SF Technotes

Supercomputers vs. COVID-19

By Michael Castelluccio
April 8, 2020
1 comments

On Monday March 23, 2020, the U.S. CTO Michael Kratsios announced the formation of the COVID-19 High Performance Computing (HPC) Consortium to fight COVID-19. He said, “And that means unleashing the full capacity of our world-class supercomputers to rapidly advance scientific research for treatments and a vaccine.”

 

Dario Gil, IBM’s director of research and a member of the coalition, described the reasons for gathering the collected power of 16 supercomputers in the effort: “These high-performance computing systems allow researchers to run very large numbers of calculations in epidemiology, bioinformatics, and molecular modeling. These experiments would take years to complete if worked by hand, or months if handled on slower, traditional computing platforms.”

 

THE HPC TEAM

 

The team is a gathering of academic, commercial, and government resources, all focusing their expertise on a single problem—the COVID-19 pandemic. The members include the following:

  • Massachusetts Institute of Technology (MIT)
  • Rensselaer Polytechnic Institute (RPI)
  • IBM
  • Amazon Web Services
  • Google Cloud
  • Microsoft
  • Hewlett Packard Enterprise
  • Five U.S. Department of Energy Labs including:
    Argonne National Laboratory
    Lawrence Livermore National Laboratory
    Los Alamos National Laboratory
    Oak Ridge National Laboratory
    Sandia National Laboratories
  • The National Science Foundation
  • NASA

The consortium is open to others willing to join the effort.

 

The massive computing power of the 16 supercomputers together represent more than 330 petaflops (one petaflop is the ability of a computer to do one thousand trillion floating point operations per second), 775,000 central processing unit cores, and 34,000 graphics processing units. The list includes IBM Summit (photo at top), the number one most powerful supercomputer in the world, along with MIT’s Supercloud, a 7-petaflops HPC cluster.

 

The RPI supercomputer AiMOS (Artificial Intelligence Multiprocessing Optimized System) is the most powerful supercomputer housed at a private university. It can perform 8 quadrillion calculations per second. According to RPI, AiMOS is “uniquely designed and optimized to help users explore new applications in artificial intelligence. In addition to the platform, Rensselaer is offering access to the expertise of [its] world-class faculty in data, artificial intelligence, networking, therapeutic interventions, materials, public health, and other areas necessary to understand and address the threat of COVID-19.”

 

The computing power along with computational scientists to ensure the hardware is used efficiently will be available to researchers. Gil says these high-performance computers were chosen not just for their vast computing capacities, but also for their ability to manage large databases in epidemiology, bioinformatics, and molecular modeling.

 

Bioinformatics is the domain of a relatively new kind of scientist, the computational biologist. The job description is formidable. According to Wikipedia, “Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques to the study of biological, ecological, behavioral, and social systems.”

 

Gil offered an example of the potential of IBM’s Summit computer in bioinformatics with work that’s already under way. “At the Oak Ridge National Laboratory and the University of Tennessee, [IBM’s Summit supercomputer] screened 8,000 compounds to find those that are most likely to bind the main ‘spike’ protein of the Coronavirus, rendering it unable to infect host cells. They were able to recommend the 77 promising small-molecule drug compounds that could now be experimentally tested.” In the press materials, Gill explained, “This is the power of accelerating discovery through computation.”

 

This video illustrates the search.

 

 

 

Paul Dabbar, undersecretary for science at the U.S. Department of Energy, also pointed to other work at the Argonne National Lab where researchers have already examined 250 million known small molecules that may affect the coronavirus.

 

THE XSEDE PORTAL

 

Kratsios said that HPC has been ramping up and “there’s already a significant amount of scientific advancement on coronavirus research we’re going to be building off of with this big public/private partnership.”

 

 

The clearing house for presenting and sharing the research of these institutions and companies is the Extreme Science and Engineering Discovery Environment (XSEDE) website at portal.xsede.org.

 

The call for projects is on the website. “Researchers are invited to submit COVID-19 related research proposals to the consortium via this online portal, which will then be reviewed for matching with computer resources from one of the partner institutions. Emphasis (will be) on projects that can ensure rapid results.”

 

The amount of research into a possible vaccine and treatment continues to grow worldwide. The World Health Organization’s website at who.int updates the latest scientific findings and knowledge on the coronavirus disease.

 



Michael Castelluccio has been the Technology Editor for Strategic Finance for 25 years. His SF Technotes blog is in its 22nd year. You can contact Mike at mcastelluccio@imanet.org.


1 + Show Comments

1 comment.
    Michael Parietti April 11, 2020 AT 10:03 am

    Awesome Article! Amazing and promising outlook on the fight to defeat the Pandemic/Apocalypse.