The History of Supercomputing vs. COVID-19

By Editorial Team

March 9, 2021

The COVID-19 pandemic poses a greater challenge to the high-performance computing community than any before. HPCwire‘s coverage of the supercomputing response to the pandemic began in early February 2020 and has since encompassed hundreds of articles involving hundreds of supercomputers, universities, and companies as they pivoted the world’s most advanced systems to battle a 21st-century plague. This timeline — regularly updated to reflect ongoing developments in the pandemic — highlights a small fraction of this important work.

 

Supercomputing vs. COVID-19

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  • Researchers use HPC to investigate the lab leak hypothesis

    As scientists increasingly ponder whether COVID-19 spread after it escaped from study by the Wuhan Institute of Virology, a team of Australian researchers releases a study (conducted using HPC cloud resources) that fails to exclude the possibility of a lab leak origin for the pandemic.

  • Simulations show grocery stores may be more COVID-safe than previously thought

    Researchers use SDSC’s Comet supercomputer to show that COVID’s viral particles may be stickier than previously thought, making spaces like grocery stores with lots of surfaces safer than previously suspected.

  • Supercomputers aid investigation into dangerous COVID variants

    Researchers from the Catholic University of America use supercomputers to investigate the mutations that lead to the differences in the most dangerous COVID-19 variants, which increasingly represent a large portion of cases around the world.

  • RIKEN continues work on new tests, new vaccines and more

    RIKEN continues to use Fugaku to conduct COVID-19 research, focusing new vaccine strategies and testing techniques for COVID-19.

  • COVID-19 HPC Consortium organizers plan a ‘National Strategic Computing Reserve’

    Some of the organizers of the COVID-19 HPC Consortium discuss the establishment of a National Strategic Computing Reserve, which would be ready to spin up the nation’s computing resources for major crises at a moment’s notice.

  • ASF keynotes explore how HPC pervaded the pandemic

    Along with the NSF, a range of experts join the Advanced Scale Forum (ASF) in a rapid-fire roundtable to discuss how advanced technologies have transformed the way humanity responded to the COVID-19 pandemic.

  • Dompé announces Ligate, Exscalate4CoV’s successor

    Dompé announces Ligate, a successor consortium to Exscalate4CoV that will focus on enhancing the Exscalate drug development platform through a wide range of partnerships.

  • World passes 100 million cases

    Global coronavirus cases pass 100 million — just three months after passing 50 million.

  • University of Chicago researchers generate first computational model of entire virus

    Researchers at the University of Chicago use supercomputing power to generate the first computational model of the entire SARS-CoV-2 virus, moving beyond the extensive modeling of key elements of the virus completed throughout the year.

  • CLIMB COVID project gets £1.2M boost to sequence global SARS-CoV-2 genomes

    With variants on the rise, the CLIMB COVID HPC-powered coronavirus sequencing project is awarded £1.2M in order to expand beyond the UK and sequence global coronavirus genomes.

  • Los Alamos researchers work to optimize vaccine distribution

    At Los Alamos National Laboratory, researchers collaborate with the New Mexico governor’s office to provide HPC-enabled epidemiological modeling for optimizing vaccine distribution.

  • First vaccine authorized for emergency use in the U.S.

    The U.S. Food and Drug Administration issues emergency authorization for Pfizer’s COVID-19 vaccine. In the following days, the first shots are administered.

  • Exscalate4CoV runs 70 billion-molecule SARS-CoV-2 simulation

    The Exscalate4CoV consortium runs what it calls “the most complex supercomputing simulation ever realized, simulating 70 billion drug molecules across 15 interaction sites on SARS-CoV-2 in 60 hours.

  • Azured scaled to record 86,400 cores for COVID-related molecular dynamics

    Microsoft Azure and the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign scale a molecular dynamics code — the same code used in the Gordon Bell Special Prize-winning simulation — to a record 86,400 cores.

  • Gordon Bell Special Prize goes to massive SARS-CoV-2 simulations

    At SC20, the Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research goes to a wide-reaching, nationwide collaboration to develop unprecedented simulations of key aspects of SARS-CoV-2. In particular, the simulations — referenced earlier in the timeline — helped to illuminate the role of the spike proteins’ glycan shields.

  • TACC details Frontera’s work to end the pandemic

    In a digital fireside chat with Nash Palaniswamy, Dan Stanzione — associate vice preisdent for research at the University of Texas at Austin and executive director of TACC — talks about the ways TACC has adapted to remote work, COVID-19 research and changes in computing over the course of 2020.

  • At SC20, experts brace for the next pandemic

    SC20 — virtual, of course — features a plenary session titled “Advanced Computing and COVID-19: It’s More Than HPC” with Rommie Amaro, Alex Vespignani, Ilkay Altintas and Rick Stevens. The distinguished panelists discuss the role that advanced technologies have played during the pandemic — and highlight the changes that will be necessary to more effectively […]

  • The COVID-19 HPC Consortium shifts to triage

    As the first vaccinations near and concerns deepen over a strong winter spike, the massive COVID-19 HPC Consortium — which at this point comprises 43 members, 91 projects and 600 petaflops of computing power — enters a new phase: one focused on benefiting COVID patients over the following six months.

  • 2020 HPCwire Awards honor a year of COVID-19 research

    During SC20 in November, the HPCwire Readers’ and Editors’ Choice awards program celebrates its 17th year of honoring outstanding achievements in high-performance computing. They incorporate of new category — Best Use of HPC in Response to Societal Plights — and COVID-19-related research wins five additional awards across four more categories, for a total of eight […]

  • Fugaku heralds a dark winter

    Riken announces the latest in a series of Fugaku-powered simulations, showing that humidity is a strong controlling factor in the spread of viral particles — and heightening worries as much of the world begins to face down the winter season.

  • Lawrence Livermore announces Mammoth cluster to fight COVID-19

    Lawrence Livermore National Laboratory announces a new, high-memory cluster called Mammoth, putting it to work on COVID-19 research right out of the gate.

  • Exscalate4CoV research leads to human trial of possible therapeutic

    The public-private supercomputing consortium Exscalate4CoV announces that its research has led to a human clinical trial of a repurposed drug called raloxifene that may hold promise as a therapeutic for COVID-19 patients.

  • Folding@home and Nvidia team to visualize the coronavirus

    Folding@home simulates more than 442,000 atoms of the viral molecule in constant motion for a microsecond, teaming with Nvidia to produce an immersive visualization of the virus’ spike proteins.

  • Lawrence Livermore upgrades its Corona cluster for coronavirus research

    Lawrence Livermore National Laboratory teams with AMD and Supermicro to upgrade its Corona supercomputing cluster to provide additional resources to scientists for COVID-19 drug discovery and vaccine research.

  • Death toll passes 1,000,000

    The pandemic passes another grim milestone: a million deaths.

  • AMD’s COVID-19 HPC Fund reaches 12 petaflops, 20+ recipients

    A few months after its first allocations, AMD’s COVID-19 HPC Fund reaches 12 petaflops of compute capacity and announced allocations to 18 additional institutions.

  • Folding@home, Rosetta@home gain Arm support

    Neocortix announces that it has successfully enabled Arm 64-bit support for both Folding@home and Rosetta@home, opening the door for billions of additional devices to join the crowdsourced computing fight against COVID-19.

  • Supercomputer research uncovers signs of ‘bradykinin storm’ in Covid patients

    After months of doctors struggling to explain bizarre Covid symptoms in patients, researchers at Oak Ridge National Laboratory use the Summit supercomputer to comb through genomic data, finding signs of a ‘bradykinin storm’ phenomenon that may explain COVID-19’s wide range of symptoms.

  • TACC supercomputers host simulations of the coronavirus ‘ladder’

    The Texas Advanced Computing Center’s Frontera and Longhorn systems host simulations aiming to pinpoint the conformational changes undergone by the spike protein when it binds to a human cell.

  • KISTI joins the COVID-19 HPC Consortium

    The Korea institute of Science and Technology Information (KISTI) joins the COVID-19 High Performance Consortium as the Consortium’s 42th member with the KISTI-5 supercomputer, Nurion.

  • Folding@home brings together over four million computers for COVID research

    Crowdsourced computing project Folding@home announces that over four million computers are now contributing their resources to the project — a hundredfold increase compared to pre-pandemic levels. The computers’ collective power is used to produce detailed protein simulations like the one above.

  • Riken joins the COVID-19 High Performance Computing Consortium

    Riken joins the COVID-19 High Performance Computing Consortium, pledging the most powerful supercomputer in the world to the cause.

  • At ISC 2020, the fight against Covid takes the stage

    At the virtual ISC 2020 conference, a focus session features Satoshi Matsuoka of RIKEN, Peter Coveney of the Centre of Excellence in Computational Biomedicine and Rick Stevens of Argonne National Laboratory discussing how their respective institutions are fighting back against COVID-19.

  • Fugaku launches early to fight Covid-19, claims top spot

    Riken’s showstopper Fugaku system launches almost a year ahead of schedule, weighing in at 415 Linpack petaflops and seizing the top spot on the Top500 list. The reason for the early launch: COVID-19 research.

  • Frontera illuminates SARS-CoV-2’s insidious sugar coating

    An interinstitutional team of researchers use the Frontera system at the Texas Advanced Computing Center to examine the sugary glycan shields that coat the coronavirus’ spike proteins, finding that the shields protect the proteins — but that, when the proteins attack a human cell, the proteins lift themselves outside of the shields.

  • AMD makes first COVID-19 HPC Fund allocations

    A month and a half after announcing its COVID-19 HPC Fund, AMD makes its first allocations and announces that the fund comprises some seven petaflops of compute power.

  • COVID-19 HPC Consortium expands to Europe

    The DOE’s COVID-19 HPC Consortium continues its rapid expansion, uniting more than 56 research teams and extending its research to supercomputing centers and programs in Europe.

  • Argonne model maps Covid spread in Chicago

    Researchers from Argonne National Laboratory introduce CityCOVID, a massive city-scale simulation populated by three million virtual individuals and millions of locations that demonstrates how COVID-19 spreads through a major city — and how it could be stymied.

  • Hacking streak forces European supercomputers offline

    In the midst of COVID-19 research, another plague strikes: malware. The malicious hacking streak forces a number of major European supercomputers offline as they remove the malware and reestablish security.

  • ACM introduces Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research

    In addition to its annual Gordon Bell Prize, the ACM announces it will award a Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research both in 2020 and 2021.

  • HPE’s cloud-based Sentinel hosts hunt for therapeutics

    Hewlett Packard Enterprise’s cloud-based Sentinel supercomputer hosts work from a team at the University of Alabama in Huntsville to model drug molecule interactions with the spike protein.

  • PRACE awards hundreds of millions of core hours to Covid research

    The Partnership for Advanced Computing in Europe (PRACE) announces over 300 million core hours’-worth of supercomputer time allocations to a wide range of projects tackling the pandemic.

  • Supercomputer quartet tackles AI-enabled drug discovery

    The Comet, Longhorn, Frontera and Summit supercomputers all assist the reorientation of a tool called DeepDriveMD for use in COVID-19 drug discovery, narrowing a billion molecules down to 30 promising candidates.

  • Australian supercomputing leaders begin battle with COVID-19

    NCI Australia announces support for three projects with a combined 40 million units of compute time on its “Gadi” supercomputer, and the Pawsey Supercomputing Centre announces support for five projects on over 1,100 cores of its Nimbus cloud.

  • Korea’s national supercomputing center dedicates resources to COVID-19

    Researchers at the Korea Institute of Science and Technology Information (KISTI) use their Nurion supercomputer to crunch drug candidates for COVID-19.

  • Supercomputing-enabled models challenge widely cited projections

    Researchers at the University of Texas at Austin apply resources from the Texas Advanced Computing Center to develop a new — and, they claim, more accurate — model than the widely-cited IHME model used by the White House.

  • AMD launches COVID-19 HPC fund

    Alongside other initiatives, AMD announces its COVID-19 HPC Fund, which begins with an initial donation of $15 million in HPC systems to institutions researching COVID-19.

  • Nvidia and AMD join the COVID-19 High Performance Computing Consortium

    Heavy-hitters Nvidia and AMD both join the newly formed COVID-19 HPC Consortium.

  • LLNL shares work-from-home stories

    Another quarantined researcher joins the This Week in HPC podcast: Jim Brase from Lawrence Livermore National Laboratory. In the episode, Brase discusses LLNL’s approaches to fighting COVID-19 on multiple fronts and Brase’s own workflow changes as COVID-19 forces LLNL to adjust its day-to-day operations.

  • Deaths pass 100,000

    Global deaths pass six digits just a few months after the first cases.

  • CSC supercomputer simulates spread in grocery stores

    A team of Finnish researchers used the Puhti supercomputer at CSC (a Finnish science and IT company) to simulate how viral particles from a cough could travel — and linger — in a grocery store aisle.

  • Pandemic wipes out HPC market growth

    Intersect360 Research revises its 2020 forecast of 7 percent growth in the HPC products and services market, projecting instead up to a 12 percent drop.

  • Frontera probes transmission on airplanes

    With uncertainty building vis-a-vis how — and where — COVID-19 is spreading, a team of researchers employs the Frontera system at the Texas Advanced Computing Center to simulate how viral particles could travel in airplanes.

  • Lawrence Livermore hunts for antibody candidates

    Lawrence Livermore National Laboratory 10³⁹ COVID-19 antibody candidates down to 20 using a combination of HPC clusters and machine learning.

  • Singapore’s National Supercomputing Center joins the fight

    Singapore’s National Supercomputing Center pledges its resources to the fight against COVID-19 through a special call for projects.

  • Frontera completes massive SARS-CoV-2 simulations

    Led by Rommie Amaro, researchers use the Frontera system at the Texas Advanced Computing Center to complete the first parts of a simulation that will eventually constitute the first all-atom model of the SARS-CoV-2 viral envelope.

  • PRACE fast-tracks COVID-19 proposals

    The Partnership for Advanced Computing in Europe announces that it is welcoming and fast-tracking proposals that contribute to the “mitigation of the impact of the COVID-19 pandemic.”

  • DOE forms COVID-19 High Performance Computing Consortium

    The Department of Energy announces the COVID-19 High Performance Computing Consortium, a massive collaboration between government and industry partners aiming to pool major supercomputing resources and allocate them to researchers.

  • CINECA reports from the front lines

    Carlo Cavazzoni, a senior staff member at Italian supercomputing organization CINECA, speaks to the This Week in HPC podcast about CINECA’s work using supercomputing to combat COVID-19 and Cavazzoni’s personal experience living near the epicenter of the Italian coronavirus outbreak.

  • GENCI offers its resources to the cause

    GENCI, the French national high-performance computing organization, announces that it is providing its computing and storage resources to COVID-19 researchers.

  • Exscalate4CoV consortium awarded €3 million to fight COVID-19

    Italian-based consortium Exscalate4CoV is awarded €3 million (~$3.39 million) by the European Commission for research projects focusing on COVID-19.

  • Summit joins the fight

    One of the earliest heavy hitters to join the research effort, ORNL’s Summit supercomputer — at the time, the most powerful publicly ranked supercomputer in the world — assesses thousands of compounds for their ability to bind to SARS-CoV-2’s spike protein.

  • NSF invites COVID-19 computing proposals

    The National Science Foundation solicits proposals through its Office of Advanced Cyberinfrastructure for projects that address COVID-19 challenges through data and/or software infrastructure development activities.

  • Tech conferences canceled

    Several major tech conferences, including Nvidia’s GPU Technology Conference and the Strata Data + AI Conference, are canceled due to the spread of COVID-19.

  • Folding@home rallies the troops

    Greg Bowman, director of the massive crowdsourced protein computing platform Folding@home, declares “We need your help!” in a plea for additional volunteer computing resources to quickly fold the proteins of SARS-CoV-2.

  • Rosetta@home load spikes

    Users of crowdsourced computing platform Rosetta@home report large increases in the number of tasks being run on their machines, and an admin confirms that the influx of jobs is due to a “mad rush” of analyses of the spike protein from partner organizations.

  • European Commission mobilizes €10 million for coronavirus research

    The European Commission announces a €10 million call for expressions of interest for projects that fight COVID-19 through vaccine development, treatment and diagnostics.

  • First confirmed U.S. case of COVID-19

    The Centers for Disease Control and Prevention (CDC) confirm the first case of COVID-19 in the state of Washington.

  • Wuhan reports the first cases of a novel coronavirus

    The Wuhan Municipal Health Commission in China reports a cluster of pneumonia cases, eventually identifying a novel coronavirus that is named SARS-CoV-2.

  • Supercomputer-powered startup identifies four promising COVID therapeutics

    Working with a variety of supercomputing resources, Massachusetts-based startup ARIScience identifies four promising therapeutics for COVID-19 patients.

December 2019

Feel like something’s missing from this timeline? Let us know at oliver@taborcommunications.com.

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