When scaling your workload is a matter of saving lives

By Werner Vogels, CTO, Amazon.com

April 20, 2020

On March 16, 2020, at 9:26 PM, I received an urgent email from my friend DJ Patil, former White House Chief Data Scientist, Head of Technology for Devoted Health, a Senior Fellow at the Belfer Center at the Harvard Kennedy School, and Advisor to Venrock Partners. You don’t get that many titles after your name unless you’re pretty good at something. For DJ, that “something” is math and computer science.

DJ was writing to me from the California crisis command center. He explained that he was working with governors from across the country to model the potential impact of COVID-19 for scenario planning. He wanted to help them answer critical questions, like “How many hospital beds will we need?” and “Can we reduce the spread if we temporarily close places where people gather?” and “Should we issue a shelter-in-place order and for how long?” While nobody can predict the future, modeling the virus with all the factors they did know was their best shot at helping leaders make informed decisions, which would impact hundreds of thousands of lives.

DJ assembled a team of volunteers that consisted of some of the brightest minds from across Silicon Valley and the country. As though following a call to arms, these professionals came together, in a personal capacity, to fight COVID-19 the best way they knew how: with data.

The good news is that they had a model. And not just any model. DJ and his team have been working with one that had been primarily developed by the world renowned Johns Hopkins Bloomberg School of Public Health (JHSPH). This model, which is an open-source project, uses state or county population numbers along with transportation data to model the number of people who potentially would be exposed, infected, and/or hospitalized. The model also considers virus spread based on a variety of non-pharmaceutical interventions, including shutting down schools and parks and issuing quarantine orders.

However, the model was running on the JHSPH on-premises infrastructure and the model pipeline couldn’t scale to run a large number of scenarios simultaneously or to meet the needs of the country (and potentially the world). It was too slow. To get the required scale and speed, DJ and his team needed to run the model in the cloud—so they moved their on-premises code to AWS. This led to another challenge: The code hadn’t been written initially with the cloud in mind, so it couldn’t fully take advantage of the scale and optimizations possible with AWS. As a result, DJ’s team spent one week porting and running a single scenario for California, which still wasn’t fast enough.

Imagine how long it would take to scale the pipeline for 49 more states. It would require at least months of work. Adding multiple scenarios with different variables would delay it even more. DJ’s team didn’t have that kind of time. In the words of Dr. Anthony Fauci, the director of the National Institute of Allergy and Infectious Diseases, “You don’t make the timeline. The virus makes the timeline.”

DJ’s team needed to be able to onboard the model pipeline and run a full report in hours rather than weeks or months. That’s why DJ reached out to me. He wanted our help optimizing the model pipeline for the cloud. Presented with an opportunity to help my friend and support a project that could save lives, I immediately said “yes.”

When I sounded the alarm internally, something amazing happened. People from across the company volunteered to help because they knew that they had the expertise that the project needed. Nobody asked, “Who is responsible for this customer?” or “Who has the bandwidth to work on this project?” Everyone sprang into action immediately.

We wanted to get that model pipeline running like it had a jet engine. The first thing we had to do was create an architecture that would fuel the model every step of the way. We began by profiling the code and re-compiling key numerical libraries.

Next, we had to help optimize the model pipeline. That’s when our specialist team, including the high performance computing (HPC) group, stepped in. These professionals help organizations solve some of the biggest data-related problems and tame the largest workloads, like in genomics, computational chemistry, machine learning, and autonomous vehicle simulation. They worked with members of DJ’s team, JHSPH, and some state employees non-stop through two weekends to optimize the model pipeline through re-architecture and deployment on AWS.

We contributed to the open-source JHSPH model to enable a Continuous Integration & Deployment (CI/CD) pipeline for container deployments on Amazon Elastic Container Registry. Also, we orchestrated scalable deployment strategies on AWS Elastic Container Service through AWS Batch and integrated several other services, including Amazon S3 and Amazon EC2 Auto Scaling. A high level of coordination with AWS was critical to bringing all these technologies together.

Figure 1: Architecture for the Scalable COVID Scenario Pipeline using AWS Batch

What was the end result?

DJ’s team has reduced the time to on-board the model pipeline and generate a full report from one week for one scenario to under 12 hours for multiple scenarios. Now, the new model created by JHSPH is being rolled out on AWS to all 50 states and internationally to help with making decisions that directly impact the global spread of COVID-19.

But this isn’t where the story ends—it’s where it begins. While the spread of the virus is now global, we have yet to grasp its full impact on human society. As we learn more about the spreading conditions of the virus, iterating over existing models will be crucial. There will be many more sleepless nights for everyone working on this initiative as they continue to scale the model to more states and countries as well as analyze the effect of mitigation strategies.

If you have relevant skills in technology, communications, and/or operations, please consider joining the U.S. Digital Response team. It’s a volunteer-run, non-partisan effort to help federal, state, and local government with technology, data, design, operations, communications, project management, and other needs during the COVID-19 crisis. https://www.usdigitalresponse.org/

 

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!

Oak Ridge Supercomputer Enables Next-Gen Jet Turbine Research

July 27, 2021

Air travel is notoriously carbon-inefficient, with many airlines going as far as to offer purchasable carbon offsets to ease the guilt over large-footprint travel. But even over just the last decade, major aircraft model Read more…

IBM and University of Tokyo Roll Out Quantum System One in Japan

July 27, 2021

IBM and the University of Tokyo today unveiled an IBM Quantum System One as part of the IBM-Japan quantum program announced in 2019. The system is the second IBM Quantum System One assembled outside the U.S. and follows 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 it seem like it's two nodes behind? For Intel, the response w Read more…

Will Approximation Drive Post-Moore’s Law HPC Gains?

July 26, 2021

“Hardware-based improvements are going to get more and more difficult,” said Neil Thompson, an innovation scholar at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL). “I think that’s something that this crowd will probably, actually, be already familiar with.” Thompson, speaking... Read more…

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

AWS Solution Channel

Accelerate innovation in healthcare and life sciences with AWS HPC

With Amazon Web Services, researchers can access purpose-built HPC tools and services along with scientific and technical expertise to accelerate the pace of discovery. Whether you are sequencing the human genome, using AI/ML for disease detection or running molecular dynamics simulations to develop lifesaving drugs, AWS has the infrastructure you need to run your HPC workloads. Read more…

PEARC21 Panel Reviews Eight New NSF-Funded HPC Systems Debuting in 2021

July 23, 2021

Over the past few years, the NSF has funded a number of HPC systems to further supply the open research community with computational resources to meet that community’s changing and expanding needs. A review of these systems at the PEARC21 conference (July 19-22) highlighted... 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…

Will Approximation Drive Post-Moore’s Law HPC Gains?

July 26, 2021

“Hardware-based improvements are going to get more and more difficult,” said Neil Thompson, an innovation scholar at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL). “I think that’s something that this crowd will probably, actually, be already familiar with.” Thompson, speaking... Read more…

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

Chameleon’s HPC Testbed Sharpens Its Edge, Presses ‘Replay’

July 22, 2021

“One way of saying what I do for a living is to say that I develop scientific instruments,” said Kate Keahey, a senior fellow at the University of Chicago a Read more…

Summer Reading: “High-Performance Computing Is at an Inflection Point”

July 21, 2021

At last month’s 11th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART), a group of researchers led by Martin Schulz of the Leibniz Supercomputing Center (Munich) presented a “position paper” in which they argue HPC architectural landscape... Read more…

PEARC21 Panel: Wafer-Scale-Engine Technology Accelerates Machine Learning, HPC

July 21, 2021

Early use of Cerebras’ CS-1 server and wafer-scale engine (WSE) has demonstrated promising acceleration of machine-learning algorithms, according to participa Read more…

15 Years Later, the Green500 Continues Its Push for Energy Efficiency as a First-Order Concern in HPC

July 15, 2021

The Green500 list, which ranks the most energy-efficient supercomputers in the world, has virtually always faced an uphill battle. As Wu Feng – custodian of the Green500 list and an associate professor at Virginia Tech – tells it, “noone" cared about energy efficiency in the early 2000s, when the seeds... 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…

AMD Chipmaker TSMC to Use AMD Chips for Chipmaking

May 8, 2021

TSMC has tapped AMD to support its major manufacturing and R&D workloads. AMD will provide its Epyc Rome 7702P CPUs – with 64 cores operating at a base cl 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…

Berkeley Lab Debuts Perlmutter, World’s Fastest AI Supercomputer

May 27, 2021

A ribbon-cutting ceremony held virtually at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) today marked the official launch of Perlmutter – aka NERSC-9 – the GPU-accelerated supercomputer built by HPE in partnership with Nvidia and AMD. 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 called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I 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 after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... 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…

Iran Gains HPC Capabilities with Launch of ‘Simorgh’ Supercomputer

May 18, 2021

Iran is said to be developing domestic supercomputing technology to advance the processing of scientific, economic, political and military data, and to strengthen the nation’s position in the age of AI and big data. On Sunday, Iran unveiled the Simorgh supercomputer, which will deliver.... Read more…

Leading Solution Providers

Contributors

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…

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…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

Microsoft to Provide World’s Most Powerful Weather & Climate Supercomputer for UK’s Met Office

April 22, 2021

More than 14 months ago, the UK government announced plans to invest £1.2 billion ($1.56 billion) into weather and climate supercomputing, including procuremen Read more…

Q&A with Jim Keller, CTO of Tenstorrent, and an HPCwire Person to Watch in 2021

April 22, 2021

As part of our HPCwire Person to Watch series, we are happy to present our interview with Jim Keller, president and chief technology officer of Tenstorrent. One of the top chip architects of our time, Keller has had an impactful career. 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…

Senate Debate on Bill to Remake NSF – the Endless Frontier Act – Begins

May 18, 2021

The U.S. Senate today opened floor debate on the Endless Frontier Act which seeks to remake and expand the National Science Foundation by creating a technology Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire