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!

Quantum Rolls – DOE Dishes $218M; NSF Awards $31M; US Releases ‘Strategic Overview’

September 24, 2018

It was quite a day for U.S. quantum computing. In conjunction with the White House Summit on Advancing American Leadership in Quantum Information Science (QIS) held today, the Department of Energy announced $218 million Read more…

By John Russell

Russian and American Scientists Achieve 50% Increase in Data Transmission Speed

September 20, 2018

As high-performance computing becomes increasingly data-intensive and the demand for shorter turnaround times grows, data transfer speed becomes an ever more important bottleneck. Now, in an article published in IEEE Tra Read more…

By Oliver Peckham

IBM to Brand Rescale’s HPC-in-Cloud Platform

September 20, 2018

HPC (or big compute)-in-the-cloud platform provider Rescale has formalized the work it’s been doing in partnership with public cloud vendors by announcing its Powered by Rescale program – with IBM as its first named Read more…

By Doug Black

HPE Extreme Performance Solutions

Introducing the First Integrated System Management Software for HPC Clusters from HPE

How do you manage your complex, growing cluster environments? Answer that big challenge with the new HPC cluster management solution: HPE Performance Cluster Manager. Read more…

IBM Accelerated Insights

Clouds Over the Ocean – a Healthcare Perspective

Advances in precision medicine, genomics, and imaging; the widespread adoption of electronic health records; and the proliferation of medical Internet of Things (IoT) and mobile devices are resulting in an explosion of structured and unstructured healthcare-related data. Read more…

Democratization of HPC Part 1: Simulation Sheds Light on Building Dispute

September 20, 2018

This is the first of three articles demonstrating the growing acceptance of High Performance Computing especially in new user communities and application areas. Major reasons for this trend are the ongoing improvements i Read more…

By Wolfgang Gentzsch

Quantum Rolls – DOE Dishes $218M; NSF Awards $31M; US Releases ‘Strategic Overview’

September 24, 2018

It was quite a day for U.S. quantum computing. In conjunction with the White House Summit on Advancing American Leadership in Quantum Information Science (QIS) Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

Nvidia Accelerates AI Inference in the Datacenter with T4 GPU

September 14, 2018

Nvidia is upping its game for AI inference in the datacenter with a new platform consisting of an inference accelerator chip--the new Turing-based Tesla T4 GPU- Read more…

By George Leopold

DeepSense Combines HPC and AI to Bolster Canada’s Ocean Economy

September 13, 2018

We often hear scientists say that we know less than 10 percent of the life of the oceans. This week, IBM and a group of Canadian industry and government partner Read more…

By Tiffany Trader

Rigetti (and Others) Pursuit of Quantum Advantage

September 11, 2018

Remember ‘quantum supremacy’, the much-touted but little-loved idea that the age of quantum computing would be signaled when quantum computers could tackle Read more…

By John Russell

How FPGAs Accelerate Financial Services Workloads

September 11, 2018

While FSI companies are unlikely, for competitive reasons, to disclose their FPGA strategies, James Reinders offers insights into the case for FPGAs as accelerators for FSI by discussing performance, power, size, latency, jitter and inline processing. Read more…

By James Reinders

Update from Gregory Kurtzer on Singularity’s Push into FS and the Enterprise

September 11, 2018

Container technology is hardly new but it has undergone rapid evolution in the HPC space in recent years to accommodate traditional science workloads and HPC systems requirements. While Docker containers continue to dominate in the enterprise, other variants are becoming important and one alternative with distinctly HPC roots – Singularity – is making an enterprise push targeting advanced scale workload inclusive of HPC. Read more…

By John Russell

TACC Wins Next NSF-funded Major Supercomputer

July 30, 2018

The Texas Advanced Computing Center (TACC) has won the next NSF-funded big supercomputer beating out rivals including the National Center for Supercomputing Ap Read more…

By John Russell

IBM at Hot Chips: What’s Next for Power

August 23, 2018

With processor, memory and networking technologies all racing to fill in for an ailing Moore’s law, the era of the heterogeneous datacenter is well underway, Read more…

By Tiffany Trader

Requiem for a Phi: Knights Landing Discontinued

July 25, 2018

On Monday, Intel made public its end of life strategy for the Knights Landing "KNL" Phi product set. The announcement makes official what has already been wide Read more…

By Tiffany Trader

CERN Project Sees Orders-of-Magnitude Speedup with AI Approach

August 14, 2018

An award-winning effort at CERN has demonstrated potential to significantly change how the physics based modeling and simulation communities view machine learni Read more…

By Rob Farber

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

By John Russell

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

AMD’s EPYC Road to Redemption in Six Slides

June 21, 2018

A year ago AMD returned to the server market with its EPYC processor line. The earth didn’t tremble but folks took notice. People remember the Opteron fondly Read more…

By John Russell

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

Sandia to Take Delivery of World’s Largest Arm System

June 18, 2018

While the enterprise remains circumspect on prospects for Arm servers in the datacenter, the leadership HPC community is taking a bolder, brighter view of the x86 server CPU alternative. Amongst current and planned Arm HPC installations – i.e., the innovative Mont-Blanc project, led by Bull/Atos, the 'Isambard’ Cray XC50 going into the University of Bristol, and commitments from both Japan and France among others -- HPE is announcing that it will be supply the United States National Nuclear Security Administration (NNSA) with a 2.3 petaflops peak Arm-based system, named Astra. Read more…

By Tiffany Trader

D-Wave Breaks New Ground in Quantum Simulation

July 16, 2018

Last Friday D-Wave scientists and colleagues published work in Science which they say represents the first fulfillment of Richard Feynman’s 1982 notion that Read more…

By John Russell

MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

TACC’s ‘Frontera’ Supercomputer Expands Horizon for Extreme-Scale Science

August 29, 2018

The National Science Foundation and the Texas Advanced Computing Center announced today that a new system, called Frontera, will overtake Stampede 2 as the fast Read more…

By Tiffany Trader

Intel Announces Cooper Lake, Advances AI Strategy

August 9, 2018

Intel's chief datacenter exec Navin Shenoy kicked off the company's Data-Centric Innovation Summit Wednesday, the day-long program devoted to Intel's datacenter Read more…

By Tiffany Trader

GPUs Power Five of World’s Top Seven Supercomputers

June 25, 2018

The top 10 echelon of the newly minted Top500 list boasts three powerful new systems with one common engine: the Nvidia Volta V100 general-purpose graphics proc Read more…

By Tiffany Trader

The Machine Learning Hype Cycle and HPC

June 14, 2018

Like many other HPC professionals I’m following the hype cycle around machine learning/deep learning with interest. I subscribe to the view that we’re probably approaching the ‘peak of inflated expectation’ but not quite yet starting the descent into the ‘trough of disillusionment. This still raises the probability that... Read more…

By Dairsie Latimer

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