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Meet Ruby the Supercomputer: Now in Service for COVID-19 and Nuclear Security Research

Ruby, a 6 petaFLOP Intel Xeon Platinum-based cluster, will be used for unclassified programmatic work in support of the National Nuclear Security Administration’s stockpile stewardship mission, open science and the search for therapeutic drugs and designer antibodies against SARS-CoV-2, the virus that causes COVID-19. Photo by Katrina Trujillo/LLNL.

Lawrence Livermore National Laboratory (LLNL), along with partners Intel, Supermicro and Cornelis Networks, have deployed “Ruby,” 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.

Funded by NNSA’s Advanced Simulation and Computing (ASC) program, the Laboratory’s Multi-programmatic and Institutional Computing (M&IC) program and the Coronavirus Aid, Relief and Economic Security (CARES) Act, the 6 petaFLOP peak, Intel® Xeon® Platinum-based cluster 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.

LLNL COVID-19 researchers 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,” 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 for Ruby include large-scale simulating of plasma dynamics and neutron production at LLNL’s MegaJOuLe Neutron Imaging Radiography system and simulations for inertial confinement fusion research conducted at the National Ignition Facility and Sandia National Laboratories’ Z-machine. 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.

“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 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.”

Expected to rank among the 100 most powerful supercomputers in the world when the updated Top500 List is announced on Nov. 16, 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 of memory.

Ruby’s nodes are interconnected using Omni-Path, the purpose-built high-performance network from Cornelis Networks. Spun out from Intel in September, Cornelis Networks continues to partner with Intel to co-optimize HPC cluster solutions based on Xeon and Omni-Path. 

San Jose-based IT company Supermicro provided the 26 racks and infrastructure needed including 376 TwinPro™ Systems and 24 Ultra Systems.

For more on Ruby, visit LLNL.

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