LLNL’s Jim Brase Explains How DOE Labs Are Fighting (and Coping with) COVID-19

April 14, 2020

The latest episode of the This Week in HPC podcast features Jim Brase, who works with the Computing Directorate at Lawrence Livermore National Laboratory (LLNL). Intersect360 Research’s Addison Snell spoke to Brase to discuss LLNL’s approaches to fighting COVID-19 on multiple fronts and Brase’s own workflow changes as COVID-19 forces LLNL to adjust its day-to-day operations. We present this lightly edited transcript alongside the podcast audio.

Addison Snell: Hi everyone, thanks for listening to another episode of This Week in HPC with Intersect360 Research, distributed in partnership with HPCwire. I’m Addison Snell with Intersect360 Research, and this week in HPC, I’ve got a special episode where I’m joined by Jim Brase, who’s in the Computing Directorate at Lawrence Livermore National Laboratory. Jim, thanks very much for joining me this week in HPC.

Jim Brase: Hey, happy to be here.

Snell: I really wanted to talk to you because we’ve had a huge focus, of course, worldwide, on the COVID-19 (or novel coronavirus) pandemic, and you’ve been involved in a lot of work going on in the national lab efforts as we’re trying to dedicate supercomputing resources to help scientists, epidemiologists, pharmaceutical companies, and so on in the general research battle against COVID-19. To start, can you talk about some of the myriad ways that supercomputing can get deployed that help researchers in the battle against the virus’ spread?

Brase: Computing is used almost across the board in understanding and building models for how we can respond to COVID-19. It’s used in analyzing the structure of the virus with systems like x-ray crystallography or cryo-electron microscopy; it’s used in understanding the interaction between the virus and human cells using things like molecular dynamics simulations; it’s used in identifying targets on the viral proteins or in the co-complexes of the virus with human proteins. You go from there to computational design and screening of large sets of molecules, of antibodies, vaccines, all the way to the epidemiological models, flow models of ventilator systems used in hospitals. HPC really is applied across a large area and set of applications for this.

Snell: Lawrence Livermore is one of the premier supercomputing sites in the United States. Can you talk about how Livermore is involved specifically, and how you’re involved specifically – are you touching all of these types of applications, are you specializing in any particular area? What’s going on at Livermore?

Brase: Yeah, we have several specific projects that we have started up based on work that we’ve been doing in computational biology and predictive models in biology for many years. We have work specifically on analyzing the viral proteins and trying to understand what the best spots on those proteins would be for targeting with either small molecules or antibodies. So we’ll take things like the new crystal structures that are coming out, combine that with the sequence information that we have for the virus, and build high-resolution models of specific interaction sites and so on.

Then we have a project that we’ve actually been working on for quite some time, which comes out of a partnership we’ve developed over the last five years called ATOM, which stands for “Advancing Therapeutic Opportunities in Medicine.” It’s a collaboration across a number of [Department of Energy] labs with the National Cancer Institute, GlaxoSmithKline and the University of California at San Francisco. The collaboration is really aimed at building a platform for accelerated molecular design for rapid production of medicines. So we’re actually taking a lot of the tools that we’ve developed there with focus on cancer applications (because NCI is a partner) and repurposing those tools and using them to develop potential new antiviral molecules for this outbreak. So that’s one of the major projects we have.

We’re doing large-scale screening of molecules, we’re doing optimization of the molecular structures to enhance their safety and their pharmacokinetic properties. Then ultimately we’re feeding those to newly emerging experimental capabilities — some at the National Labs, some at partners like UCSF — to actually test those and validate which designs might actually be useful for application here. So that’s another area of work.

Finally, we have a very similar project that we’re doing in the computational design of antibodies. So these are large molecules, complexes of proteins, that interact with the virus and stop its operation and can do that very effectively and rapidly. So these are designs of much larger molecules than we’re doing for the small-molecule antiviral drugs, but ones which can be produced fairly rapidly and don’t have as many of the potential safety issues and therefore can be approved faster. So working on antibody treatments like this has been a particular area of focus for us as well.

We have a number of designs ready to go on this front that are being manufactured right now, and we’re hoping to get initial experimental feedback on those antibodies as soon as the next few weeks. We’re really excited about this, and hopefully we get good results out of this – at least results that we can feed back into the designs for the next round of work. We’re pretty optimistic about that approach.

Snell: This really strikes at the heart of what’s going on with regard to the urgency in this project. Oftentimes when people talk about scientific research, there’s a lot for the good of humanity and building our general scientific knowledge that has some future benefit that we might not fully understand. But now we’re talking about a project that’s real and present in our lives right now, and we look at daily trackers that tell us how many cases, how many lives lost, and people really want scientists to catch up as fast as we can. So what’s going on now, do we have early results coming out of the lab?

Brase: Yeah, we have designs that we’ve done, we have those starting experimental testing now, so the urgency on this is very high right now. As you said, we’ve been talking about this and working on this for a number of years, in various application areas. It’s been clear to us as we’ve looked at the possible threats that face us in these areas that a pandemic infectious disease like this is a likely thing. It’s happened before, it’s happening now, it’ll happen again. Being prepared to rapidly produce specifically designed therapeutics is a capability that we really strongly need in this country and in the world to be prepared for this. Viral diseases like this will continue to emerge and we need to have the tools in place to be able to respond rapidly. 

Snell: And as we pointed out, you’ve got access to some of the most powerful supercomputing resources in the world with Sierra and other supercomputers. How subscribed are you with this kind of work right now? Are things getting reprioritized, are non-COVID-19 projects getting put on hold, where are we in supply versus demand of supercomputing power?

Brase: Lawrence Livermore and our sister DOE labs host the most powerful supercomputers in the world. We are absolutely prioritizing these systems to work on COVID-19. There’s no higher priority for our computing resources right now. I wouldn’t say we’ve stopped all the other research that we’re doing: we work on a lot of very important and high-priority national security problems at Livermore, a lot of leading-edge science problems, those are still continuing. But the teams that are working on COVID-19 response, whether it’s in specific therapeutic design, in trying to understand the function and structure of the virus – those are getting the top priority. 

Snell: You made an excellent point with regard to the importance of these applications, not only for COVID-19 but also for other application areas, like, for example, national security. I talked to Carlo Cavazzoni of CINECA in Italy a couple of weeks ago on an episode of this podcast, and he was right in the epicenter of the Italian outbreak there that was so devastating. We are in northern California which is one of the original hotspots in the United States and it’s interesting to look at how it’s affecting us both professionally and personally. What’s considered essential when it comes to Lawrence Livermore National Lab? How are things operating now? How are you coping?

Brase: As far as the lab goes, we’ve been on minimal safe operations for several weeks now where the first priority is to maintain the safety of the lab and the people who are there. We’re continuing to run our computer systems, we’re continuing to have some minimal level of lab operations, particularly in areas that are related to the COVID-19 response, and there are a few specific national security priority projects that are continuing to operate at a fairly low rate but getting the important work that they’re doing done at a reasonable level. For me personally, being in the computing department at Livermore, I can pretty much work remotely as well as I can there most of the time. But just getting used to working completely through virtual meetings and so on has been a little bit of a learning experience, and we’re looking forward to getting back to whatever the new normal will look like sometime in the next weeks and months here. 

Snell: And we’re all trying to figure out what that new normal is going to look like. It feels to me a lot like things are changing very dynamically on a daily basis — sometimes the world looks different by evening than it did first thing in the morning. How do you think this might evolve your work at Livermore over the coming weeks? I know this is also a priority at the entire DOE level, there’s a consortium evolved here. How do you see this evolving?

Brase: One thing that I hope we’ll see is a continuing prioritization of building up a sustainable capability for rapid response, having the open data and transparent research on how we design new molecules for medicines and so on. As you mentioned, this has also fostered some really new and unprecedented levels of cooperation on getting things like computing resources to groups all around the world that can take advantage of them. The DOE has really come together as part of this COVID-19 HPC Consortium to help with that. That’s something I hope is a sustainable result as well: seeing the levels of cooperation that we’re seeing between agencies, between labs and so on is great.

Snell: I’ve been speaking with Jim Brase, who’s managing multiple computing projects within the Computing Directorate at Lawrence Livermore National Laboratory. Jim, thank you very much for taking some time out of your very busy schedule to join me on the podcast today. I’ll let you get back to work, I’m very grateful for the important work that you’re helping to oversee.

Brase: My pleasure, Addison, good to talk to you. 

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!

SC21 Was Unlike Any Other — Was That a Good Thing?

December 3, 2021

For a long time, the promised in-person SC21 seemed like an impossible fever dream, the assurances of a prominent physical component persisting across years of canceled conferences, including two virtual ISCs and the virtual SC20. With the advent of the Delta variant, Covid surges in St. Louis and contention over vaccine requirements... Read more…

The Green500’s Crystal Anniversary Sees MN-3 Crystallize Its Winning Streak

December 2, 2021

“This is the 30th Green500,” said Wu Feng, custodian of the Green500 list, at the list’s SC21 birds-of-a-feather session. “You could say 15 years of Green500, which makes it, I guess, the crystal anniversary.” Indeed, HPCwire marked the 15th anniversary of the Green500 – which ranks supercomputers by flops-per-watt, rather than just by flops – earlier this year with... Read more…

AWS Arm-based Graviton3 Instances Now in Preview

December 1, 2021

Three years after unveiling the first generation of its AWS Graviton chip-powered instances in 2018, Amazon Web Services announced that the third generation of the processors – the AWS Graviton3 – will power all-new Amazon Elastic Compute 2 (EC2) C7g instances that are now available in preview. Debuting at the AWS re:Invent 2021... Read more…

Nvidia Dominates Latest MLPerf Results but Competitors Start Speaking Up

December 1, 2021

MLCommons today released its fifth round of MLPerf training benchmark results with Nvidia GPUs again dominating. That said, a few other AI accelerator companies participated and, one of them, Graphcore, even held a separ Read more…

HPC Career Notes: December 2021 Edition

December 1, 2021

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it’s a promotion, new company hire, or even an accolade, we’ Read more…

AWS Solution Channel

Running a 3.2M vCPU HPC Workload on AWS with YellowDog

Historically, advances in fields such as meteorology, healthcare, and engineering, were achieved through large investments in on-premises computing infrastructure. Upfront capital investment and operational complexity have been the accepted norm of large-scale HPC research. Read more…

At SC21, Experts Ask: Can Fast HPC Be Green?

November 30, 2021

HPC is entering a new era: exascale is (somewhat) officially here, but Moore’s law is ending. Power consumption and other sustainability concerns loom over the enormous systems and chips of this new epoch, for both cost and compliance reasons. Reconciling the need to continue the supercomputer scale-up while reducing HPC’s environmental impacts... Read more…

SC21 Was Unlike Any Other — Was That a Good Thing?

December 3, 2021

For a long time, the promised in-person SC21 seemed like an impossible fever dream, the assurances of a prominent physical component persisting across years of canceled conferences, including two virtual ISCs and the virtual SC20. With the advent of the Delta variant, Covid surges in St. Louis and contention over vaccine requirements... Read more…

The Green500’s Crystal Anniversary Sees MN-3 Crystallize Its Winning Streak

December 2, 2021

“This is the 30th Green500,” said Wu Feng, custodian of the Green500 list, at the list’s SC21 birds-of-a-feather session. “You could say 15 years of Green500, which makes it, I guess, the crystal anniversary.” Indeed, HPCwire marked the 15th anniversary of the Green500 – which ranks supercomputers by flops-per-watt, rather than just by flops – earlier this year with... Read more…

Nvidia Dominates Latest MLPerf Results but Competitors Start Speaking Up

December 1, 2021

MLCommons today released its fifth round of MLPerf training benchmark results with Nvidia GPUs again dominating. That said, a few other AI accelerator companies Read more…

At SC21, Experts Ask: Can Fast HPC Be Green?

November 30, 2021

HPC is entering a new era: exascale is (somewhat) officially here, but Moore’s law is ending. Power consumption and other sustainability concerns loom over the enormous systems and chips of this new epoch, for both cost and compliance reasons. Reconciling the need to continue the supercomputer scale-up while reducing HPC’s environmental impacts... Read more…

Raja Koduri and Satoshi Matsuoka Discuss the Future of HPC at SC21

November 29, 2021

HPCwire's Managing Editor sits down with Intel's Raja Koduri and Riken's Satoshi Matsuoka in St. Louis for an off-the-cuff conversation about their SC21 experience, what comes after exascale and why they are collaborating. Koduri, senior vice president and general manager of Intel's accelerated computing systems and graphics (AXG) group, leads the team... 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…

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…

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…

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…

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…

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…

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…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire