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!

Energy Exascale Earth System Model Version 2 Promises Twice the Speed

October 18, 2021

The Energy Exascale Earth System Model (E3SM) is an ongoing Department of Energy (DOE) earth system modeling, simulation and prediction project aiming to “assert and maintain an international scientific leadership posi 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…

Royalty-free stock illustration ID: 1938746143

MosaicML, Led by Naveen Rao, Comes Out of Stealth Aiming to Ease Model Training

October 15, 2021

With more and more enterprises turning to AI for a myriad of tasks, companies quickly find out that training AI models is expensive, difficult and time-consuming. Finding a new approach to deal with those cascading challenges is the aim of a new startup, MosaicML, that just came out of stealth... Read more…

NSF Awards $11M to SDSC, MIT and Univ. of Oregon to Secure the Internet

October 14, 2021

From a security standpoint, the internet is a problem. The infrastructure developed decades ago has cracked, leaked and been patched up innumerable times, leaving vulnerabilities that are difficult to address due to cost Read more…

SC21 Announces Science and Beyond Plenary: the Intersection of Ethics and HPC

October 13, 2021

The Intersection of Ethics and HPC will be the guiding topic of SC21's Science & Beyond plenary, inspired by the event tagline of the same name. The evening event will be moderated by Daniel Reed with panelists Crist Read more…

AWS Solution Channel

Cost optimizing Ansys LS-Dyna on AWS

Organizations migrate their high performance computing (HPC) workloads from on-premises infrastructure to Amazon Web Services (AWS) for advantages such as high availability, elastic capacity, latest processors, storage, and networking technologies; Read more…

Quantum Workforce – NSTC Report Highlights Need for International Talent

October 13, 2021

Attracting and training the needed quantum workforce to fuel the ongoing quantum information sciences (QIS) revolution is a hot topic these days. Last week, the U.S. National Science and Technology Council issued a report – The Role of International Talent in Quantum Information Science... 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…

Royalty-free stock illustration ID: 1938746143

MosaicML, Led by Naveen Rao, Comes Out of Stealth Aiming to Ease Model Training

October 15, 2021

With more and more enterprises turning to AI for a myriad of tasks, companies quickly find out that training AI models is expensive, difficult and time-consuming. Finding a new approach to deal with those cascading challenges is the aim of a new startup, MosaicML, that just came out of stealth... Read more…

Quantum Workforce – NSTC Report Highlights Need for International Talent

October 13, 2021

Attracting and training the needed quantum workforce to fuel the ongoing quantum information sciences (QIS) revolution is a hot topic these days. Last week, the U.S. National Science and Technology Council issued a report – The Role of International Talent in Quantum Information Science... Read more…

Eni Returns to HPE for ‘HPC4’ Refresh via GreenLake

October 13, 2021

Italian energy company Eni is upgrading its HPC4 system with new gear from HPE that will be installed in Eni’s Green Data Center in Ferrera Erbognone (a provi Read more…

The Blueprint for the National Strategic Computing Reserve

October 12, 2021

Over the last year, the HPC community has been buzzing with the possibility of a National Strategic Computing Reserve (NSCR). An in-utero brainchild of the COVID-19 High-Performance Computing Consortium, an NSCR would serve as a Merchant Marine for urgent computing... Read more…

UCLA Researchers Report Largest Chiplet Design and Early Prototyping

October 12, 2021

What’s the best path forward for large-scale chip/system integration? Good question. Cerebras has set a high bar with its wafer scale engine 2 (WSE-2); it has 2.6 trillion transistors, including 850,000 cores, and was fabricated using TSMC’s 7nm process on a roughly 8” x 8” silicon footprint. Read more…

What’s Next for EuroHPC: an Interview with EuroHPC Exec. Dir. Anders Dam Jensen

October 7, 2021

One year after taking the post as executive director of the EuroHPC JU, Anders Dam Jensen reviews the project's accomplishments and details what's ahead as EuroHPC's operating period has now been extended out to the year 2027. Read more…

University of Bath Unveils Janus, an Azure-Based Cloud HPC Environment

October 6, 2021

The University of Bath is upgrading its HPC infrastructure, which it says “supports a growing and wide range of research activities across the University.” 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…

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…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months... 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…

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…

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…

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…

Leading Solution Providers

Contributors

AMD-Xilinx Deal Gains UK, EU Approvals — China’s Decision Still Pending

July 1, 2021

AMD’s planned acquisition of FPGA maker Xilinx is now in the hands of Chinese regulators after needed antitrust approvals for the $35 billion deal were receiv 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…

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…

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…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer 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…

Frontier to Meet 20MW Exascale Power Target Set by DARPA in 2008

July 14, 2021

After more than a decade of planning, the United States’ first exascale computer, Frontier, is set to arrive at Oak Ridge National Laboratory (ORNL) later this year. Crossing this “1,000x” horizon required overcoming four major challenges: power demand, reliability, extreme parallelism and data movement. Read more…

Intel Unveils New Node Names; Sapphire Rapids Is Now an ‘Intel 7’ CPU

July 27, 2021

What's a preeminent chip company to do when its process node technology lags the competition by (roughly) one generation, but outmoded naming conventions make i Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire