IBM has unleashed its currently top-rated supercomputer, Summit, to simulate 8,000 chemical compounds in a matter of days in a hunt for something that will impact the COVID-19 infection process by binding to the virus’s spike, a key early step in coming up with an effective vaccine or cure. In the first few days Summit already identified 77 small-molecule compounds, such as medications and natural compounds, that have shown the potential to impair COVID-19’s ability to dock with and infect host cells.
POWER9 Summit Supercomputer battles COVID-19
The US Dept of Energy turned to the IBM Summit supercomputer to help in the fight against COVID-19 that appears almost unstoppable as it has swept through 84 countries on every continent except Antarctica, according to IBM. The hope is that by quickly culling the most likely initial chemical candidates, the lab researchers could get an early jump on the search for an effective cure.
As IBM explains it, viruses infect cells by binding to them and using a ‘spike’ to inject their genetic material into the host cell. When trying to understand new biological compounds, like viruses, researchers in wet labs grow the micro-organism and see how it reacts in real-life to the introduction of new compounds, but this can be a slow process without computers that can perform fast digital simulations to narrow down the range of potential variables.And even then there are challenges.
Computer simulations can examine how different variables react with different viruses, but when each of these individual variables can be comprised of millions or even billions of unique pieces of data and compounded by the need to be run in multiple simulations this isn’t trivial. Very quickly this can become a very time-intensive process, especially if you are using commodity hardware.
But, IBM continued, by using Summit, researchers were able to simulate 8,000 compounds in a matter of days to model which bone might impact that infection process by binding to the virus’s spike. As of last week, they have identified dozens of small-molecule compounds, such as medications and natural compounds, that have shown the potential to impair COVID-19’s ability to dock with and infect host cells.
“Summit was needed to rapidly get the simulation results we needed. It took us a day or two whereas it would have taken months on a normal computer,” said Jeremy Smith, Governor’s Chair at the University of Tennessee, director of the UT/ORNL Center for Molecular Biophysics, and principal researcher in the study. “Our results don’t mean that we have found a cure or treatment for COVID-19. But we are very hopeful that our computational findings will both inform future studies and provide a framework that the subsequent researchers can use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.”
After the researchers turn over the most likely possibilities to the medical scientists they are still a long way from finding a cure. The medical folks will take them into the physical wet lab and do whatever they do to determine whether a compound might work or not.
Eventually, if they are lucky, they will end up with something promising, which then has to be tested against the coronavirus and COVID-19. Published experts suggest this can take a year or two or more.
Summit gave the researchers a jump start with its massive data processing capability, enabled through its 4,608 IBM Power Systems AC922 server nodes, each equipped with two IBM POWER9 CPUs and six NVIDIA Tensorcore V100 GPUs, giving it a peak performance of 200 petaflops, in effect more powerful than one million high-end laptops.
Might quantum computing have sped up the process even more? IBM didn’t report throwing one of its quantum machines at the problem, relying instead on Summit, which has already been acclaimed as the world’s fastest supercomputer.
Nothing stays the same in the high performance computing world. HEXUS reports that when time is of the essence and lives are at stake, the value of supercomputers is highly evident. Now a new one, is being touted as the world’s first 2 Exaflops+ supercomputer, is set to begin operations in 2023. This AMD-powered giant, HEXUS notes, is claimed to be about 10x faster than Summit. That’s good to know, but let’s hope the medical researchers have already beaten the Coronavirus and COVID-19 by then.
DancingDinosaur is Alan Radding, a veteran information technology analyst, writer, and ghost-writer. Follow DancingDinosaur on Twitter, @mainframeblog, and see more of his work at http://technologywriter.com/
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