Oct. 7, 2020 — With funding from the Coronavirus Aid, Relief and Economic Security (CARES) Act, Lawrence Livermore National Laboratory, chipmaker AMD and information technology company Supermicro have upgraded the supercomputing cluster Corona, providing additional resources to scientists for COVID-19 drug discovery and vaccine research.
The recent addition of nearly 1,000 AMD Radeon Instinct MI50 GPU accelerators to the National Nuclear Security Administration’s Corona system — named for the total solar eclipse of 2017 — more than doubles the speed of the cluster from about 4.5 petaFLOPS to in excess of 11 petaFLOPS of peak performance, increasing the amount of available compute cycles and enabling the system to better handle the complex simulations performed as part of LLNL’s research on COVID-19 antibodies and antiviral compounds.
“The Corona system is a major advance in our capability for predictive biomedical modeling for COVID-19,” said LLNL Deputy Associate Director for Programs Jim Brase, who heads the Lab’s COVID-19 research and rapid response effort. “It allows us to develop advanced simulations of the structure and function of virus and to use large-scale machine learning to discover and optimize new therapeutics. This performance boost will help the Corona system lead the way in accelerating pandemic response.”
Signed into law in late March, the CARES Act in part provided funding to the Department of Energy national laboratories for COVID-19 research, including the development of disease countermeasures and vaccines.
Delivered to LLNL in 2018, the Corona high performance computing (HPC) system is used for unclassified open science applications. Since the pandemic began, the system has become an essential tool for LLNL’s COVID-19 work, particularly for researchers attempting to discover and design antibodies capable of binding to SARS-CoV-2, the virus that causes COVID-19. Antibody candidates showing promise in simulations for blocking the virus from human receptors and preventing infection are being synthesized and tested.
“The expansion of Corona allows us to routinely run the computationally intensive molecular dynamics simulations to obtain the free energy between antibodies-antigens, an important feature in machine learning for narrowing down the mutant antibodies that might bind to the SARS-CoV-2 spike protein,” said LLNL COVID-19 researcher Felice Lightstone. “Additionally, Corona is being used to calculate features and conformations of more than one billion chemical compounds to screen against four binding sites in the SARS-CoV-2 proteins by machine learning and molecular docking studies.”
Technicians installed an additional 121 AMD EPYC 7002 series-based CPU nodes with 968 of AMD’s state-of-the-art Radeon Instinct MI50 GPU accelerators into the Corona system, with each node containing six GPUs. Optimized for large-scale deep learning, the AMD MI50 accelerators deliver up to 26.5 teraFLOPS of native peak theoretical half-precision or up to 13.3 teraFLOPS of single-precision peak theoretical floating-point performance, combined with 32GB of high-bandwidth memory.
“AMD is proud to deploy, along with LLNL and Supermicro, the technology devoted to accelerating this critical COVID-19 research,” said Brad McCredie, corporate vice president, Data Center GPU and Accelerated Processing at AMD. “With the high-performance computing capabilities offered by AMD processors, we aim to help researchers find creative ways to fight or cure COVID-19 much sooner.”
San Jose-based IT company Supermicro provided the motherboards, servers and racks necessary for the expansion.
“We are very pleased to be selected by LLNL for the Corona supercomputing cluster expansion, giving industry-leading resources to scientists for COVID-19 drug discovery and vaccine research,” said Charles Liang, president and CEO of Supermicro. “Supermicro delivered a turn-key large-scale cluster of Supermicro 4U GPU servers with 2-socket AMD processors and eight AMD GPUs. It’s exciting to support this global initiative and continue our focus on developing industry-leading systems for advanced computational workloads found in HPC environments.”
In addition to work by LLNL scientists, the Corona system is being offered to researchers worldwide through the COVID-19 HPC Consortium, which makes free compute cycles available to COVID-19 researchers from outside institutions. The consortium involves more than a dozen member institutions in government, industry and academia and is spearheaded by the White House Office of Science and Technology Policy, the U.S. Department of Energy and IBM.
AMD also will be donating computing cycles on the Corona system to LLNL COVID-19 researchers and projects for approved projects as part of its COVID-19 HPC Fund.
Source: Lawrence Livermore National Laboratory