Azure Scaled to Record 86,400 Cores for Molecular Dynamics

By Oliver Peckham

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign (UIUC) to test the limits of Azure’s scalability on a key molecular dynamics tool. The result: successful scaling across a staggering 86,400 CPU cores — a virtual cluster with nearly 5 peak petaflops of performance.

The code at hand was Nanoscale Molecular Dynamics (NAMD), developed in-house at UIUC. NAMD, nicknamed “the computational microscope,” has played a major role in COVID-19 research this year and was at the heart of the massive simulations of the coronavirus that yesterday won the 2020 ACM Gordon Bell Special Prize in HPC-Based COVID-19 Research. Azure in fact hosted similar simulations of SARS-CoV-2’s viral envelope and spike proteins as part of a project funded by the COVID-19 HPC Consortium.

The efforts focused on scaling Azure’s HBv2 virtual machines, each of which was equipped with 120 AMD Epyc 7002-series CPU cores, 480GB of memory and – crucially – 200 Gbps Nvidia HDR InfiniBand. Using the HBv2 VMs, the team scaled NAMD on 20 million-atom and 210 million-atom systems. The 210 million-atom system scaled up to 720 nodes, achieving what Azure claims is the largest HPC simulation ever on the public cloud by an order of magnitude.

“The team found not only could HBv2 clusters meet the researchers’ requirements, but that performance and scalability on Azure rivaled and in some cases surpassed the capabilities of the Frontera supercomputer, ranked 8th on the June 2020 Top500 list,” wrote Evan Burness, principal program manager for Azure HPC. 

Image courtesy of Microsoft Azure.

The successful scaling bodes well for future molecular dynamics projects in the cloud, as the test was intended to evaluate HBv2 VMs for future SARS-CoV-2 simulations.

“Our NIH center has put in years of programming effort towards developing fast scalable codes in NAMD,” said David Hardy, a senior research programmer at UIUC. “These efforts along with the UCX [communication layer] support in Charm++ [the library NAMD uses for parallelization] allowed us to get good performance and scaling for NAMD on the Microsoft Azure Rome cluster without any other modifications to the source code.” 

Looking ahead, Azure will likely begin to deploy new hardware soon. Recently, the cloud provider announced that it would be using next-generation AMD Epyc CPUs – codenamed “Milan” – to power future HB-series virtual machines for HPC use cases. AMD is currently preparing to ship the Milan-series CPUs.

Header image: a still from a NAMD simulation of SARS-CoV-2. Image courtesy of UIUC.

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!

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

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from its predecessors, including the red-hot H100 and A100 GPUs. 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. While Nvidia may not spring to mind when thinking of the quant Read more…

2024 Winter Classic: Meet the HPE Mentors

March 18, 2024

The latest installment of the 2024 Winter Classic Studio Update Show features our interview with the HPE mentor team who introduced our student teams to the joys (and potential sorrows) of the HPL (LINPACK) and accompany Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the field was normalized for boys in 1969 when the Apollo 11 missi Read more…

Apple Buys DarwinAI Deepening its AI Push According to Report

March 14, 2024

Apple has purchased Canadian AI startup DarwinAI according to a Bloomberg report today. Apparently the deal was done early this year but still hasn’t been publicly announced according to the report. Apple is preparing Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimization algorithms to iteratively refine their parameters until Read more…

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

March 18, 2024

Nvidia's latest and fastest GPU, code-named 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…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the fi Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimizat Read more…

PASQAL Issues Roadmap to 10,000 Qubits in 2026 and Fault Tolerance in 2028

March 13, 2024

Paris-based PASQAL, a developer of neutral atom-based quantum computers, yesterday issued a roadmap for delivering systems with 10,000 physical qubits in 2026 a Read more…

India Is an AI Powerhouse Waiting to Happen, but Challenges Await

March 12, 2024

The Indian government is pushing full speed ahead to make the country an attractive technology base, especially in the hot fields of AI and semiconductors, but Read more…

Charles Tahan Exits National Quantum Coordination Office

March 12, 2024

(March 1, 2024) My first official day at the White House Office of Science and Technology Policy (OSTP) was June 15, 2020, during the depths of the COVID-19 loc Read more…

AI Bias In the Spotlight On International Women’s Day

March 11, 2024

What impact does AI bias have on women and girls? What can people do to increase female participation in the AI field? These are some of the questions the tech 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…

Analyst Panel Says Take the Quantum Computing Plunge Now…

November 27, 2023

Should you start exploring quantum computing? Yes, said a panel of analysts convened at Tabor Communications HPC and AI on Wall Street conference earlier this y 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…

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

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…

Training of 1-Trillion Parameter Scientific AI Begins

November 13, 2023

A US national lab has started training a massive AI brain that could ultimately become the must-have computing resource for scientific researchers. Argonne N 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…

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…

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…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire