New LLNL supercomputer tackles nuclear security, COVID-19 research

November 12, 2020 //By Rich Pell
New supercomputer to tackle nuclear security, COVID-19 research
Lawrence Livermore National Laboratory (LLNL), along with partners Intel, Supermicro, and Cornelis Networks, has deployed a high-performance computing (HPC) cluster that will perform functions for the National Nuclear Security Administration (NNSA) and support the Laboratory’s COVID-19 research.

The 6-petaFLOP peak Intel Xeon Platinum-based cluster, called "Ruby," will be used for unclassified programmatic work in support of NNSA's stockpile stewardship mission, LLNL open science, and the search for therapeutic drugs and designer antibodies against SARS-CoV-2, 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," says Chris Clouse, acting program director for LLNL’s ASC 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."

Early applications for Ruby, says the organization, include large-scale simulating of plasma dynamics and neutron production at LLNL's MegaJOuLe Neutron Imaging Radiography system (MJOLNIR) and simulations for inertial confinement fusion (ICF) research conducted at the National Ignition Facility and Sandia National Laboratories’ Z-machine facility. Additional work will be done on asteroid detection, moon formation, high-fidelity fission, and other basic science discovery through LLNL's Computing Grand Challenge and Laboratory Directed Research and Development (LDRD) programs.

LLNL COVID-19 researchers also have begun using Ruby to compute the molecular docking calculations needed for discovering small molecules capable of binding to protein sites in the structure of SARS-CoV-2 for drug discovery purposes.

"Ruby is excellent for running the molecular docking calculations," says 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."

Ruby is a liquid-cooled cluster consisting of more than 1,500 nodes, each outfitted with Intel Xeon Platinum 8276L processors with Intel Deep Learning Boost and 192 gigabytes (GB) of memory. It is

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