The Week in HPC Research

By Nicole Hemsoth

February 21, 2013

The top research stories of the week have been hand-selected from prominent journals and leading conference proceedings. Here’s another diverse set of items, including one on GPU programming, distributed file systems, exhaustive search with parallel agents, the benefits of invasive computing, and an HPC cloud proof-of-concept.

Extending OpenMP for GPU Programming

The International Journal of Computational Science and Engineering (Volume 8, Number 1/2013) includes an interesting research item from Seyong Lee (Computer Science and Mathematics Division, Oak Ridge National Laboratory) and Rudolf Eigenmann (School of Electrical and Computer Engineering, Purdue University). The duo have developed a directive-based OpenMP extension to address programmability and tunability issues relevant to the GPGPU developer community.

GPGPU computing provides an inexpensive parallel computing platform for compute-intensive applications, yet programming complexity can challenge developers hindering more widespread adoption, the authors note. “Even though the compute unified device architecture (CUDA) programming model offers better abstraction, developing efficient GPGPU code is still complex and error–prone,” they argue.

Thus the authors propose a new programming interface, called OpenMPC, comprised of standard OpenMP and a new set of compiler directives and environment variables that have been extended for CUDA. They argue that OpenMPC, a directive–based, high–level programming model, offers better programmability and tunability for GPGPU code.

“We have developed a fully automatic compilation and user–assisted tuning system supporting OpenMPC. In addition to a range of compiler transformations and optimisations, the system includes tuning capabilities for generating, pruning, and navigating the search space of compilation variants. Evaluation using 14 applications shows that our system achieves 75% of the performance of the hand–coded CUDA programmes (92% if excluding one exceptional case),” they write.

Next >>

Six Distributed File Systems

A trio of French scientists provide a thorough analysis of six distributed file systems in this recent 39-page research paper, appearing in the HAL/INRIA open archive. The authors, one from SysFera and two from Laboratoire MIS at the Universite de Picardie Jules Verne, start with the observation that a large number of HPC applications rely on distributed computing environments to process and analyze large amounts of data. (Examples provided include probabilistic analysis, weather forecasting and aerodynamic research.) They further note the emergence of new infrastructures designed to handle the increased computational demand. Most of these new architectures, the authors assert, involve some manner of distributed computing, such that the computing process is spread among the nodes of a large distributed computing platform.

Furthermore the team believes that the growing body of scientific data will likewise necessitate innovations in distributed storage. “Easy to use and reliable storage solutions” are essential for scientific computing, they argue, and the community already has a “well-tried solution to this issue,” in the form of Distributed File Systems (DFSs).

The paper offers a comparison of six modern DFSs as to three fundamental issues: scalability, transparency and fault tolerance. For their study, the authors selected popular, widely-used and frequently updated DFSs: HDFS, MooseFS, iRODS, Ceph, GlusterFS, and Lustre.

Next >>

Exhaustive Search with Parallel Agents

In a recent paper, Macedonia researcher Toni Draganov Stojanovski from University for Information Science And Technology in the Republic of Macedonia sets out to examine the performance of exhaustive search when it is conducted with many search agents working in parallel.

Stojanovski and his research team observe that the advance of manycore processors and more sophisticated distributed processing offers more opportunities for exhaustive search via the use of multiple search agents. While there are a selection of elegant algorithms available for solving complex problems, exhaustive search remains as the best or only solution for real-life problems with no regular structure.

The paper reviews the performance that is achieved using the exhaustive search approach in conjunction with several different search agents with special attention to the following parameters:

• Differences in speeds of search agents.

• Length of allocated search subregions.

• Type of communication between central server and agents.

The findings reveal that the performance of the search improves with the increase in the level of mutual assistance between agents. Furthermore, nearly identical performance outcomes can be achieved with homogeneous and heterogeneous search agents as long as “the lengths of subregions allocated to individual search regions follow the differences in the speeds of heterogeneous search agents.” The research team also demonstrate how to achieve the optimum search performance by means of increasing the dimension of the search region.

The work appears in the January issue of the Turkish Journal of Electrical Engineering & Computer Sciences.

Next >>

The Benefits of Invasive Computing

In their paper, titled Invasive Computing on High Performance Shared Memory Systems, three researchers from the Department of Informatics, at Garching, Germany, offer new approaches for improving the throughput of runtime-adaptive applications on cutting-edge HPC systems. Their work was published as a chapter in Facing the Multicore Challenge III.

According to the team, there are multiple issues at play:

A first issue is the, in general, missing information about the actual impact of unforeseeable workload by adaptivity and of the unknown number of time steps or iterations on the runtime of adaptive applications. Another issue is that resource scheduling on HPC systems is currently done before an application is started and remains unchanged afterwards, even in case of varying requirements. Furthermore, an application cannot be started after another running application allocated all resources.

The authors propose a solution that involves the design of algorithms that adapt their use of resources during runtime, e.g., by relinquishing or adding compute cores. In the event that concurrent applications are competing for resources, they recommend that an appropriate resource management solution be adopted.

To improve the throughput of runtime-adaptive applications, the computer scientists employed invasive paradigms that start applications and schedule resources during runtime. Scheduling work can be achieved through the use of a global resource manager, and scalability graphs help improve load balancing of multiple applications. In the case of adaptive simulations, several scalability graphs are employed.

The paper includes a proof-of-concept that demonstrates runtime/throughput results for a fully adaptive shallow-water simulation.

Next >>

Easy to Use Cloud Service

Among the many HPC cloud research pieces that were published this week was an Australian endeavor that seeks to transform complicated HPC applications into easy-to-use SaaS cloud services. Researchers Adam K.L. Wonga and Andrzej M. Goscinskia from the School of Information Technology at Deakin University in Australia set out to develop and test a unified framework for HPC applications as services in clouds.

The duo acknowledge the benefits of HPC cloud. Scalable, affordable and accessible on demand, the use of HPC resources in a cloud environment have been a natural fit for many scientific disciplines, including biology, medicine, chemistry, they write. Still they have observed a steep learning curve when it comes to preparing for and deploying HPC applications in the cloud. This they say has stood in the way of many innovative HPC-backed discoveries.

To remedy this situation and improve ease of use and access to HPC resources, the researchers are looking to the world of Web-based tools, but as they write “high-performance computational research are both unique and complex, which make the development of web-based tools for this research difficult.”

The paper describes their approach to developing a unified cloud framework – one that makes it easier for various domain users to deploy HPC applications in public clouds as services. Their proof-of-concept integrates three components:

(i) Amazon EC2 public cloud for providing HPC infrastructure.

(ii) a HPC service software library for accessing HPC resources.

(iii) the Galaxy web-based platform for exposing and accessing HPC application services.

The authors conclude that “this new approach can reduce the time and money needed to deploy, expose and access discipline HPC applications in clouds.”

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!

SC Bids Farewell to Denver, Heads to Dallas for 30th

November 17, 2017

After a jam-packed four-day expo and intensive six-day technical program, SC17 has wrapped up another successful event that brought together nearly 13,000 visitors to the Colorado Convention Center in Denver for the larg Read more…

By Tiffany Trader

SC17 Keynote – HPC Powers SKA Efforts to Peer Deep into the Cosmos

November 17, 2017

This week’s SC17 keynote – Life, the Universe and Computing: The Story of the SKA Telescope – was a powerful pitch for the potential of Big Science projects that also showcased the foundational role of high performance computing in modern science. It was also visually stunning. Read more…

By John Russell

How Cities Use HPC at the Edge to Get Smarter

November 17, 2017

Cities are sensoring up, collecting vast troves of data that they’re running through predictive models and using the insights to solve problems that, in some cases, city managers didn’t even know existed. Speaking Read more…

By Doug Black

HPE Extreme Performance Solutions

Harness Scalable Petabyte Storage with HPE Apollo 4510 and HPE StoreEver

As a growing number of connected devices challenges IT departments to rapidly collect, manage, and store troves of data, organizations must adopt a new generation of IT to help them operate quickly and intelligently. Read more…

SC17 Student Cluster Competition Configurations: Fewer Nodes, Way More Accelerators

November 16, 2017

The final configurations for each of the SC17 “Donnybrook in Denver” Student Cluster Competition have been released. Fortunately, each team received their equipment shipments on time and undamaged, so the teams are r Read more…

By Dan Olds

SC Bids Farewell to Denver, Heads to Dallas for 30th

November 17, 2017

After a jam-packed four-day expo and intensive six-day technical program, SC17 has wrapped up another successful event that brought together nearly 13,000 visit Read more…

By Tiffany Trader

SC17 Keynote – HPC Powers SKA Efforts to Peer Deep into the Cosmos

November 17, 2017

This week’s SC17 keynote – Life, the Universe and Computing: The Story of the SKA Telescope – was a powerful pitch for the potential of Big Science projects that also showcased the foundational role of high performance computing in modern science. It was also visually stunning. Read more…

By John Russell

How Cities Use HPC at the Edge to Get Smarter

November 17, 2017

Cities are sensoring up, collecting vast troves of data that they’re running through predictive models and using the insights to solve problems that, in some Read more…

By Doug Black

Student Cluster LINPACK Record Shattered! More LINs Packed Than Ever before!

November 16, 2017

Nanyang Technological University, the pride of Singapore, utterly destroyed the Student Cluster Competition LINPACK record by posting a score of 51.77 TFlop/s a Read more…

By Dan Olds

Hyperion Market Update: ‘Decent’ Growth Led by HPE; AI Transparency a Risk Issue

November 15, 2017

The HPC market update from Hyperion Research (formerly IDC) at the annual SC conference is a business and social “must,” and this year’s presentation at S Read more…

By Doug Black

Nvidia Focuses Its Cloud Containers on HPC Applications

November 14, 2017

Having migrated its top-of-the-line datacenter GPU to the largest cloud vendors, Nvidia is touting its Volta architecture for a range of scientific computing ta Read more…

By George Leopold

HPE Launches ARM-based Apollo System for HPC, AI

November 14, 2017

HPE doubled down on its memory-driven computing vision while expanding its processor portfolio with the announcement yesterday of the company’s first ARM-base Read more…

By Doug Black

OpenACC Shines in Global Climate/Weather Codes

November 14, 2017

OpenACC, the directive-based parallel programming model used mostly for porting codes to GPUs for use on heterogeneous systems, came to SC17 touting impressive Read more…

By John Russell

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

Leading Solution Providers

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

Intel Launches Software Tools to Ease FPGA Programming

September 5, 2017

Field Programmable Gate Arrays (FPGAs) have a reputation for being difficult to program, requiring expertise in specialty languages, like Verilog or VHDL. Easin Read more…

By Tiffany Trader

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This