A Toolkit for Materials Scientific Cloud Computing

By Ian Armas Foster

July 5, 2013

There are two elements in improving high performance computing with regard to scientific computing. The first is well covered over on HPCwire, and examines how the latest advancements in the greatest supercomputers push the boundaries of modeling and computation. The second component deals with making the applications that run those models and simulations more accessible to scientists who may not have access to those top-end supercomputers.

Recognizing this, researchers from the physics department at the University of Washington at Seattle, through a grant from the National Science Foundation, created what they call a ‘virtual platform’ for scientific cloud computing, or SC2VP, which they simply named “SC2IT” for scientific cloud computing interface tools.

“The main elements of our new platform include a virtual cloud computer blueprint or AMI, which contains preinstalled and optimized scientific codes and utilities.”

The platform, according to the researchers, is meant to simulate the parallelism and extensive data storage capabilities of a large supercomputer in a cloud environment, with the emphasis being to cater toward the material sciences. “This blueprint,” the researchers noted, “contains libraries, compilers, a parallel computing environment, and preconfigured applications typically useful for materials scientists. E.g. these applications can calculate structural and electronic properties of materials.”

What is important to note here is that the physicists built their toolkit with creating an HPC cluster as their top priority. Building a virtual machine is, according to the physicists, is not as difficult as making that cluster run high performance scientific applications. As they noted, “launching a set of virtual machines from a cloud provider is easy but does not produce a fully functional HPC cluster… To truly bring advanced science to a broad class of end users, another step is necessary beyond launching a parallel MS program on a cloud cluster.”

That next level, according to the researchers, involves congregating various scientific computing codes that optimize certain types of problems. These codes already exist through previous computational research, but the trick was incorporating them en masse in a toolset that would allow them to be deployed on a virtual cluster.

“The development of novel scientific software is often modular: computational scientists link existing codes together and combine them with new developments to produce state-of-the-art results.”

The particular existing codes they used included a Density Functional Theory code, whose purpose is to assess and order the dynamic motion relationships among the coordinates in a material, essentially building a model of how a substance moves. With that, they added two codes to calculate a material’s vibrational tendencies, including “a new module to next derive vibrational properties; and thirdly, an existing spectroscopy code to finally calculate an X-ray spectrum incorporating the vibrational information.”

Below is a screenshot of how the researchers implemented the spectroscopy code through the Graphical User Interface (GUI) hey set up. The red arrow denotes where the user can identify upon which resources the implementation would ideally run.

Materials science has grown rapidly over the last decade, simply because the resolution and precision with which one can observe and test substances has seen a marked increase. However, as is seen in genomics, another popular scientific cloud computing use case, those materials and their associated tests represent a lot of information to be stored and processed. Being able to run those computations and store the necessary data in the cloud would promote cost-effectiveness, providing access to researchers without extensive in-house HPC resources.

It also incidentally fosters collaboration, as retrieving data from a virtual cluster in the cloud is simpler than transmitting entire datasets over a user’s limited bandwidth or (still fairly common today) sending physical hard drives with copies of the large datasets in the mail.

While the focus is on materials science, it is the hope of the University of Washington physicists that this approach of aggregating optimized codes and tools can be applied to other fields of study. “We embedded the interface and blueprint in a GUI environment that enables MS end users to perform specific SCC calculations with a few mouse clicks. The same approach can be followed for SCC enhancement of GUIs for other fields of research.”

Again, this approach could prove useful to fields like genomics, where datasets are exploding and the incentive to run experiments quickly is high. The researchers here designed their toolset to run on the Amazon Elastic Compute Cloud, representing an eye toward completing high performance applications. “We tested the performance of this setup to prove that HPC calculations for materials science can be done efficiently in a cloud environment.”

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, Micro Debut Quad-Level Cell NAND Flash

May 22, 2018

Chipmakers continue to gear designs toward AI and other demanding cloud workloads that take advantage of datacenter flash storage capacity. To that end, memory specialist Micron Technology Inc. began shipping compact sol Read more…

By George Leopold

Japan Meteorological Agency Takes Delivery of Pair of Crays

May 21, 2018

Cray has supplied two identical Cray XC50 supercomputers to the Japan Meteorological Agency (JMA) in northwestern Tokyo. Boasting more than 18 petaflops combined peak computing capacity, the new systems will extend the a Read more…

By Tiffany Trader

ASC18: Final Results Revealed & Wrapped Up

May 17, 2018

It was an exciting week at ASC18 in Nanyang, China. The student teams braved extreme heat, extremely difficult applications, and extreme competition in order to cross the cluster competition finish line. The gala awards ceremony took place on Wednesday. The auditorium was packed with student teams, various dignitaries, the media, and other interested parties. So what happened? Read more…

By Dan Olds

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

IBM Accelerated Insights

Mastering the Big Data Challenge in Cognitive Healthcare

Patrick Chain, genomics researcher at Los Alamos National Laboratory, posed a question in a recent blog: What if a nurse could swipe a patient’s saliva and run a quick genetic test to determine if the patient’s sore throat was caused by a cold virus or a bacterial infection? Read more…

ASC18: Tough Applications & Tough Luck

May 17, 2018

The applications at the ASC18 Student Cluster Competition were tough. Tougher than the $3.99 steak special at your local greasy spoon restaurant. The apps are so tough that even Chuck Norris backs away from them slowly. Read more…

By Dan Olds

Japan Meteorological Agency Takes Delivery of Pair of Crays

May 21, 2018

Cray has supplied two identical Cray XC50 supercomputers to the Japan Meteorological Agency (JMA) in northwestern Tokyo. Boasting more than 18 petaflops combine Read more…

By Tiffany Trader

ASC18: Final Results Revealed & Wrapped Up

May 17, 2018

It was an exciting week at ASC18 in Nanyang, China. The student teams braved extreme heat, extremely difficult applications, and extreme competition in order to cross the cluster competition finish line. The gala awards ceremony took place on Wednesday. The auditorium was packed with student teams, various dignitaries, the media, and other interested parties. So what happened? Read more…

By Dan Olds

Spring Meetings Underscore Quantum Computing’s Rise

May 17, 2018

The month of April 2018 saw four very important and interesting meetings to discuss the state of quantum computing technologies, their potential impacts, and th Read more…

By Alex R. Larzelere

Quantum Network Hub Opens in Japan

May 17, 2018

Following on the launch of its Q Commercial quantum network last December with 12 industrial and academic partners, the official Japanese hub at Keio University is now open to facilitate the exploration of quantum applications important to science and business. The news comes a week after IBM announced that North Carolina State University was the first U.S. university to join its Q Network. Read more…

By Tiffany Trader

Democratizing HPC: OSC Releases Version 1.3 of OnDemand

May 16, 2018

Making HPC resources readily available and easier to use for scientists who may have less HPC expertise is an ongoing challenge. Open OnDemand is a project by t Read more…

By John Russell

PRACE 2017 Annual Report: Exascale Aspirations; Industry Collaboration; HPC Training

May 15, 2018

The Partnership for Advanced Computing in Europe (PRACE) today released its annual report showcasing 2017 activities and providing a glimpse into thinking about Read more…

By John Russell

US Forms AI Brain Trust

May 11, 2018

Amid calls for a U.S. strategy for promoting AI development, the Trump administration is forming a senior-level panel to help coordinate government and industry research efforts. The Select Committee on Artificial Intelligence was announced Thursday (May 10) during a White House summit organized by the Office of Science and Technology Policy (OSTP). Read more…

By George Leopold

Emerging Advanced Scale Tech Trends Focus of Annual Tabor Conference

May 9, 2018

At Tabor Communications' annual Advanced Scale Forum (ASF) held this week in Austin, the focus was on enterprise adoption of HPC-class technologies and high performance data analytics (HPDA). It’s a confab that brings together end users (CIOs, IT planners, department heads) and vendors and encourages... Read more…

By the Editorial Team

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

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

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

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

AI Cloud Competition Heats Up: Google’s TPUs, Amazon Building AI Chip

February 12, 2018

Competition in the white hot AI (and public cloud) market pits Google against Amazon this week, with Google offering AI hardware on its cloud platform intended Read more…

By Doug Black

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

Leading Solution Providers

HPC and AI – Two Communities Same Future

January 25, 2018

According to Al Gara (Intel Fellow, Data Center Group), high performance computing and artificial intelligence will increasingly intertwine as we transition to Read more…

By Rob Farber

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

CFO Steps down in Executive Shuffle at Supermicro

January 31, 2018

Supermicro yesterday announced senior management shuffling including prominent departures, the completion of an audit linked to its delayed Nasdaq filings, and Read more…

By John Russell

Deep Learning Portends ‘Sea Change’ for Oil and Gas Sector

February 1, 2018

The billowing compute and data demands that spurred the oil and gas industry to be the largest commercial users of high-performance computing are now propelling Read more…

By Tiffany Trader

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Sympo Read more…

By Staff

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