Advanced Clustering and AMD CPUs Help Folding@home project study Covid-19 proteins

Posted on August 4, 2020

Dr. Greg Bowman of Washington University School of Medicine in St. Louis has turned the focus of the Folding@home project, which is the largest crowd-sourced computational biology project the world has ever seen, over to the study of Covid-19.

Dr. Greg Bowman inspects Advanced Clustering hardware that has helped analyze huge data sets.

Bowman, an associate professor of biochemistry and molecular biophysics at university, is relying on tens of thousands of home computers to study the complexities of disease through the Folding@home project. At the moment, the Folding@home team is using 5 million devices powered by 4.5 million CPUs (31 million CPU cores) along with half a million GPUs to study Covid-19.

With more than 100 simulation projects currently underway via Folding@home to study the Covid-19 proteins, one of Dr. Bowman’s biggest challenges is data analysis. To solve that problem, he has turned to Advanced Clustering Technologies to provide high performance computing hardware equal to the task of analyzing his huge datasets.

“We are bringing in 6TB of data per hour,” Bowman said. “It’s a huge amount of data to analyze, so we need significant hardware on our end to run the analysis. As we bring in this equipment, the question will be, ‘How fast can we humans decide on the next step.’ The technology is there to support us. We just need to be able to make those decisions. That’s exactly where we want to be as scientists.”

The HPC equipment Bowman is acquiring for his project will be quite an upgrade. The new system is built upon Advanced Clustering Technologies’ ACTblade e230, which provides up to four independent AMD EPYC compute nodes with 8 drives in one chassis. This blade combines storage, networking and computing in a single system to increase scalability and reduce datacenter complexity.

“Most of the data analysis we’re currently doing relies on six-year-old high performance computing machines that offer 240 cpu cores. The new machines will use AMD EPYC 7742 processors providing 1,500 cpu cores. That’s a nice boost of our throughput.”

Click here to access the complete Folding@home case study.

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