What’s New in HPC Research: Face Detection, DNA Nanotechnology, Visualization & More

By Oliver Peckham

April 18, 2020

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here.


Benchmarking machine learning accelerators

As machine learning becomes a more common tool of the trade in HPC, the field of available hardware accelerators (such as CPUs, GPUs, FPGAs and others) has substantially grown. In this paper, a team of authors from MIT’s Lincoln Laboratory Supercomputing Center survey the state of these processors and accelerators for machine learning, identifying trends in power consumption, precision and more.

Authors: Albert Reuther, Peter Michaleas, Michael Jones, Vijay Gadepally, Siddharth Samsi and Jeremy Kepner.

Using supercomputing to predict the structure and dynamics of DNA systems

Designing and synthesizing DNA using nanotechnology is a burgeoning field, but computational requirements remain a substantial bottleneck for researchers. These authors – a duo from the University of Illinois at Urbana-Champaign – applied a supercomputing-driven multi-resolution simulation framework, called “MrDNA,” that is able to produce an atom-scale structure of a self-assembled DNA nanosystem in just half an hour. 

Authors: Christopher Maffeo and Aleksei Aksimentiev

Building a shared HPC resource center across a university system

More and more, high-performance computing resources are becoming an essential item for university departments – and not just the computer scientists. This paper from George Washington University explores the university’s experiences in planning and establishing its first HPC center and presents a set of lessons learned for other universities aiming to acquire HPC resources.

Authors: Glen MacLachlan, Jason Hurlburt, Marco Suarez, Kai Leung Wong, William Burke, Terrence Lewis, Andrew Gallo, Jaroslav Flidr, Raoul Gabiam, Janis Nicholas and Brian Ensor.

Optimizing HPC for face detection

Object detection algorithms often have high computational requirements. In this paper, written by a team from the Autonomous University of Tamaulipas, the authors apply a parallelization strategy using Lustre and MPI to conduct face detection on an HPC cluster. The authors found a substantial reduction in the read time of image files and a similarly large improvement in processing speed. 

Authors: Hugo Eduardo Camacho Cruz, Julio Cesar González Mariño and Jesús Humberto Foullon Peña.

Improving high-performance visualization

Visualization is often important to translate research results into something more accessible and usable. The authors – a trio from Virginia Tech – present a workflow that aims to tackle two issues in scientific visualization: rendering scalability and scalability of the representations themselves. To improve these areas, the authors leveraged tools like subsampling and parallel rendering, testing their workflow on HPC clusters.

Authors: Ayat Mohammed, Nicholas F. Polys and Duncan Farrah. 

Using HPC for processing EEG data

Electroencephalograms (EEGs) are important tests for diagnosing brain conditions like seizures, epileopsy, tumors and more. These authors — a team from the University of California San Diego and the École Polytechnique Fédérale de Lausanne — describe how EEGLAB, an open-source signal processing environment for EEGs, was integrated with the Neuroscience Gateway (NSG), allowing researchers to run EEGLAB on HPC resources through the XSEDE network.

Authors: RamónMartínez-Cancino, Arnaud Delorme, Dung Truong, Fiorenzo Artoni, Kenneth Kreutz-Delgado, Subhashini Sivagnanam, Kenneth Yoshimoto, Amitava Majumdar and Scott Makeig.

Evaluating HPC needs in Danube region countries

With supercomputing becoming a necessity for global competitiveness, some countries are finding themselves at a disadvantage. This study, conducted by researchers from Serbia, Slovenia, and Bosnia and Herzegovina, examines the HPC needs of countries in the Danube region (such as the authors’ own countries, as well as Bulgaria, the Czech Republic and many others). The authors aimed to determine the most significant criteria for the introduction of HPC in each country, outlining the nations’ individualized needs.

Authors: Milovan Tomašević, Lucija Lapuh, Željko Stević, Dragiša Stanujkić and Darjan Karabašević.


Do you know about research that should be included in next month’s list? If so, send us an email at [email protected]. We look forward to hearing from you.

Subscribe to HPCwire's Weekly Update!

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

Intel Speeds NAMD by 1.8x: Saves Xeon Processor Users Millions of Compute Hours

August 12, 2020

Potentially saving datacenters millions of CPU node hours, Intel and the University of Illinois at Urbana–Champaign (UIUC) have collaborated to develop AVX-512 optimizations for the NAMD scalable molecular dynamics cod Read more…

By Rob Farber

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yesterday, Intel reported an Optane and DAOS-based system finishe Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows users to virtually “walk” around the massive supercomputer Read more…

By Oliver Peckham

Supercomputer Simulations Examine Changes in Chesapeake Bay

August 8, 2020

The Chesapeake Bay, the largest estuary in the continental United States, weaves its way south from Maryland, collecting waters from West Virginia, Delaware, DC, Pennsylvania and New York along the way. Like many major e Read more…

By Oliver Peckham

Student Success from ‘Scratch’: CHPC’s Proof is in the Pudding

August 7, 2020

Happy Sithole, who directs the South African Centre for High Performance Computing (SA-CHPC), called the 13th annual CHPC National conference to order on December 1, 2019, at the Birchwood Conference Centre in Kempton Pa Read more…

By Elizabeth Leake

AWS Solution Channel

University of Adelaide Provides Seamless Bioinformatics Training Using AWS

The University of Adelaide, established in South Australia in 1874, maintains a rich history of scientific innovation. For more than 140 years, the institution and its researchers have had an impact all over the world—making vital contributions to the invention of X-ray crystallography, insulin, penicillin, and the Olympic torch. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

New GE Simulations on Summit to Advance Offshore Wind Power

August 6, 2020

The wind energy sector is a frequent user of high-power simulations, with researchers aiming to optimize wind flows and energy production from the massive turbines. Now, researchers at GE are preparing to undertake a lar Read more…

By Oliver Peckham

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yeste Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows use Read more…

By Oliver Peckham

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community Read more…

By Hartwig Anzt and Jack Dongarra

Implement Photonic Tensor Cores for Machine Learning?

August 5, 2020

Researchers from George Washington University have reported an approach for building photonic tensor cores that leverages phase change photonic memory to implem Read more…

By John Russell

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Machines, Connections, Data, and Especially People: OAC Acting Director Amy Friedlander Charts Office’s Blueprint for Innovation

August 3, 2020

The path to innovation in cyberinfrastructure (CI) will require continued focus on building HPC systems and secure connections between them, in addition to the Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi Read more…

By John Russell

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This