understand the nature of COVID-19.

"The IBM Clinical Development system has been made available -- without charge -- to national health agencies to reduce the time and cost of clinical trials by providing data and analysis from web-enabled devices," she said. "And our cognitive Operational Risk Insight tool has been made available to not-for-profit organisations."


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