How Charm++ is helping scientists study COVID-19

Charm++ crucial to 305-million atom simulation of COVID-19’s protein envelope

One of the largest and highest-resolution COVID-19 simulations in the world has Charm++ at its heart. The work relied on NAMD, a powerful molecular dynamics code, that leverages Charm++’s runtime system to decompose computational simulations into smaller chunks, distribute those chunks across processors, and dynamically load balance the computation to ensure maximum efficiency. The team responsible for these astounding runs recently won the 2020 ACM Gordon Bell Special Prize for High-Performance Computing Based on COVID-19 Research.

COVID-19 simulations have been running on supercomputers at Oak Ridge National Lab and the Texas Advanced Computing Center since the spring of 2020 -- just weeks after initial x-ray crystallography and electron microscopy images were completed.

The largest of the runs simulated more than 305 million atoms and more than a trillion timesteps. Watch the Gordon Bell Special Prize-winning team’s talk on these extraordinary supercomputing runs, given at the 2020 Supercomputing Conference.

“This was such an exciting project, and it really illustrates the fact that the Charmworks team supports world-changing parallel simulations like these across a variety of fields -- molecular dynamics, fluid dynamics, structural mechanics, adaptive mesh refinement, discrete event simulation, and more. We’re ready to help companies and academic

Image Credit: Amaro Lab UCSD

                                                                                                                        researchers  whether they’re  running on a  small cluster or the largest supercomputers in the world,” said Sanjay Kale, CEO of Charmworks.

That ultrafast work included targeted improvements to Charm++ and a new version of NAMD, fine-tuned to make the tools yet better suited to modeling COVID. Charm++’s native IBM PAMI and UCX messaging were crucial, speeding the transmission of data across the systems’ interconnects. They yielded a 20 percent performance increase in the new versions.

The NAMD/Charm++ based simulations looked at the virus’ entire protein envelope and the spikes that dot it. Scientists call these spikes the “main infection machinery.” When they attach to the ACE2 receptor in humans, that contact initiates the cascade of infection processes that make people sick. The simulations showed the structure and conformation of the glycan sugars that shield the spikes. Because these glycan sugars protect the spikes, they are a major target for interventions and therapies for COVID-19 and other viruses that attack humans -- and they are too small to be seen using imaging technologies in experiments.

Charmworks’ suite of tools lets you expand your code across more processors efficiently and effectively – so you can deliver faster, higher-resolution insights for your company.

 

Develop, maintain, or run parallel simulation applications – whether you’re on a small cluster or a massive supercomputer? We can help you with:

  • Automatic dynamic load balancing.

  • Improved communication performance.

  • Fault tolerance and power costs.

Email us to get started!

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