PRACE Awards Hundreds of Millions of Core Hours to COVID-19 Research Projects

By Staff report

April 29, 2020

A month after announcing that it was fast-tracking COVID-19 research proposals, the Partnership for Advanced Computing in Europe (PRACE) has detailed its first major round of awardees. The newly announced projects, part of PRACE’s “HPCvsVirus” initiative, will be receiving over 300 million core hours of computational power to advance understanding of COVID-19 and possible drug treatments or vaccines. “And,” PRACE wrote in its announcement, “this is only the beginning.”

Within the first week of its fast-tracked proposal review process, PRACE had already announced its first approved project: COVID-HP, a project utilizing 20 million core hours on the Joliot-Curie Rome supercomputer (a 6.6-peak petaflops system hosted by GENCI) to research inhibitors targeting key proteins in the virus and certain nucleic acid sequences in its genome. 

Now, just a couple of weeks later, at least fourteen other projects have joined its ranks, all receiving massive computing time allocations from PRACE.


Awardees studying proteins

The University of Jyväskylä

Researchers from the University of Jyväskylä in Finland will work to analyze COVID-19’s infamous spike protein, aiming to inhibit the protein using aptamers or by targeting its RNA-dependent RNA polymerase. The team was awarded 15 million core hours on the Joliot-Curie Rome supercomputer.

The École Polytechnique at Lausanne

A study from the École Polytechnique at Lausanne in Switzerland will use molecular dynamics to examine the small membrane protein (E) of the coronavirus, which is key to its viral assembly process. The project was awarded ten million core hours on the Piz Daint supercomputer (21.2 Linpack petaflops) at the Swiss National Supercomputing Centre (CSCS).

The University of Tuscia

A team from the University of Tuscia in Italy will investigate the interaction between the ACE2 receptor and the spike protein using molecular dynamics, comparing the results to predecessors from bats and pangolins. PRACE awarded these researchers with three million core hours on the Marconi100 supercomputer (a new, GPU-equipped partition of the Marconi system) at CINECA.

The University of Barcelona targets changes in the spike protein

Researchers from the University of Barcelona will seek small molecules to interfere with conformational changes in the spike protein and to better-characterize those changes in the structure and energy of the spike protein. The researchers were awarded 15.3 million core hours on the Hawk supercomputer (26 peak petaflops) at the Gauss Centre for Supercomputing (GCS).

The University of Southern Denmark

A professor from the University of Southern Denmark will lead another study of the spike protein, using molecular dynamics simulations to examine the “molecular hotspots” of the protein and aiming to identify strategies to limit the protein’s abilities. This study received an allocation of 35 million core hours on Piz Daint.

The Cyprus University of Technology

This six-month project will use molecular dynamics to study COVID-19 proteins, identify relevant protein motions, and mutate the proteins with the aim of producing epitope vaccines. This research has received an allocation of 16 million hours on Joliot-Curie Rome.


Awardees studying peptides

Nuritas

A team led by a researcher from Irish biotech firm Nuritas will work to identify peptides that can bond to as many targets as possible in the virus. This six-month project was awarded 40 million core hours on Piz Daint.

University College London

A professor from University College London will lead a project studying the design of peptide-based binders to block interactions between the spike protein and the ACE2 receptor, aiming to use machine learning to design those peptides. PRACE awarded the project 30 million core hours on Hawk.

The Spanish Research Council 

A team from the Spanish Research Council (CIB-CSIC) will also study peptide inhibitors, giving priority to the generic drug library. This project was awarded 25 million core hours on Marconi100.


Awardees studying the main protease

The University of Florence

A professor from the University of Florence will lead a team virtually designing inhibitors against the virus’ replication process, targeting its main protease. The researchers were awarded 20 million core hours on Marconi100.

The University of Valencia

A team from the University of Valencia is also working to develop inhibitors for COVID-19’s main protease, building a foundation for those inhibitors by building a complex structural model that will allow for computational study of these enzymes. PRACE awarded 46 million core hours to this project, split evenly between MareNostrum 4 (6.5 Linpack petaflops) and MareNostrum 4 P9 (1.1 Linpack petaflops) at the Barcelona Supercomputing Center (BSC).


Other awardees

Nostrum Biodiscovery

Researchers from Spanish biotech firm Nostrum Biodiscovery will study hundreds of millions of molecules for their potential to inhibit COVID-19, using a hierarchical approach to quickly filter down to the most promising compounds. They were awarded four million core hours at the SuperMUC-NG supercomputer (19.5 Linpack petaflops) at GCS.

The Polytechnic University of Catalonia

This study, led by a professor from the Polytechnic University of Catalonia, will use supercomputing to help develop serological antibody tests. The project has received 40 million core hours on Joliot-Curie.

The Barcelona Supercomputing Center

Finally, the “CardioVascular-COVID” project, led by researchers from the Barcelona Supercomputing Center, will examine the effects of antimalarial drugs (like hydroxychloroquine) on cardiovascular systems, with the aim if improving treatment of cardiac patients suffering from COVID-19. The team has received 7.8 million core hours on Joliot-Curie Rome.


“These projects,” PRACE wrote, “will provide new lead compounds and targets for further in vitro and in vivo studies of [COVID-19], new insights for those drugs currently undergoing clinical studies and also possible new strategies for drug repositioning to treat SARS-CoV-2 infections.”

To read more about any of the projects, click here.

Subscribe to HPCwire's Weekly Update!

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

Jack Dongarra on SC21, the Top500 and His Retirement Plans

November 29, 2021

HPCwire's Managing Editor sits down with Jack Dongarra, Top500 co-founder and Distinguished Professor at the University of Tennessee, during SC21 in St. Louis to discuss the 2021 Top500 list, the outlook for global exascale computing, and what exactly is going on in that Viking helmet photo. Read more…

SC21: Larry Smarr on The Rise of Supernetwork Data Intensive Computing

November 26, 2021

Larry Smarr, founding director of Calit2 (now Distinguished Professor Emeritus at the University of California San Diego) and the first director of NCSA, is one of the seminal figures in the U.S. supercomputing community. What began as a personal drive, shared by others, to spur the creation of supercomputers in the U.S. for scientific use, later expanded into a... Read more…

Three Chinese Exascale Systems Detailed at SC21: Two Operational and One Delayed

November 24, 2021

Details about two previously rumored Chinese exascale systems came to light during last week’s SC21 proceedings. Asked about these systems during the Top500 media briefing on Monday, Nov. 15, list author and co-founder Jack Dongarra indicated he was aware of some very impressive results, but withheld comment when asked directly if he had... Read more…

SC21’s Student Cluster Competition Winners Announced

November 19, 2021

SC21 may have been the first major supercomputing conference to return to in-person activities, but not everything returned to the live menu: the Student Cluster Competition – held virtually at ISC 2020, SC20 and ISC 2021 – was again held virtually at SC21. Nevertheless, Students@SC Chair Jay Lofstead took the physical stage at SC21 on Thursday to announce the... Read more…

MLPerf Issues HPC 1.0 Benchmark Results Featuring Impressive Systems (Think Fugaku)

November 19, 2021

Earlier this week MLCommons issued results from its latest MLPerf HPC training benchmarking exercise. Unlike other MLPerf benchmarks, which mostly measure the training and inference performance of systems that are availa Read more…

AWS Solution Channel

Royalty-free stock illustration ID: 1616974732

Using the Slurm REST API to integrate with distributed architectures on AWS

The Slurm Workload Manager by SchedMD is a popular HPC scheduler and is supported by AWS ParallelCluster, an elastic HPC cluster management service offered by AWS. Read more…

Gordon Bell Special Prize Goes to World-Shaping COVID Droplet Work

November 18, 2021

For the second (and, hopefully, final) year in a row, SC21 included a second major research award alongside the ACM 2021 Gordon Bell Prize: the Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research. Last year, the first iteration of this award went to simulations of the SARS-CoV-2 spike protein; this year, the prize went... Read more…

Jack Dongarra on SC21, the Top500 and His Retirement Plans

November 29, 2021

HPCwire's Managing Editor sits down with Jack Dongarra, Top500 co-founder and Distinguished Professor at the University of Tennessee, during SC21 in St. Louis to discuss the 2021 Top500 list, the outlook for global exascale computing, and what exactly is going on in that Viking helmet photo. Read more…

SC21: Larry Smarr on The Rise of Supernetwork Data Intensive Computing

November 26, 2021

Larry Smarr, founding director of Calit2 (now Distinguished Professor Emeritus at the University of California San Diego) and the first director of NCSA, is one of the seminal figures in the U.S. supercomputing community. What began as a personal drive, shared by others, to spur the creation of supercomputers in the U.S. for scientific use, later expanded into a... Read more…

Three Chinese Exascale Systems Detailed at SC21: Two Operational and One Delayed

November 24, 2021

Details about two previously rumored Chinese exascale systems came to light during last week’s SC21 proceedings. Asked about these systems during the Top500 media briefing on Monday, Nov. 15, list author and co-founder Jack Dongarra indicated he was aware of some very impressive results, but withheld comment when asked directly if he had... Read more…

SC21’s Student Cluster Competition Winners Announced

November 19, 2021

SC21 may have been the first major supercomputing conference to return to in-person activities, but not everything returned to the live menu: the Student Cluster Competition – held virtually at ISC 2020, SC20 and ISC 2021 – was again held virtually at SC21. Nevertheless, Students@SC Chair Jay Lofstead took the physical stage at SC21 on Thursday to announce the... Read more…

MLPerf Issues HPC 1.0 Benchmark Results Featuring Impressive Systems (Think Fugaku)

November 19, 2021

Earlier this week MLCommons issued results from its latest MLPerf HPC training benchmarking exercise. Unlike other MLPerf benchmarks, which mostly measure the t Read more…

Gordon Bell Special Prize Goes to World-Shaping COVID Droplet Work

November 18, 2021

For the second (and, hopefully, final) year in a row, SC21 included a second major research award alongside the ACM 2021 Gordon Bell Prize: the Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research. Last year, the first iteration of this award went to simulations of the SARS-CoV-2 spike protein; this year, the prize went... Read more…

2021 Gordon Bell Prize Goes to Exascale-Powered Quantum Supremacy Challenge

November 18, 2021

Today at the hybrid virtual/in-person SC21 conference, the organizers announced the winners of the 2021 ACM Gordon Bell Prize: a team of Chinese researchers leveraging the new exascale Sunway system to simulate quantum circuits. The Gordon Bell Prize, which comes with an award of $10,000 courtesy of HPC pioneer Gordon Bell, is awarded annually... Read more…

SC21 Keynote: Internet Pioneer Vint Cerf on Shakespeare, Chatbots, and Being Human

November 17, 2021

Unlike the deep technical dives of many SC keynotes, Internet pioneer Vint Cerf steered clear of the trenches and took leisurely stroll through a range of human-machine interactions, touching on ML’s growing capabilities while noting potholes to be avoided if possible. Cerf, of course, is co-designer with Bob Kahn of the TCP/IP protocols and architecture of the internet. He’s heralded... Read more…

IonQ Is First Quantum Startup to Go Public; Will It be First to Deliver Profits?

November 3, 2021

On October 1 of this year, IonQ became the first pure-play quantum computing start-up to go public. At this writing, the stock (NYSE: IONQ) was around $15 and its market capitalization was roughly $2.89 billion. Co-founder and chief scientist Chris Monroe says it was fun to have a few of the company’s roughly 100 employees travel to New York to ring the opening bell of the New York Stock... Read more…

Enter Dojo: Tesla Reveals Design for Modular Supercomputer & D1 Chip

August 20, 2021

Two months ago, Tesla revealed a massive GPU cluster that it said was “roughly the number five supercomputer in the world,” and which was just a precursor to Tesla’s real supercomputing moonshot: the long-rumored, little-detailed Dojo system. Read more…

Esperanto, Silicon in Hand, Champions the Efficiency of Its 1,092-Core RISC-V Chip

August 27, 2021

Esperanto Technologies made waves last December when it announced ET-SoC-1, a new RISC-V-based chip aimed at machine learning that packed nearly 1,100 cores onto a package small enough to fit six times over on a single PCIe card. Now, Esperanto is back, silicon in-hand and taking aim... Read more…

US Closes in on Exascale: Frontier Installation Is Underway

September 29, 2021

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, held by Zoom this week (Sept. 29-30), it was revealed that the Frontier supercomputer is currently being installed at Oak Ridge National Laboratory in Oak Ridge, Tenn. The staff at the Oak Ridge Leadership... Read more…

AMD Launches Milan-X CPU with 3D V-Cache and Multichip Instinct MI200 GPU

November 8, 2021

At a virtual event this morning, AMD CEO Lisa Su unveiled the company’s latest and much-anticipated server products: the new Milan-X CPU, which leverages AMD’s new 3D V-Cache technology; and its new Instinct MI200 GPU, which provides up to 220 compute units across two Infinity Fabric-connected dies, delivering an astounding 47.9 peak double-precision teraflops. “We're in a high-performance computing megacycle, driven by the growing need to deploy additional compute performance... Read more…

Intel Reorgs HPC Group, Creates Two ‘Super Compute’ Groups

October 15, 2021

Following on changes made in June that moved Intel’s HPC unit out of the Data Platform Group and into the newly created Accelerated Computing Systems and Graphics (AXG) business unit, led by Raja Koduri, Intel is making further updates to the HPC group and announcing... Read more…

Intel Completes LLVM Adoption; Will End Updates to Classic C/C++ Compilers in Future

August 10, 2021

Intel reported in a blog this week that its adoption of the open source LLVM architecture for Intel’s C/C++ compiler is complete. The transition is part of In Read more…

Killer Instinct: AMD’s Multi-Chip MI200 GPU Readies for a Major Global Debut

October 21, 2021

AMD’s next-generation supercomputer GPU is on its way – and by all appearances, it’s about to make a name for itself. The AMD Radeon Instinct MI200 GPU (a successor to the MI100) will, over the next year, begin to power three massive systems on three continents: the United States’ exascale Frontier system; the European Union’s pre-exascale LUMI system; and Australia’s petascale Setonix system. Read more…

Leading Solution Providers

Contributors

Hot Chips: Here Come the DPUs and IPUs from Arm, Nvidia and Intel

August 25, 2021

The emergence of data processing units (DPU) and infrastructure processing units (IPU) as potentially important pieces in cloud and datacenter architectures was Read more…

D-Wave Embraces Gate-Based Quantum Computing; Charts Path Forward

October 21, 2021

Earlier this month D-Wave Systems, the quantum computing pioneer that has long championed quantum annealing-based quantum computing (and sometimes taken heat fo Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer... Read more…

HPE Wins $2B GreenLake HPC-as-a-Service Deal with NSA

September 1, 2021

In the heated, oft-contentious, government IT space, HPE has won a massive $2 billion contract to provide HPC and AI services to the United States’ National Security Agency (NSA). Following on the heels of the now-canceled $10 billion JEDI contract (reissued as JWCC) and a $10 billion... Read more…

The Latest MLPerf Inference Results: Nvidia GPUs Hold Sway but Here Come CPUs and Intel

September 22, 2021

The latest round of MLPerf inference benchmark (v 1.1) results was released today and Nvidia again dominated, sweeping the top spots in the closed (apples-to-ap Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit tec Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

2021 Gordon Bell Prize Goes to Exascale-Powered Quantum Supremacy Challenge

November 18, 2021

Today at the hybrid virtual/in-person SC21 conference, the organizers announced the winners of the 2021 ACM Gordon Bell Prize: a team of Chinese researchers leveraging the new exascale Sunway system to simulate quantum circuits. The Gordon Bell Prize, which comes with an award of $10,000 courtesy of HPC pioneer Gordon Bell, is awarded annually... Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire