Supercomputer Modeling Shows How COVID-19 Spreads Through Populations

By Oliver Peckham

May 30, 2020

As many states begin to loosen the lockdowns and stay-at-home orders that have forced most Americans inside for the past two months, researchers are poring over the data, looking for signs of the dreaded second peak of the pandemic. Much uncertainty remains in this analysis: COVID-19 is such a new virus that researchers are largely uncertain how it spreads, and thus are uncertain how the spread will be affected by various policy measures (or lack thereof). Now, researchers at Argonne National Laboratory have applied supercomputing power to analyze how the virus spreads through populations.

Mobility patterns generated by the CityCOVID model. Image courtesy of Argonne.

The Argonne researchers – Jonathan Ozik and Charles Macal – led a team to develop epidemiological models to simulate COVID-19’s spread through city-scale representations of Chicago. The simulated Chicagoan environment was populated by nearly three million individuals traveling around 1.2 million locations, each offering an opportunity for infection. The research team ran these models for a simulated year, iterating on them each day as new real-world data became available.

“The workflow ingests updated epidemiological data – for instance, that published daily by the Chicago Department of Public Health – which serve as empirical target trajectories. By comparing these with outputs generated from ensemble model runs, we are able to estimate the pandemic’s underlying parameters,” Ozik said in an interview with Argonne’s Nils Heinonen. ​“It is these calibrated parameters that enable us to run different scenarios with the model.”

The CityCOVID model had strong computational requirements due to its complexity. “This is the most detailed granular simulation of COVID-19 that exists right now in terms of modeling individuals who could be in various disease states, including infectious or hospitalized,” Macal said.

To power the simulation, the researchers turned to Argonne’s Theta supercomputer, which has reserved 250 nodes for COVID-19 research. Theta is a Cray XC40 system that delivers 6.9 Linpack petaflops, placing it 28th on the most recent Top500 list of the world’s most powerful publicly ranked computers. The epidemiological simulations have used more than 800 nodes of Theta simultaneously. 

“With this model, you have potentially many people interacting in many different ways: some might be infected, some might be susceptible, and they mix in different proportions in a variety of different locations – there are different locations like schools and workplaces where very different parts of the population interface,” Ozik said. ​“The multitude of possibilities the model presents make it quite qualitatively different from – and quantitatively more complex than – a statistical model or more simplified compartmental models, which are much faster to run.”

The model will allow researchers to understand COVID-19’s spread on a more granular level, potentially lending valuable insight into which policies might work to stem the spread of the virus – and which don’t. 

“What are good ways to ease off the social distancing measures?” Ozik said. ​“Everybody’s interested in that for very obvious reasons, but we don’t want to do something that will just create another calamity a few months down the road.”

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industry updates delivered to you every week!

A Big Memory Nvidia GH200 Next to Your Desk: Closer Than You Think

February 22, 2024

Students of the microprocessor may recall that the original 8086/8088 processors did not have floating point units. The motherboard often had an extra socket for an optional 8087 math coprocessor. The math coprocessor ma Read more…

IonQ Reports Advance on Path to Networked Quantum Computing

February 22, 2024

IonQ reported reaching a milestone in its efforts to use entangled photon-ion connectivity to scale its quantum computers. IonQ’s quantum computers are based on trapped ions which feature long coherence times and qubit Read more…

Apple Rolls out Post Quantum Security for iOS

February 21, 2024

Think implementing so-called Post Quantum Cryptography (PQC) isn't important because quantum computers able to decrypt current RSA codes don’t yet exist? Not Apple. Today the consumer electronics giant started rolling Read more…

GenAI Having Major Impact on Data Culture, Survey Says

February 21, 2024

While 2023 was the year of GenAI, the adoption rates for GenAI did not match expectations. Most organizations are continuing to invest in GenAI but are yet to derive any substantial value from it. However, the GenAI hyp Read more…

QED-C Issues New Quantum Benchmarking Paper

February 20, 2024

The Quantum Economic Development Consortium last week released a new paper on benchmarking – Quantum Algorithm Exploration using Application-Oriented Performance Benchmarks – that builds on earlier work and is an eff Read more…

AWS Solution Channel

Shutterstock 2283618597

Deep-dive into Ansys Fluent performance on Ansys Gateway powered by AWS

Today, we’re going to deep-dive into the performance and associated cost of running computational fluid dynamics (CFD) simulations on AWS using Ansys Fluent through the Ansys Gateway powered by AWS (or just “Ansys Gateway” for the rest of this post). Read more…

Atom Computing Reports Advance in Scaling Up Neutral Atom Qubit Arrays

February 15, 2024

The scale-up challenge facing quantum computing (QC) is daunting and varied. It’s commonly held that 1 million qubits (or more) will be needed to deliver practical fault tolerant QC. It’s also a varied challenge beca Read more…

A Big Memory Nvidia GH200 Next to Your Desk: Closer Than You Think

February 22, 2024

Students of the microprocessor may recall that the original 8086/8088 processors did not have floating point units. The motherboard often had an extra socket fo Read more…

Apple Rolls out Post Quantum Security for iOS

February 21, 2024

Think implementing so-called Post Quantum Cryptography (PQC) isn't important because quantum computers able to decrypt current RSA codes don’t yet exist? Not Read more…

QED-C Issues New Quantum Benchmarking Paper

February 20, 2024

The Quantum Economic Development Consortium last week released a new paper on benchmarking – Quantum Algorithm Exploration using Application-Oriented Performa Read more…

The Pulse of HPC: Tracking 4.5 Million Heartbeats of 3D Coronary Flow

February 15, 2024

Working in Duke University's Randles Lab, Cyrus Tanade, a National Science Foundation graduate student fellow and Ph.D. candidate in biomedical engineering, is Read more…

It Doesn’t Get Much SWEETER: The Winter HPC Computing Festival in Corpus Christi

February 14, 2024

(Main Photo by Visit Corpus Christi CrowdRiff) Texas A&M University's High-Performance Research Computing (HPRC) team hosted the "SWEETER Winter Comput Read more…

Q-Roundup: Diraq’s War Chest, DARPA’s Bet on Topological Qubits, Citi/Classiq Explore Optimization, WEF’s Quantum Blueprint

February 13, 2024

Yesterday, Australian start-up Diraq added $15 million to its war chest (now $120 million) to build a fault tolerant computer based on quantum dots. Last week D Read more…

2024 Winter Classic: Razor Thin Margins in HPL/HPCG

February 12, 2024

The first task for the 11 teams in the 2024 Winter Classic student cluster competition was to run and optimize the LINPACK and HPCG benchmarks. As usual, the Read more…

2024 Winter Classic: We’re Back!

February 9, 2024

The fourth edition of the Winter Classic Invitational Student Cluster Competition is up and running. This year, we have 11 teams of eager students representin Read more…

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

Leading Solution Providers

Contributors

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire