PSC: Anton 2 Supercomputer Available for COVID-19 Research, Bridges Supercomputer Aids in Drug Development and Investigates COVID-Related Tweets

April 27, 2020

April 27, 2020 — A specialized Anton 2 supercomputer, developed by D. E. Shaw Research and hosted at PSC, is now available for urgent research with the potential to impact the national COVID-19 response, thanks to agreements between D. E. Shaw Research, PSC and its funding organizations, and collaborating centers. The availability of this unparalleled resource for simulating the motions and interactions of large biomolecules with each other and with smaller molecules such as candidate drugs could contribute to understanding of the virus that causes COVID-19 and potentially help accelerate development of treatments, preventives, and possibly vaccines.

Anton was developed by D. E. Shaw Research to execute molecular dynamics simulations of biomolecules (e.g., proteins, nucleic acids, and lipids) orders of magnitude faster than was previously possible. Anton’s speed allows scientists to simulate these complex biomolecular systems, and their interactions with natural signaling molecules and drug candidates, over ultra-long timescales, enabling observation of important biological events. The Anton 2 system hosted at PSC has been provided without cost by D. E. Shaw Research for non-commercial use by the U.S. research community, and PSC supports the community’s use of this resource with operational funding from the National Institutes of Health.

Applications for computer time on the Anton 2 at PSC are being accepted through the COVID-19 HPC Consortium. The consortium also allocates COVID-19 research time on PSC’s large Bridges supercomputing platform as well as on other consortium members’ computers.

Information on applying for COVID-19 research time on Anton 2.

COVID Consortium Project Applies AI on Bridges to Antiviral Drug Development

A Carnegie Mellon University team is using artificial intelligence (AI) on PSC’s Bridges-AI platform to investigate possible candidates to fight the virus that causes COVID-19. As part of PSC’s membership in the COVID-19 High Performance Computing Consortium, a group led by Prof. Olexandr Isayev of the CMU Department of Chemistry is combining AI with computational chemistry using the AI-specialized GPU nodes on Bridges-AI. Their unique approach may be as much as a million times faster than the usual quantum mechanical calculations needed for such simulations.

The CMU scientists aim to apply AI-accelerated simulations to aid the design and repurposing of antiviral drugs specific to the virus. To achieve this goal, they must first understand the interactions of drugs and other small molecules with the virus’s proteins. Their step-wise approach will first analyze via AI a library of molecules that can be purchased from chemical companies, preparing them for automated screening in the computer. The best candidates from this screening will then be simulated on the supercomputer using a method called molecular dynamics, also enhanced with AI. Top hits from that final screening will be tested in partners’ laboratories.

The project presents an efficient strategy to discover new antiviral drugs with higher accuracy and potentially reduced cost compared with traditional drug discovery. Isayev’s work also raises the possibility of broader applications to real-world drug discovery pipelines. All screening datasets will be deposited to the COVID-19 Data Lake database, so other researchers can benefit from them as soon as possible.

Isayev has also incorporated COVID-19 research into his Special Topics in Computational Chemistry: Machine Learning course at CMU’s Mellon College of Science.

Bridges is funded by the National Science Foundation. PSC offers the platform to the open research community at no cost to scientists. Information on obtaining computing time on PSC and other systems via the COVID-19 High Performance Computing Consortium can be found here.

Bridges Powers Investigation of COVID-related Tweets

Investigators at the Pennsylvania State University have begun using PSC’s Bridges platform to study whether people’s use of Twitter can provide clues as to the course and severity of the COVID-19 pandemic. The goal is to extract information—such as whether tweets about COVID-associated symptoms could be a warning sign of an outbreak—that will help public health and government decision makers determine when and what responses can contain spread of the virus.

The project, led by Guangqing Chi of the Penn State Computational and Spatial Analysis Core, involves collecting and analyzing a massive amount of publicly available Twitter data in a given region using Bridges and Penn State’s ICDS Advanced CyberInfrastructure supercomputer. An aspect of Bridges that proved important to the work was its Hadoop-friendly nodes. Hadoop, a popular cloud-based tool for analyzing data, will not run on most supercomputers. Bridges allowed the researchers to scale up Hadoop tools they had developed on smaller computers by seamlessly moving them to the PSC resource.

More details on the Penn State project.

About the Pittsburgh Supercomputing Center

PSC is a joint effort of Carnegie Mellon University and the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry and is a leading partner in XSEDE (Extreme Science and Engineering Discovery Environment), the National Science Foundation cyber-infrastructure program.


Source: Pittsburgh Supercomputing Center

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industry updates delivered to you every week!

MLPerf Inference 4.0 Results Showcase GenAI; Nvidia Still Dominates

March 28, 2024

There were no startling surprises in the latest MLPerf Inference benchmark (4.0) results released yesterday. Two new workloads — Llama 2 and Stable Diffusion XL — were added to the benchmark suite as MLPerf continues Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing power it brings to artificial intelligence.  Nvidia's DGX Read more…

Call for Participation in Workshop on Potential NSF CISE Quantum Initiative

March 26, 2024

Editor’s Note: Next month there will be a workshop to discuss what a quantum initiative led by NSF’s Computer, Information Science and Engineering (CISE) directorate could entail. The details are posted below in a Ca Read more…

Waseda U. Researchers Reports New Quantum Algorithm for Speeding Optimization

March 25, 2024

Optimization problems cover a wide range of applications and are often cited as good candidates for quantum computing. However, the execution time for constrained combinatorial optimization applications on quantum device Read more…

NVLink: Faster Interconnects and Switches to Help Relieve Data Bottlenecks

March 25, 2024

Nvidia’s new Blackwell architecture may have stolen the show this week at the GPU Technology Conference in San Jose, California. But an emerging bottleneck at the network layer threatens to make bigger and brawnier pro Read more…

Who is David Blackwell?

March 22, 2024

During GTC24, co-founder and president of NVIDIA Jensen Huang unveiled the Blackwell GPU. This GPU itself is heavily optimized for AI work, boasting 192GB of HBM3E memory as well as the the ability to train 1 trillion pa Read more…

MLPerf Inference 4.0 Results Showcase GenAI; Nvidia Still Dominates

March 28, 2024

There were no startling surprises in the latest MLPerf Inference benchmark (4.0) results released yesterday. Two new workloads — Llama 2 and Stable Diffusion Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing po Read more…

NVLink: Faster Interconnects and Switches to Help Relieve Data Bottlenecks

March 25, 2024

Nvidia’s new Blackwell architecture may have stolen the show this week at the GPU Technology Conference in San Jose, California. But an emerging bottleneck at Read more…

Who is David Blackwell?

March 22, 2024

During GTC24, co-founder and president of NVIDIA Jensen Huang unveiled the Blackwell GPU. This GPU itself is heavily optimized for AI work, boasting 192GB of HB Read more…

Nvidia Looks to Accelerate GenAI Adoption with NIM

March 19, 2024

Today at the GPU Technology Conference, Nvidia launched a new offering aimed at helping customers quickly deploy their generative AI applications in a secure, s Read more…

The Generative AI Future Is Now, Nvidia’s Huang Says

March 19, 2024

We are in the early days of a transformative shift in how business gets done thanks to the advent of generative AI, according to Nvidia CEO and cofounder Jensen Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, codenamed Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. Wh Read more…

Alibaba Shuts Down its Quantum Computing Effort

November 30, 2023

In case you missed it, China’s e-commerce giant Alibaba has shut down its quantum computing research effort. It’s not entirely clear what drove the change. Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

DoD Takes a Long View of Quantum Computing

December 19, 2023

Given the large sums tied to expensive weapon systems – think $100-million-plus per F-35 fighter – it’s easy to forget the U.S. Department of Defense is a Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Leading Solution Providers

Contributors

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

Google Introduces ‘Hypercomputer’ to Its AI Infrastructure

December 11, 2023

Google ran out of monikers to describe its new AI system released on December 7. Supercomputer perhaps wasn't an apt description, so it settled on Hypercomputer Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

Intel Won’t Have a Xeon Max Chip with New Emerald Rapids CPU

December 14, 2023

As expected, Intel officially announced its 5th generation Xeon server chips codenamed Emerald Rapids at an event in New York City, where the focus was really o Read more…

IBM Quantum Summit: Two New QPUs, Upgraded Qiskit, 10-year Roadmap and More

December 4, 2023

IBM kicks off its annual Quantum Summit today and will announce a broad range of advances including its much-anticipated 1121-qubit Condor QPU, a smaller 133-qu Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire