On the ‘Frontera’ Lines of COVID-19 Research

By Oliver Peckham

November 18, 2020

The Texas Advanced Computing Center (TACC) and its juggernaut Frontera system (ranked ninth on the most recent Top500 list) have been on the front lines of COVID-19 research for around eight months – and Frontera itself had only entered full production six months prior. Dan Stanzione, associate vice president for research at the University of Texas at Austin and executive director of TACC, has been there for all of it.

Dan Stanzione, TACC

In advance of some big news for Frontera (more on that later), Stanzione sat down for a digital “fireside chat” with Nash Palaniswamy (general manager for AI and HPC solutions and sales at Intel) to talk about the ways TACC has adapted to remote work, COVID-19 research and changes in computing over the course of 2020.

“I think we’ve had a really outstanding first year [with Frontera],” Stanzione said. “It’s been full the whole time. Tremendous demand, very high utilization, great reliability.” Frontera, he said, had supported over a million jobs across “70 to 80” teams, ranging from single-node jobs to jobs that used around 7,900 of the system’s 8,008 Intel Cascade Lake-based nodes. These jobs have ranged from tornado dynamics to hypersonic aircraft to materials design – and, Stanzione said, “this year in particular, an awful lot of drug discovery.”

“We’ve had a ton of use related to COVID,” he continued. “In fact, beginning maybe the last week of February or so and running through maybe the end of August, about 30 percent of what we were running was COVID-related one way or another. It started to drop off a little bit as we made it through the early stages of some of the projects. Across TACC, we’ve supported 50 to 60 COVID-related projects – 28 of those have been on Frontera this year.”


“… about 30 percent of what we were running was COVID-related one way or another.”


The projects, Stanzione said, had included everything from the microscale (“we do whole-virion modeling, we do a lot of molecular docking, look at the atom-by-atom level of how the virus moves, how it gets into a cell, how you might bind to it in order to build vaccines”) to the macroscale (“looking at society and people where we’re looking at mobility data, cell phone-related data, mapping epidemiological models to how much people are moving around and interacting”). In fact, he said, TACC still uses Frontera to run daily forecasts of those epidemiological models for policy-makers.

By way of example, Stanzione highlighted work by Rommie Amaro’s team at the University of California, San Diego.

“The first thing that we did was characterize the spike on top of the virus particle – that’s what everyone was doing – and then you scale that out to a few hundred million atoms and you get the whole virion,” he said. “And then you look at that over time, because that spike actually wiggles around some, and that motion turns out to be really important. [Amaro] discovered that that spike kind of hides in a coating of sugar.”

Understanding that the spike emerged from this coating “every four microseconds or so,” he explained, was key to designing effective drugs. That work has since been utilized by researchers like Rick Stevens at Argonne National Laboratory who are working to use hybrid simulation-AI pipelines to engage in rapid drug discovery. “This blend of simulation and AI has really proven to be very powerful and perhaps more effective than either one of those techniques would have done on its own, particularly in the drug discovery case,” he said. (To learn more about the COVID-19 research from Amaro and Stevens, read HPCwire‘s coverage of their SC20 panel.)


“This blend of simulation and AI has really proven to be very powerful and perhaps more effective than either one of those techniques would have done on its own.”


“I think we’ve put easily ten million node hours of Frontera time into COVID-related work at this point,” Stanzione estimated, adding that in addition to 30 percent of TACC’s computing time, COVID-19 research had occupied around a third of TACC’s staff. The COVID-19 research has also been making full use of Frontera’s various technologies – its Intel Optane DC persistent memory, for instance, was used to effectively create “multiple terabytes of RAM” for a COVID-19 project conducted by the Cleveland Clinic.

Frontera, of course, is not the only system at TACC. Second most-notable is the Stampede2 supercomputer, a 10.7-Linpack petaflops system that debuted just two years before Frontera. Stanzione said that while Frontera has taken over the “few largest computational problems,” Stampede2 is even busier: it recently crossed the 2,000-project line, he said, and in August, hosted its 8,000th user. Stanzione assured that Stampede2 – which has hosted over five million jobs across four years – has “two good years” ahead of it before TACC starts thinking about Stampede3.

Stanzione also commented on how remote work and the pandemic generally have changed the workflow at TACC.

“We’ve dealt with what everyone has dealt with in terms of the pandemic and switching to largely remote work,” he said. “Obviously we’ve kept a footprint here in the building near the datacenter all the time, just to keep an eye on the hardware. … But most everybody else has transitioned to remote work. Given the nature of the computational work we do, I think we were well-prepared to do that.”

“While we’re seeing the huge volume of demand, we’re also seeing different kinds of demand,” he continued. TACC, he explained, had been spending a lot of time building out web and other interfaces for its systems to smooth out remote workflows. “We have a project now where we’re using Google Docs and natural language processing as a way to specify computation on the machine.”

Accordingly, TACC has been hiring in a variety of areas during the pandemic, with its total staff now numbering over 180. “We’re always hiring great people,” he said, “so for anybody out there who’s looking for something to do, TACC might have a place for you.”

And TACC’s staff isn’t the only thing getting upsized: Frontera itself will also be receiving a major upgrade, announced this week at SC20. The upgrade will add 396 Dell R640 server nodes, each containing two Intel Xeon 8280 Cascade Lake CPUs and 192GB of DDR4 memory: an identical configuration to Frontera’s existing 8,008 nodes, which deliver, in aggregate, 23.5 Linpack petaflops. The new hardware provides an additional ~1.15 Linpack petaflops, although TACC currently has no plans to redo the benchmarking. The expansion is aimed at increasing Frontera’s capacity for urgent computing like COVID-19 research and natural disaster analysis.

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!

Watch Nvidia’s GTC21 Keynote with Jensen Huang Livestreamed Here, Monday at 8:30am PT

April 9, 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.S. Entity List bars U.S. firms from supplying key technolog Read more…

Argonne Supercomputing Supports Caterpillar Engine Design

April 8, 2021

Diesel fuels still account for nearly ten percent of all energy-related U.S. carbon emissions – most of them from heavy-duty vehicles like trucks and construction equipment. Energy efficiency is key to these machines, 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 training and inference servers that will power the upcoming 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…

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…

What’s New in HPC Research: Tundra, Fugaku, µHPC & More

April 6, 2021

In this regular feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. 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…

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…

RIKEN’s Ongoing COVID Research Includes New Vaccines, New Tests & More

April 6, 2021

RIKEN took the supercomputing world by storm last summer when it launched Fugaku – which became (and remains) the world’s most powerful supercomputer – ne 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…

AI Systems Summit Keynote: Brace for System Level Heterogeneity Says de Supinski

April 1, 2021

Heterogeneous computing has quickly come to mean packing a couple of CPUs and one-or-many accelerators, mostly GPUs, onto the same node. Today, a one-such-node system has become the standard AI server offered by dozens of vendors. This is not to diminish the many advances... 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