At ISC, the Fight Against COVID-19 Took the Stage – and Yes, Fugaku Was There

By Oliver Peckham

June 23, 2020

With over nine million infected and nearly half a million dead, the COVID-19 pandemic has seized the world’s attention for several months. It has also dominated the supercomputing sector, with COVID-related research receiving major allocations on nearly every research supercomputer in the world (and many industrial supercomputers). It’s not surprising, then, that at ISC 2020, the virtual conference opened, revealed the new Top500 list – and then got straight to COVID-19.

In the focus session, three speakers addressed how HPC is fighting back against the coronavirus: Satoshi Matsuoka of RIKEN, which just nabbed the top spot in the Top500 with its Fugaku system; Peter Coveney of the Centre of Excellence in Computational Biomedicine, which is working to make HPC and machine learning actionable in a rapid drug development workflow; and Rick Stevens of Argonne National Laboratory, where researchers are working with the COVID-19 HPC Consortium to comb through billions of molecules.

Satoshi Matsuoka highlights Fugaku’s role in COVID-19 research

Satoshi Matsuoka

Fugaku, the most powerful supercomputer in the world, is in business early thanks to COVID-19. The system – situated at Riken in Japan – was scheduled to launch in 2021. When the pandemic struck, plans changed. “It was decided by [Japan’s] Ministry of Education, Culture, Sports, Science and Technology that we will utilize [not only supercomputers that are already available] but also [deploy Fugaku early], almost a year ahead of schedule, to combat COVID-19,” explained Matsuoka, director of the Riken Center for Computational Science (R-CCS).

The Fugaku supercomputer

Fugaku’s showstopping 415 Linpack petaflops are close to triple the performance of the runner-up, Oak Ridge’s newly dethroned Summit system. At 158,976 nodes, Fugaku is the largest system ever created in terms of nodes, footprint and power consumption. The software, Matsuoka said, is “quite standard,” allowing for broad usability without much Fugaku-specific tweaking.

“They’re largely divided into two areas,” Matsuoka said of Fugaku’s COVID-19 workloads. “One is medical-pharma – so trying to see how the virus behaves, what are the effective drugs, especially how we can repurpose existing drugs and so forth and also how a vaccine is made. So these are molecular-level investigations of the virus and its countermeasures. The other is more macroscopic – so we’re trying to see how these viruses are transmitted and what are the mitigation measures and how it will impact society.”

Matsuoka highlighted several of the COVID-19 projects taking advantage of Fugaku’s early arrival. One Riken researcher, for instance, is studying conformational changes of the spike protein using a highly scalable molecular dynamics code. Another researcher is using fragment molecular orbital calculations to investigate the energy levels of the spike protein, scaling across hundreds of thousands of Fugaku’s CPUs. “On [Fugaku’s predecessor] the K computer,” Matsuoka said, “this calculation would have taken days, weeks, multiple weeks – on Fugaku, … they have been able to do this in just three hours.”

Other researchers are using Fugaku to run socially oriented simulations, such as simulating droplets in indoor spaces like trains or simulating the spread effects of using face masks or contact tracing applications, Matsuoka said – and, of course, there are more to come. “So if you have any good ideas,” he said, “go to the website and you can apply.” 

A Riken-led simulation of virus droplets in train cabins. Image courtesy of Satoshi Matsuoka.

Peter Coveney describes a new, HPC- and AI-driven model for drug development

Peter Coveney

Coveney, the second speaker, runs the Centre of Excellence in Computational Biomedicine (CompBioMed), an initiative funded by the European Union that is currently redirecting its research efforts and computational research to the study of and drug development for COVID-19. Coveney (who also teaches at University College London) stressed the need to “invert the model [of drug development] as it currently exists” using advanced IT.

“The opportunities there are enormous,” Coveney said. “What we’re really trying to do is transform the approach to biomedicine, to be able to move it from a highly empirical approach … to putting a priority on the predictions that come out of computers.”

But to do that, he said, the computational results had to be actionably accurate – and perhaps even more difficult, they had to be quickly produced. Molecular screening, however – the crux of computational drug design, whereby compounds are fitted to targets on the virus’ proteins – is labor-intensive, time-consuming and expensive ($1 to $10 a compound, with billions of compounds to screen for COVID-19).

Coveney outlined how CompBioMed worked with over 40 partners around the world to streamline the computational drug design pipeline. CompBioMed gained access to a wide range of supercomputers, from SuperMUC-NG (the most powerful supercomputer in the EU) to Piz Daint, Archer, Summit, Frontera, Theta and more. The researchers used a piece of middleware called Radical Cybertools to run workflows across a large number of nodes on multiple machines.

With computing power in hand, CompBioMed focused on how to ensure “validation, verification and uncertainty quantification” (or “VVUQ”) in the pipeline. “This is designed in general to raise confidence in HPC simulation,” Coveney said.

To effectively leverage the computing power and ensure “VVUQ,” CompBioMed combined machine learning with molecular dynamics. Machine learning was used first to whittle down the near-infinite list of candidate molecules. “We have to do searches in a hurry,” Coveney said. “We want to use computationally very fast methods that are also cheap … to search huge libraries of molecules, to explore chemical space, to predict new molecules and so on.” 

The ensemble molecular dynamics process. Image courtesy of Peter Coveney.

Then, with the list whittled down, CompBioMed used molecular dynamics simulations – 20 to 30 of them at a time. As Coveney explained, a single molecular dynamics simulation could have a large number of errors. “But if you run many of them concurrently … we can run those on very large supercomputers all at the same time,” Coveney said. “Then we can make reliable predictions that get fed back to another stage of the machine learning.”

The best candidate compounds from this process are then submitted to medical research labs for further testing. “We are already discovering many tens to hundreds of potential compounds that can be investigated by our experimental colleagues,” Coveney said. “And indeed, that’s happening already.”

“We’re trying to change the way medicine is actually understood and applied,” Coveney concluded. “We want to make the subject more amenable to scientific investigation, that it should revolve around theory, modeling and simulation in addition to experimental research.”

Rick Stevens dives into the COVID-19 HPC Consortium and machine learning-enabled research

Rick Stevens

Finally, Stevens took the virtual stage. Stevens – associate laboratory director at Argonne National Laboratory – has been working closely with the COVID-19 HPC Consortium, a public-private effort to pool supercomputing resources for COVID-19 research. Currently, the effort has over 40 members, comprising some 483 petaflops of resources, 50,000 GPUs, 136,000 nodes and five million CPU cores. 

As Stevens explained, the projects being tackled by the consortium fall into three broad categories: first, basic science, including things like analyzing the virus’ structure, protein functions and virus evolution; second, therapeutics (“the largest group”), aiming to discovery drug targets on the virus, design drugs and discover repurposable drugs; and finally, patient care – “things more related to optimizing the healthcare system or epidemiology.”

Stevens outlined some of the key work, especially where it intersected with Argonne. “If you’re gonna work on this problem, you need to understand the enemy,” Stevens said, describing how Argonne has used its Advanced Photon Source (APS) to identify new structures of COVID-19, which in turn produce new drug targets for simulations to examine. 

Like Coveney, Stevens highlighted the intersections of AI and supercomputing as viable pathways for processing massive amounts of compounds in a relatively short time frame. For instance, he said, researchers were using AI to reconcile models of proteins from various sources to produce even more accurate models. In the spring, Argonne also began assembling a large database – around 60 TB – containing descriptors, images and more for over four billion compounds, with the aim of producing massive datasets for machine learning applications.

“One of the strategies that we have is to use a combination of high-throughput virtual docking … to generate scores – generate them on thousands or millions of data points,” Stevens said, “but then use that data to train machine learning models and do inference on a much larger scale.” As in Coveney’s research, the most promising hits are then sent for wet lab screening. 

Argonne’s pipeline for COVID-19 drug discovery. Image courtesy of Rick Stevens.

Stevens also discussed the use of machine learning to understand the “trajectories” of molecular dynamics simulations and the use of reinforcement learning to essentially build drug molecules from the ground up, adding to them iteratively to improve the docking score.

“One of the overall challenges here, of course, is that there’s over 10⁶⁰ possible drugs,” Steven said, “and you can only test at the end of the day, in humans, a small fraction of these.” But now, with AI and supercomputing converging to create a new model of rapid drug design, that might be enough.

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