Researchers use ALCF resources to model the spread of COVID-19

Argonne researchers lead highly detailed COVID-19 modeling initiatives to understand how the virus spreads as a result of populations.

With COVID-19 drastically altering everyday existence for men and women across the planet, the U.S. Section of Energy’s (DOE) Argonne Countrywide Laboratory has moved promptly to join the international battle versus the pandemic. Between the laboratory’s most potent methods for scientific study is the supercomputer Theta, housed at the Argonne Management Computing Facility (ALCF), a DOE Office of Science User Facility. Over 250 nodes on the machine were quickly reserved for multipronged study into the ailment.

Led by Argonne computational scientist Jonathan Ozik and Argonne Distinguished Fellow Charles (Chick) Macal, one of these branches of study oversees the improvement of epidemiological styles to simulate the distribute of COVID-19 throughout the population.

“This is the most in-depth granular simulation of COVID-19 that exists ideal now in terms of modeling men and women who could be in many ailment states, like infectious or hospitalized.” — Chick Macal, Argonne Distinguished Fellow

The styles are metropolis-scale simulations of Chicago, populated with just under three million agents that represent men and women going about their everyday schedules and navigating some one.2 million internet sites (properties, universities, workplaces, and so on) that every existing options for them to fulfill, or colocate — that is, options for publicity. Next publicity, an agent can grow to be infected in a severe way, depending on an agent’s profile, which contains age attributes. A selected quantity of the infected agents then perish.

These styles — running for a simulated calendar year — are revised and enhanced on a everyday basis, in accordance with the most up-to-date info and data. These updates are going towards a fully automatic workflow.

“The workflow ingests current epidemiological info — for occasion, that published everyday by the Chicago Section of General public Overall health — which provide as empirical target trajectories. By evaluating these with outputs generated from ensemble product runs, we are in a position to estimate the pandemic’s fundamental parameters,” Ozik claimed. ​“It is these calibrated parameters that help us to run unique scenarios with the product.”

“This is the most in-depth granular simulation of COVID-19 that exists ideal now in terms of modeling men and women who could be in many ailment states, like infectious or hospitalized,” Macal claimed.

The styles go after strains of inquiry that will be common to everyone subsequent the virus in the information media — for illustration, the variance in outcome yielded by applying social distancing measures for even so numerous additional times or weeks.

“What are fantastic methods to relieve off the social distancing measures?” Ozik asked. ​“Everybody’s fascinated in that for extremely apparent motives, but we really do not want to do some thing that will just create a further calamity a few months down the street.”

The considerable computational calls for of the undertaking outcome from the models’ stochastic (randomly established) elements, which govern the fundamental uncertainties and parameters of the simulation. These parameters govern agent behaviors, as perfectly as ailment development dynamics and transmissibility. Within just the product, transmissibility encapsulates the probability that a inclined agent is infected, dependent on the quantity of time that two agents invest collectively.

“With this product, you have potentially numerous men and women interacting in numerous unique methods: some may be infected, some may be inclined, and they combine in unique proportions in a wide variety of unique places — there are unique places like universities and workplaces where by extremely unique parts of the population interface,” Ozik described. ​“The multitude of options the product offers make it very qualitatively unique from — and quantitatively a lot more complex than — a statistical product or a lot more simplified compartmental styles, which are much a lot quicker to run.”

With optimization assistance from ALCF staff, simulation runs on Theta have utilized a lot more than 800 nodes at when. As component of the automatic workflow, subsequent these simulation runs, output info are transferred to Petrel (a assistance furnished by Argonne and Globus, a University of Chicago-run non-gain committed to info administration) for archival storage and submit-processing this submit-processing is concluded on Bebop, a higher-efficiency computing cluster operated by Argonne’s Laboratory Computing Source Centre that the crew also leverages for simulation runs.

“It’s the huge image that we’re attempting to capture with these simulations,” Macal claimed. ​“How can we innovate and lead by creating data unavailable everywhere else? We want to have an impact on the selections that are staying manufactured about social distancing and opening culture again up.”

Supply: ANL