In the pursuit of COVID-19 treatments, high-performance computing steps up
GridMarkets runs its high-performance rendering platform on Oracle Cloud Infrastructure, helping drug researchers simulate molecular reactions to COVID-19.
By Sasha Banks-Louie | October 2020
As the new coronavirus continues its infectious rampage, extreme pressure is on drug-makers to quickly introduce new vaccines and treatments that can stop the spread of COVID-19.
Running computer-generated simulations that help discover those new drugs takes massive computing power. But with businesses still largely in the mode of working remotely, accessing such resources if they’re in an on-premises data center is much harder. Plus, most on-premises servers aren’t built for the kind of speed the COVID-19 crisis demands. It can take months to run some of the most processor-intensive jobs on those systems.
“Modeling billions of molecule combinations against the key proteins that COVID-19 needs to reproduce requires enormous calculations,” said computational chemist Andrew Jennings during a recent roundtable discussion hosted by Oracle, called HPC in Healthcare. Jennings has worked with top pharmaceutical and biotech companies to research COVID-19 antibodies and small-molecule drugs. “Many big pharma companies don’t have the clusters they need to handle these workloads,” he said.
During the Zoom-based roundtable, Jennings told host Karan Batta, vice president of high-performance computing at Oracle, that he relies on the cloud-based animation rendering platform GridMarkets. He started testing it in 2018 and is now completing his molecular simulations for COVID-19 in less than 24 hours. GridMarkets runs on Oracle Cloud Infrastructure.
Jennings explained how he uses GridMarkets to simulate the reactions between different molecules and proteins—a process called docking—and then tests multiple compounds until he finds one that completely binds to the target cell structure’s surface, inhibiting the protease and stopping the COVID-19 virus from replicating.
“With Oracle Cloud Infrastructure, there’s no need to queue requests or schedule simulations. Our customers can access an unlimited number of machines, CPUs, or GPUs whenever they need them—without having to pay for unused capacity when they don’t.”
Without a single vaccine yet approved to prevent COVID-19, Jennings’ work to help speed the development of small-molecule drugs is critically important now, since they could potentially slow the spread of infection.
Oracle’s Karan Batta talks with GridMarkets about running drug discovery workloads on Oracle HPC Cloud.
Along with Batta and Jennings was Mark Ross, who cofounded GridMarkets in 2011, joined the Oracle for Startups program in 2018, and now runs the GridMarkets rendering platform on high-performance servers located in Oracle Cloud data centers around the world. “With Oracle Cloud Infrastructure, we can respond immediately with however many machines and specific configurations our customers need to run their jobs,” Ross told Batta. “What this means for our customers is that there’s no waiting, no queuing,” he said. When users submit jobs to GridMarkets, they can pick economy options, which limit the number of machines they can choose from, at a very low cost. Users who have more urgent needs can select from an unlimited number of virtual machines, CPUs, and GPUs that can run their jobs run instantly. “Our partnership with Oracle completely eliminates that old paradigm of deciding which priority a submission is.”
Such flexible, pay-for-use capacity is also how GridMarkets keeps its own costs low. “We don’t own or maintain any hardware, and we’re paying 70% less to spin up an instance on Oracle Cloud Infrastructure than we did running workloads on Amazon Web Services or Google Cloud,” Ross said.
Jennings sees no end in sight for his work, even if there’s a successful vaccine. Although drug researchers haven’t yet seen mutations that make the virus deadlier, modeling any new mutations as they’re discovered could play a key role in controlling the risk of mutations that render treatments or vaccines ineffective.
One of the capabilities Jennings likes most about GridMarkets is he can access all the resources he needs from wherever he is working. “I can select how many machines I want to run my simulations, and then immediately hit go,” Jennings said. In a matter of seconds, GridMarkets configures the software and compute resources, and it encrypts the data. When the job is finished, the machine shuts down, so there are no lingering costs. “None of this ties up local resources, I don’t have to be sitting behind a company’s firewall, and I can do it from home on a laptop.”
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Photography: Getty Images
