Exposing the secrets of a deadly virus with the power of HPC

California research team draws on the power of a supercomputer from Dell Technologies and Intel to understand the structure and behavior of the SARS-CoV-2 virus.


The fight against the deadly COVID-19 disease is a collective effort drawing on the resources of scientists, laboratories and high performance computing centers around the world. This is very much the case at the University of California at San Diego, where a team of researchers is leveraging the massive computational power of a supercomputer at the Texas Advanced Computing Center (TACC) to expose the secrets of the SARS-CoV-2 virus, which causes COVID-19.

This team is led by Dr. Rommie Amaro, a distinguished professor in theoretical and computational chemistry at UC San Diego, working in conjunction with scientists in national research labs who are part of this shared quest to innovate with data. Dr. Amaro explains that her team is using the simulation power of a TACC supercomputer to churn through massive amounts of data to see things that can’t be observed under even the most powerful microscopes.

“One of the main things we’re working on in my group is to try to see things that experimentalists can’t see,” Dr. Amaro says. “We’re trying to get really detailed views into living systems. In particular, one of our goals is to understand more about the structure of the SARS-CoV-2 virus and its molecular piece parts, and how they come together into a working whole. And so we’re using computational simulation to give us insights beyond where we can get with experiments.”

The secrets of a sugary shield

Much of the research conducted by Dr. Amaro and her team revolves around a sugary molecular shield on the SARS-CoV-2 virus, made up of a substance known as glycans. SARS-CoV-2 and other viruses use this spiked sugary cloak to attack the cells of a human host. In essence, the glycans trick the human immune system into seeing them as harmless.

The breakthrough simulations and modeling conducted by the UC San Diego research team have shown the world what the sugary coating actually looks like and how it tries to hide itself from human immune systems. These efforts reveal that the glycans prime the coronavirus for infection by changing the shape of their spike protein. Scientists hope this basic research will add to the arsenal of knowledge needed to defeat the COVID-19 disease.

“When we know how it’s hiding, that gives us a chance to try to understand how we can do a better job in making things like vaccines to detect the virus in the body,” Dr. Amaro says. “Hopefully we can translate those understandings into things that will be useful either in the clinic or the street — for example, if we’re trying to reduce transmission for what we know now about aerosols and wearing masks.”

Drawing on the power of HPC

For these data- and compute-intensive scientific investigations, Dr. Amaro and her colleagues draw on the computational power of the TACC Frontera supercomputer. With a peak-performance rating of 38.7 petaflops, Frontera is currently the 9th fastest supercomputer in the world.[1]

Dell Technologies provided the primary computing system for Frontera, based on Dell EMC PowerEdge C6420 servers. The initial implementation of the system has more than 8,000 two-socket nodes, more than 16,000 Intel® Xeon® Scalable processors and 448,448 cores. In addition, Frontera incorporates several technical innovations, including Intel® Optane™ DC Persistent Memory for some large-memory nodes, CoolIT Systems high-density Direct Contact Liquid Cooling and a high performance HDR 200 Gb/s InfiniBand interconnect.

With the Frontera supercomputer, and community codes like the nanoscale molecular dynamics (NAMD) engine, Dr. Amaro and her colleagues were able to scale their compute problem across many hundreds and even thousands of nodes. And in further work, they were able to simulate the entire virus itself, which has about 300 million atoms.

“This is an enormous problem that would not be possible to even think about computing on any sort of normal desktop or laptop, or any sort of cluster that one generally has access to,” Dr. Amaro says. “It really takes the ability to scale many simulations across many hundreds and even thousands of nodes in order to make progress in this space.”

To Learn More

Find out more about Dr. Amaro’s work in the case study. For a closer look at the capabilities of the Frontera supercomputer at Texas Advanced Computing Center, see the Dell Technologies case study “A New ‘Frontera.’”

Explore more HPC  Solutions from Dell Technologies and Intel.

[1] Source: TOP500 List – November 2020.


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