Lawrence Livermore National Laboratory has deployed another high-performance computing cluster to perform functions for the National Nuclear Security Administration and support the laboratory’s COVID-19 research.
Nicknamed “Ruby,” the liquid cooled HPC, with more than 1,500 nodes, is expected to rank among the 100 most powerful supercomputers in the world when an updated list is announced this week.
Ruby will be used for unclassified work related to computer reliability testing and maintenance of the nation’s nuclear weapons stockpile, and the search for therapeutic drugs and designer antibodies against the virus that causes COVID-19.
“Ruby provides a substantial computing resource in our open collaboration zone, which has experienced a heavy increase in demand due to an uptick in telecommuting and a growth in external collaborations,” said Chris Clouse, acting program director for LLNL’s Advanced Simulation and Computing program. “A resource like Ruby provides a venue for leveraging expertise and tools in the open community for areas that are important to our programmatic missions.”
COVID-19 researchers have already begun using Ruby for the immense calculations needed for discovering small molecules capable of binding to protein sites in the structure of the coronavirus.
“Ruby is excellent for running the molecular docking calculations,” said LLNL Biochemical and Biophysical Systems Group Leader Felice Lightstone, who heads the
COVID-19 small molecule work. “Our early access on Ruby is allowing us to screen about 130 million compounds per day when using the entire machine. As our COVID-19 therapeutic effort moves toward optimizing compounds we have identified as promising, Ruby allows us to maximize the throughput of our new designs.”
Other early applications include large-scale simulating of plasma dynamics and neutron production at and simulations for inertial confinement fusion (ICF) research. LLNL said additional work will be done on asteroid detection, moon formation, and high-fidelity fission.
LLNL is partnering with Intel, Supermicro and Cornelis Networks.
“The Ruby supercomputer is a great example of how the tech industry comes together to solve some of science’s largest challenges,” said Trish Damkroger, vice president and general manager of the high-performance computing organization at Intel. “Working closely with LLNL, Supermicro and Cornelis Networks has allowed us to deploy Ruby, which will make significant contributions in the area of COVID-19 research.”