Global Supercomputing Is Mobilizing Against COVID-19

By Oliver Peckham

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled, and supercomputer facilities have even begun preemptively restricting visitor access. But tech is striking back, and hard: day by day, more and more organizations are dedicating supercomputing power toward the effort to diagnose, understand and fight back against COVID-19.

The first step was diagnosis

Before supercomputers began spinning up to find a cure, researchers were scrambling to simply diagnose the disease as cases in China’s Hubei province spun out of control. With limited (and rapidly iterated) test kits available, Chinese researchers turned to AI and supercomputing for answers. They trained an AI model on China’s first petascale supercomputer, Tianhe-1, with the aim of distinguishing between the CT scans of pneumonic patients with COVID-19 and patients with non-COVID-19 pneumonia. In a paper, the researchers reported nearly 80% accuracy when testing this method against external datasets, dramatically outperforming early test kits as well as human radiologists. 

The Summit supercomputer.

The big gun was brought out early

One of the first systems to join the fight was the world’s most powerful publicly-ranked supercomputer: Summit. Oak Ridge National Laboratory (ORNL) pitted Summit’s 148 Linpack petaflops of performance against a crucial “spike” protein on the coronavirus that researchers believe may be key to disabling its ability to infect. Testing how various compounds interact with key virus components can be an extremely time-consuming task, so the researchers – a team from ORNL’s Center for Molecular Biophysics –  were granted a discretionary time allocation on Summit, which allowed them to cycle through 8,000 compounds within a few days

Using Summit, the research time identified 77 compounds that may be promising candidates for testing by medical researchers. “Summit was needed to rapidly get the simulation results we needed. It took us a day or two whereas it would have taken months on a normal computer,” said Jeremy Smith, director of UT/ORNL CMB and principal researcher for the study. The researchers are preparing to repeat the study using a new, higher-quality model of the spike protein recently made available.

Major organizations have opened their doors – and wallets – for coronavirus computing proposals

Last week, the National Science Foundation (NSF) issued a Dear Colleague Letter expressing interest in proposals for “non-medical, non-clinical-care research that can be used immediately to be understand how to model and understand the spread of COVID-19; to inform and educate about the science of virus transmission and prevention; and to encourage the development of processes and actions to address this global challenge.” Two days later, it issued another Dear Colleague Letter specifically inviting rapid response research proposals for COVID-19 computing activities through its Office of Advanced Cyberinfrastructure. As a complement to existing funding opportunities, the NSF also invited requests for supplemental funding. 

Even with their quick response, though, the NSF weren’t the first to open their pocketbooks. In January, the European Commission announced a €10 million call for expressions of interest for projects that fight COVID-19 through vaccine development, treatment and diagnostics. Then, on the same day as the latest NSF Dear Colleague Letter, they announced an additional €37.5 million in funding. 

€3 million of this funding has already been allocated to the Exscalate4CoV (E4C) program in Italy – one of the hardest-hit countries. E4C is operating through Exscalate, a supercomputing platform that uses a chemical library of over 500 billion molecules to conduct pathogen research. Specifically, E4C is aiming to identify candidate molecules for drugs, help design a biochemical and cellular screening test, identify key genomic regions in COVID-19 and more. 

Beyond E4C, the EU also highlighted “on-demand, large-scale virtual screening” of potential drugs and antibodies at the HPC Centre of Excellence for Computational Biomolecular Research, as well as “prioritized and immediate access” to supercomputers operated by the EuroHPC Joint Undertaking. Presumably, as the NSF and European Commission funding opportunities are leveraged, high-performance computing will play an increasingly large role in the fight against the coronavirus.

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!

Nvidia Aims Clara Healthcare at Drug Discovery, Imaging via DGX

April 12, 2021

Nvidia Corp. continues to expand its Clara healthcare platform with the addition of computational drug discovery and medical imaging tools based on its DGX A100 platform, related InfiniBand networking and its AGX develop Read more…

Nvidia Serves Up Its First Arm Datacenter CPU ‘Grace’ During Kitchen Keynote

April 12, 2021

Today at Nvidia’s annual spring GPU technology conference, held virtually once more due to the ongoing pandemic, the company announced its first ever Arm-based CPU, called Grace in honor of the famous American programmer Grace Hopper. Read more…

Nvidia Debuts BlueField-3 – Its Next DPU with Big Plans for an Expanded Role

April 12, 2021

Nvidia today announced its next generation data processing unit (DPU) – BlueField-3 – adding more substance to its evolving concept of the DPU as a full-fledged partner to CPUs and GPUs in delivering advanced computi Read more…

Nvidia’s Newly DPU-Enabled SuperPOD Is a Multi-Tenant, Cloud-Native Supercomputer

April 12, 2021

At GTC 2021, Nvidia has announced an upgraded iteration of its DGX SuperPods, calling the new offering “the first cloud-native, multi-tenant supercomputer.” The newly announced SuperPods come just two years after the Read more…

Tune in to Watch Nvidia’s GTC21 Keynote with Jensen Huang – Recording Now Available

April 12, 2021

Join HPCwire right here on Monday, April 12, at 8:30 am PT to see the Nvidia GTC21 keynote from Nvidia’s CEO, Jensen Huang, livestreamed in its entirety. Hosted by HPCwire, you can click to join the Huang keynote on our livestream to hear Nvidia’s expected news and... Read more…

AWS Solution Channel

Volkswagen Passenger Cars Uses NICE DCV for High-Performance 3D Remote Visualization

 

Volkswagen Passenger Cars has been one of the world’s largest car manufacturers for over 70 years. The company delivers more than 6 million automobiles to global customers every year, from 50 production locations on five continents. Read more…

The US Places Seven Additional Chinese Supercomputing Entities on Blacklist

April 8, 2021

As tensions between the U.S. and China continue to simmer, the U.S. government today added seven Chinese supercomputing entities to an economic blacklist. The U.S. Entity List bars U.S. firms from supplying key technolog Read more…

Nvidia Serves Up Its First Arm Datacenter CPU ‘Grace’ During Kitchen Keynote

April 12, 2021

Today at Nvidia’s annual spring GPU technology conference, held virtually once more due to the ongoing pandemic, the company announced its first ever Arm-based CPU, called Grace in honor of the famous American programmer Grace Hopper. Read more…

Nvidia Debuts BlueField-3 – Its Next DPU with Big Plans for an Expanded Role

April 12, 2021

Nvidia today announced its next generation data processing unit (DPU) – BlueField-3 – adding more substance to its evolving concept of the DPU as a full-fle Read more…

Nvidia’s Newly DPU-Enabled SuperPOD Is a Multi-Tenant, Cloud-Native Supercomputer

April 12, 2021

At GTC 2021, Nvidia has announced an upgraded iteration of its DGX SuperPods, calling the new offering “the first cloud-native, multi-tenant supercomputer.” Read more…

Tune in to Watch Nvidia’s GTC21 Keynote with Jensen Huang – Recording Now Available

April 12, 2021

Join HPCwire right here on Monday, April 12, at 8:30 am PT to see the Nvidia GTC21 keynote from Nvidia’s CEO, Jensen Huang, livestreamed in its entirety. Hosted by HPCwire, you can click to join the Huang keynote on our livestream to hear Nvidia’s expected news and... Read more…

The US Places Seven Additional Chinese Supercomputing Entities on Blacklist

April 8, 2021

As tensions between the U.S. and China continue to simmer, the U.S. government today added seven Chinese supercomputing entities to an economic blacklist. The U Read more…

Habana’s AI Silicon Comes to San Diego Supercomputer Center

April 8, 2021

Habana Labs, an Intel-owned AI company, has partnered with server maker Supermicro to provide high-performance, high-efficiency AI computing in the form of new Read more…

Intel Partners Debut Latest Servers Based on the New Intel Gen 3 ‘Ice Lake’ Xeons

April 7, 2021

Fresh from Intel’s launch of the company’s latest third-generation Xeon Scalable “Ice Lake” processors on April 6 (Tuesday), Intel server partners Cisco, Dell EMC, HPE and Lenovo simultaneously unveiled their first server models built around the latest chips. And though arch-rival AMD may... Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

CERN Is Betting Big on Exascale

April 1, 2021

The European Organization for Nuclear Research (CERN) involves 23 countries, 15,000 researchers, billions of dollars a year, and the biggest machine in the worl Read more…

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu 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…

Saudi Aramco Unveils Dammam 7, Its New Top Ten Supercomputer

January 21, 2021

By revenue, oil and gas giant Saudi Aramco is one of the largest companies in the world, and it has historically employed commensurate amounts of supercomputing Read more…

Quantum Computer Start-up IonQ Plans IPO via SPAC

March 8, 2021

IonQ, a Maryland-based quantum computing start-up working with ion trap technology, plans to go public via a Special Purpose Acquisition Company (SPAC) merger a Read more…

Leading Solution Providers

Contributors

Can Deep Learning Replace Numerical Weather Prediction?

March 3, 2021

Numerical weather prediction (NWP) is a mainstay of supercomputing. Some of the first applications of the first supercomputers dealt with climate modeling, and Read more…

Livermore’s El Capitan Supercomputer to Debut HPE ‘Rabbit’ Near Node Local Storage

February 18, 2021

A near node local storage innovation called Rabbit factored heavily into Lawrence Livermore National Laboratory’s decision to select Cray’s proposal for its CORAL-2 machine, the lab’s first exascale-class supercomputer, El Capitan. Details of this new storage technology were revealed... Read more…

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

African Supercomputing Center Inaugurates ‘Toubkal,’ Most Powerful Supercomputer on the Continent

February 25, 2021

Historically, Africa hasn’t exactly been synonymous with supercomputing. There are only a handful of supercomputers on the continent, with few ranking on the Read more…

The History of Supercomputing vs. COVID-19

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 t Read more…

HPE Names Justin Hotard New HPC Chief as Pete Ungaro Departs

March 2, 2021

HPE CEO Antonio Neri announced today (March 2, 2021) the appointment of Justin Hotard as general manager of HPC, mission critical solutions and labs, effective Read more…

AMD Launches Epyc ‘Milan’ with 19 SKUs for HPC, Enterprise and Hyperscale

March 15, 2021

At a virtual launch event held today (Monday), AMD revealed its third-generation Epyc “Milan” CPU lineup: a set of 19 SKUs -- including the flagship 64-core, 280-watt 7763 part --  aimed at HPC, enterprise and cloud workloads. Notably, the third-gen Epyc Milan chips achieve 19 percent... Read more…

Microsoft, HPE Bringing AI, Edge, Cloud to Earth Orbit in Preparation for Mars Missions

February 12, 2021

The International Space Station will soon get a delivery of powerful AI, edge and cloud computing tools from HPE and Microsoft Azure to expand technology experi Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire