Using Blue Waters Supercomputer to Better Understand Ebola Transmission

September 14, 2016

The following is a blog post by Hannah Remmert.

Sept. 14 — Most of us in the United States likely feel safe from Ebola—West Africa feels like it’s worlds away. We’re located very far geographically from the countries with the highest frequency of infections, like Liberia, Sierra Leone, and Guinea, and many of us aren’t likely to be traveling to those places any time soon. But what about in the airports? Could you come into contact with someone who has contracted Ebola and find yourself infected?

Florida State University professor Ashok Srinivasan is researching a way to prevent that scenario from ever happening, or at least making sure that it is a lot less likely to occur with the help of the Blue Waters supercomputer.

When people travel via air, they inevitably come into contact with many people between standing in line for security, rushing to get in line to board their flight, and sitting close to many people during the flight itself. Thus, Srinivasan and his team, consisting of Sirish Namilae from Embry-Riddle Aeronautical University and Robert Pahle, Anuj Mubayi, and Matthew Scotch from Arizona State University, are evaluating airlines policies regarding flights, and if a change to these policies could have an effect on the likelihood of infection transmission.

“We’re looking at whether a change in procedures and policies related to air travel can reduce the likelihood of infection transmission in planes, because a lot of infections, for example SARS (severe acute respiratory syndrome), influenza, and so on, are spread through planes primarily. So we want to see if we can change the boarding procedure, how seating arrangements are made, the type of plane and so on, so that the likelihood of an epidemic is reduced,” explains Srinivasan.

What they’ve found is that changing the boarding procedure can significantly reduce the likelihood of infection transmission.

“The boarding procedure is often designed for efficiency. A lot of the procedures that are very good in terms of efficiency, that is, getting people into the seats very fast, are also very bad for disease transmission because they bring people close together. So policies that take a little longer to board the plane also tend to reduce the likelihood of infection transmission.”

This discovery could not have been possible without the help of Blue Waters. Srinivasan and his team were able to run 70,000 cores for each simulation, which would take about 20 minutes per core, or about 25,000 hours of computing, which would be over 1,000 days. And that’s for just one model. What they found was that their models needed refining. The original model of passenger movement was designed for evacuation, not the normal boarding and disembarkation behavior they needed. This required them to refine the original model a few times to get a more realistic simulation of human movement. Without Blue Waters, the time needed just to create the correct model would have taken many years.

And Srinivasan was happy about more than just the technological capacities of Blue Waters.

“Well, on the whole, the support team that came with Blue Waters was very useful. They supported and enabled us to appropriately scale our simulations, whereas with some of the other supercomputers, we didn’t have the service ecosystem that would allow us to do that, even if the hardware had resources available.”

The research Srinivasan and his team are doing is unique in that many of the other researchers studying Ebola are focused on the scientific understanding of the virus and its transmission, whereas Srinivasan is focusing on how the policies and procedures engrained in our society can affect transmission. When there are massive outbreaks of disease and infection, flights are affected. In late 2014, many people were pushing to ban flights from Ebola-infected areas. “By fine-tuning certain policies and procedures, we can avoid detrimental impacts not only to human health but to our economies.”


Source: Hannah Remmert, NCSA

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!

LANL Researchers Simulate Billion-Atom Biomolecule

April 23, 2019

Simulating large biomolecules has long been challenging. Now, researchers from Los Alamos National Laboratory, RIKEN Center for Computational Science in Japan, the New Mexico Consortium, and New York University have succ Read more…

By John Russell

Students Gird for Cluster Mayhem at ASC19

April 23, 2019

Final cluster configurations have been set, and competitors in the ASC19 Student Supercomputer Challenge have started running the various AI models and HPC benchmarks that will determine who is declared champion. But if Read more…

By Alex Woodie

Student Cluster Season Opener: ASC19

April 22, 2019

Calling all computer sports fans! Now hear this:  The 2019 Student Cluster Competition season is officially underway with the beginning of the ASC19 event on Tuesday, April 22nd. For you millions of student cluster c Read more…

By Dan Stark

HPE Extreme Performance Solutions

HPE and Intel® Omni-Path Architecture: How to Power a Cloud

Learn how HPE and Intel® Omni-Path Architecture provide critical infrastructure for leading Nordic HPC provider’s HPCFLOW cloud service.

powercloud_blog.jpgFor decades, HPE has been at the forefront of high-performance computing, and we’ve powered some of the fastest and most robust supercomputers in the world. Read more…

IBM Accelerated Insights

Bridging HPC and Cloud Native Development with Kubernetes

The HPC community has historically developed its own specialized software stack including schedulers, filesystems, developer tools, container technologies tuned for performance and large-scale on-premises deployments. Read more…

A Beginner’s Guide to the ASC19 Finals

April 22, 2019

Three thousand watts. That's how much power the competitors in the 2019 ASC Student Supercomputer Challenge here in Dalian, China, have to work with. Everybody would like more juice to run compute-intensive HPC simulatio Read more…

By Alex Woodie

A Beginner’s Guide to the ASC19 Finals

April 22, 2019

Three thousand watts. That's how much power the competitors in the 2019 ASC Student Supercomputer Challenge here in Dalian, China, have to work with. Everybody Read more…

By Alex Woodie

At ASF 2019: The Virtuous Circle of Big Data, AI and HPC

April 18, 2019

We've entered a new phase in IT -- in the world, really -- where the combination of big data, artificial intelligence, and high performance computing is pushing Read more…

By Alex Woodie with Doug Black and Tiffany Trader

Interview with 2019 Person to Watch Michela Taufer

April 18, 2019

Today, as part of our ongoing HPCwire People to Watch focus series, we are highlighting our interview with 2019 Person to Watch Michela Taufer. Michela -- the Read more…

By HPCwire Editorial Team

Intel Gold U-Series SKUs Reveal Single Socket Intentions

April 18, 2019

Intel plans to jump into the single socket market with a portion of its just announced Cascade Lake microprocessor line according to one media report. This isn Read more…

By John Russell

BSC Researchers Shrink Floating Point Formats to Accelerate Deep Neural Network Training

April 15, 2019

Sometimes calculating solutions as precisely as a computer can wastes more CPU resources than is necessary. A case in point is with deep learning. In early stag Read more…

By Ken Strandberg

Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

The insatiable appetite for higher throughput and lower latency – particularly where edge analytics and AI, network functions, or for a range of datacenter ac Read more…

By Doug Black

Nvidia Doubles Down on Medical AI

April 9, 2019

Nvidia is collaborating with medical groups to push GPU-powered AI tools into clinical settings, including radiology and drug discovery. The GPU leader said Monday it will collaborate with the American College of Radiology (ACR) to provide clinicians with its Clara AI tool kit. The partnership would allow radiologists to leverage AI techniques for diagnostic imaging using their own clinical data. Read more…

By George Leopold

Digging into MLPerf Benchmark Suite to Inform AI Infrastructure Decisions

April 9, 2019

With machine learning and deep learning storming into the datacenter, the new challenge is optimizing infrastructure choices to support diverse ML and DL workfl Read more…

By John Russell

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

ClusterVision, European HPC specialists that have built and installed over 20 Top500-ranked systems in their nearly 17-year history, appear to be in the midst o Read more…

By Tiffany Trader

Intel Reportedly in $6B Bid for Mellanox

January 30, 2019

The latest rumors and reports around an acquisition of Mellanox focus on Intel, which has reportedly offered a $6 billion bid for the high performance interconn Read more…

By Doug Black

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

By Tiffany Trader

Looking for Light Reading? NSF-backed ‘Comic Books’ Tackle Quantum Computing

January 28, 2019

Still baffled by quantum computing? How about turning to comic books (graphic novels for the well-read among you) for some clarity and a little humor on QC. The Read more…

By John Russell

IBM Quantum Update: Q System One Launch, New Collaborators, and QC Center Plans

January 10, 2019

IBM made three significant quantum computing announcements at CES this week. One was introduction of IBM Q System One; it’s really the integration of IBM’s Read more…

By John Russell

Deep500: ETH Researchers Introduce New Deep Learning Benchmark for HPC

February 5, 2019

ETH researchers have developed a new deep learning benchmarking environment – Deep500 – they say is “the first distributed and reproducible benchmarking s Read more…

By John Russell

Leading Solution Providers

SC 18 Virtual Booth Video Tour

Advania @ SC18 AMD @ SC18
ASRock Rack @ SC18
DDN Storage @ SC18
HPE @ SC18
IBM @ SC18
Lenovo @ SC18 Mellanox Technologies @ SC18
NVIDIA @ SC18
One Stop Systems @ SC18
Oracle @ SC18 Panasas @ SC18
Supermicro @ SC18 SUSE @ SC18 TYAN @ SC18
Verne Global @ SC18

IBM Bets $2B Seeking 1000X AI Hardware Performance Boost

February 7, 2019

For now, AI systems are mostly machine learning-based and “narrow” – powerful as they are by today's standards, they're limited to performing a few, narro Read more…

By Doug Black

The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

How do you know if an HPC system, particularly a larger-scale system, is well-suited for deep learning workloads? Today, that’s not an easy question to answer Read more…

By John Russell

Arm Unveils Neoverse N1 Platform with up to 128-Cores

February 20, 2019

Following on its Neoverse roadmap announcement last October, Arm today revealed its next-gen Neoverse microarchitecture with compute and throughput-optimized si Read more…

By Tiffany Trader

Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

By Tiffany Trader

France to Deploy AI-Focused Supercomputer: Jean Zay

January 22, 2019

HPE announced today that it won the contract to build a supercomputer that will drive France’s AI and HPC efforts. The computer will be part of GENCI, the Fre Read more…

By Tiffany Trader

Oil and Gas Supercloud Clears Out Remaining Knights Landing Inventory: All 38,000 Wafers

March 13, 2019

The McCloud HPC service being built by Australia’s DownUnder GeoSolutions (DUG) outside Houston is set to become the largest oil and gas cloud in the world th Read more…

By Tiffany Trader

Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

The insatiable appetite for higher throughput and lower latency – particularly where edge analytics and AI, network functions, or for a range of datacenter ac Read more…

By Doug Black

UC Berkeley Paper Heralds Rise of Serverless Computing in the Cloud – Do You Agree?

February 13, 2019

Almost exactly ten years to the day from publishing of their widely-read, seminal paper on cloud computing, UC Berkeley researchers have issued another ambitious examination of cloud computing - Cloud Programming Simplified: A Berkeley View on Serverless Computing. The new work heralds the rise of ‘serverless computing’ as the next dominant phase of cloud computing. Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This