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Primeur weekly 2016-07-25

Special

SpiNNaker and BrainScaleS neuromorphic systems ready for non-expert use in stochastic inference computing ...

Beyond Moore's Law panelists address business maturity of new technologies, future developments, neuromorphic chip training, and memristors ...

Focus

D-Wave works with its customers Lockheed, Google and Los Alamos to design better quantum software ...

Altair's Bill Nitzberg to present PBS Pro open source license version, PBS Simulator and PBS Cloud Manager ...

Quantum computing

Russian physicists discover a new approach for building quantum computers ...

RMIT researchers make leap in measuring quantum states ...

Focus on Europe

Guiding EU researchers along the last mile to Open Digital Science ...

Digital Humanities and Urban Climate proposals win NLeSC-Lorentz Workshop competition ...

European Horizon 2020 Work Programme update supports competitiveness through open science ...

6th Irish Supercomputer List shows Irish HPC capacity doubles with new no. 1 and three new TOP500-class machines ...

PRACE to look for Peer-Review Officer ...

7th International HPC Summer School took place in Ljubljana, Slovenia ...

Middleware

Inria joins the OpenMP ARB ...

Hardware

Gigabyte announces official release of production-ready Cavium ThunderX-based servers ...

The University of Tokyo selects Mellanox EDR InfiniBand to accelerate its newest supercomputer ...

Smallest hard disk to date writes information atom by atom ...

A mini-antenna for the data processing of tomorrow ...

Hangzhou C-SKY Microsystems joins EEMBC Executive Board ...

Electron spin control: Levitated nanodiamond is research gem ...

The Scripps Research Institute leverages powerful end-to-end DDN storage to help reveal secrets to new medical treatments ...

Applications

MSC Software partners with Italian Campania Region Technological Aerospace District for the development of aeronautical programmes ...

Deloitte Advisory Cyber Risk Services and Cray offer advanced Cyber Reconnaissance and Analytics services ...

Strathclyde mathematician wins prize for research into speeding up stroke diagnosis ...

Underlying molecular networks suggest new targets to combat brain cancer ...

An accelerated pipeline to open materials research ...

Rice wins interdisciplinary Big Data grant ...

Study uses text-mining to improve market intelligence on startups ...

The Cloud

The HNSciCloud Pre-Commercial Procurement tender is out: you can bid now ...

CSC and IBM expand strategic alliance with collaboration utilizing IBM Cloud for z to enable clients' move to Cloud ...

An accelerated pipeline to open materials research

This image shows ORNL software engineer Eric Lingerfelt (right) and Stephen Jesse (left) of ORNL's Center for Nanophase Materials Sciences led the development of the Bellerophon Environment for Analysis of Materials (BEAM), an ORNL platform that combines the lab's state-of-the art imaging technologies with advanced data analytics and high-performance computing to accelerate materials science research. Credit: ORNL.21 Jul 2016 Oak Ridge - Using today's advanced microscopes, scientists are able to capture exponentially more information about the materials they study compared to a decade ago - in greater detail and in less time. While these new capabilities are a boon for researchers, helping to answer key questions that could lead to next-generation technologies, they also present a new problem: How to make effective use of all this data?

At the Department of Energy's Oak Ridge National Laboratory (ORNL), researchers are engineering a solution by creating a novel infrastructure uniting the lab's state-of-the art imaging technologies with advanced data analytics and high-performance computing (HPC). Pairing experimental power and computational might holds the promise of accelerating research and enabling new opportunities for discovery and design of advanced materials, knowledge that could lead to better batteries, atom-scale semiconductors, and efficient photovoltaics, to name a few applications. Developing a distributed software system that delivers these advanced capabilities in a seamless manner, however, requires an extra layer of sophistication.

Enter the Bellerophon Environment for Analysis of Materials (BEAM), an ORNL platform that combines scientific instruments with web and data services and HPC resources through a user-friendly interface. Designed to streamline data analysis and workflow processes from experiments originating at DOE Office of Science User Facilities at ORNL, such as the Center for Nanophase Materials Sciences (CNMS) and Spallation Neutron Source (SNS), BEAM gives materials scientists a direct pipeline to scalable computing, software support, and high-performance Cloud storage services provided by ORNL's Compute and Data Environment for Science (CADES). Additionally, BEAM offers users a gateway to world-class supercomputing resources at the Oak Ridge Leadership Computing Facility (OLCF) - another DOE Office of Science User Facility.

The end result for scientists is near-real-time processing, analysis, and visualization of large experimental datasets from the convenience of a local workstation - a drastic improvement over traditional, time-consuming data-analysis practices.

"Processes that once took days now take a matter of minutes", stated ORNL software engineer Eric Lingerfelt, BEAM's lead developer. "Once researchers upload their data into BEAM's online data management system, they can easily and intuitively execute advanced analysis algorithms on HPC resources like CADES's compute clusters or the OLCF's Titan supercomputer and quickly visualize the results. The speedup is incredible, but most importantly the work can be done remotely from anywhere, anytime."

A team led by Eirc Lingerfelt and CNMS's Stephen Jesse began developing BEAM in 2015 as part of the ORNL Institute for Functional Imaging Materials, a lab initiative dedicated to strengthening the ties between imaging technology, HPC, and data analytics.

Many of BEAM's core concepts, such as its layered infrastructure, Cloud data management, and real-time analysis capabilities, emerged from a previous DOE project called Bellerophon - a computational workflow environment for HPC core collapse supernova simulations - led by the OLCF's Bronson Messer and developed by Lingerfelt. Initially released in 2010, Bellerophon's database has grown to include more than 100,000 data files and 1.5 million real-time rendered images of more than 40 different core-collapse supernova models.

Applying and expanding Bellerophon's compute and data strategies to the materials realm, however, presented multiple new technical hurdles. "We spent an entire year creating and integrating the BEAM infrastructure with instruments at CNMS", Eric Lingerfelt stated. "Now scientists are just starting to use it."

Through BEAM, researchers gain access to scalable algorithms--code developed by ORNL mathematicians and computational scientists to shorten the time to discovery. Additionally, BEAM offers users improved data-management capabilities and common data formats that make tagging, searching, and sharing easier. Lowering these barriers for the materials science community not only helps with verification and validation of current findings but also creates future opportunities for scientific discovery. "As we add new features and data-analysis tools to BEAM, users will be able to go back and run those on their data", Eric Lingerfelt stated.

One of the first data processing workflows developed for BEAM demonstrates its far-reaching potential for accelerating materials science.

At CNMS, users from around the world make use of the centre's powerful imaging instruments to study materials in atomic detail. Conducting analysis of users' data, however, oftentimes slowed scientific progress. One common analysis process required users to format data derived from an imaging technique called band excitation atomic force microscopy. Conducted on a single workstation, the analysis oftentimes took days. "Sometimes people would take their measurement and couldn't analyze it even in the weeks they were here", Stephen Jesse stated.

By transferring the microscopy data to CADES computing via the BEAM interface, CNMS users gained a 1,000-fold speedup in their analysis, reducing the work to a matter of minutes. A specialized fitting algorithm, which was re-implemented for utilization on HPC resources by ORNL mathematician Eirik Endeve, played a key role in tightening the feedback loop users relied upon to judge whether adjustments needed to be made to their experiment. "We literally reduced a year of data analysis to 10 hours", Eric Lingerfelt stated.

BEAM is also proving its worth at SNS - the most intense pulsed neutron beam system in the world - by tightening the interplay between theory and experiment. Working with Jose Borreguero from the Center for Accelerating and Modeling Materials at SNS, the BEAM team created a workflow that allows near-real-time comparison of simulation and neutron scattering data leveraging CADES computing. The feedback helps neutron scientists fine-tune their simulations and guides subsequent experiments. In the future, machine-learning algorithms could fully automate the process, freeing up scientists to focus on other parts of their work. "Humans, however, will still be at the center of the scientific process", Eric Lingerfelt stated.

"We're not here to replace every single step in the workflow of a scientific experiment, but we want to develop tools that complement things that scientists are already doing", he stated.

Now that BEAM's infrastructure is in place, Eric Lingerfelt's team is collaborating with advanced mathematics, data, and visualization experts at ORNL to regularly augment the software's toolbox.

"Once we've created a fully functioning suite, we want to open BEAM up to other material scientists who may have their own analysis codes but don't have the expertise to run them on HPC", Eric Lingerfelt stated. "Down the line we would like to have an open science materials-analysis library where people can validate analysis results publicly."

Currently Eric Lingerfelt's team is developing a suite of algorithms to conduct multivariate analysis, a highly complex, multidimensional analytic process that sifts through vast amounts of information taken from multiple instruments on the same material sample.

"You need HPC for this type of analysis to even be possible", Stephen Jesse stated. "We're gaining the ability to analyze high-dimension datasets that weren't analyzable before, and we expect to see properties in materials that weren't visible before."

The project was supported in part by ORNL's Laboratory Directed Research and Development programme.
Source: DOE/Oak Ridge National Laboratory

Back to Table of contents

Primeur weekly 2016-07-25

Special

SpiNNaker and BrainScaleS neuromorphic systems ready for non-expert use in stochastic inference computing ...

Beyond Moore's Law panelists address business maturity of new technologies, future developments, neuromorphic chip training, and memristors ...

Focus

D-Wave works with its customers Lockheed, Google and Los Alamos to design better quantum software ...

Altair's Bill Nitzberg to present PBS Pro open source license version, PBS Simulator and PBS Cloud Manager ...

Quantum computing

Russian physicists discover a new approach for building quantum computers ...

RMIT researchers make leap in measuring quantum states ...

Focus on Europe

Guiding EU researchers along the last mile to Open Digital Science ...

Digital Humanities and Urban Climate proposals win NLeSC-Lorentz Workshop competition ...

European Horizon 2020 Work Programme update supports competitiveness through open science ...

6th Irish Supercomputer List shows Irish HPC capacity doubles with new no. 1 and three new TOP500-class machines ...

PRACE to look for Peer-Review Officer ...

7th International HPC Summer School took place in Ljubljana, Slovenia ...

Middleware

Inria joins the OpenMP ARB ...

Hardware

Gigabyte announces official release of production-ready Cavium ThunderX-based servers ...

The University of Tokyo selects Mellanox EDR InfiniBand to accelerate its newest supercomputer ...

Smallest hard disk to date writes information atom by atom ...

A mini-antenna for the data processing of tomorrow ...

Hangzhou C-SKY Microsystems joins EEMBC Executive Board ...

Electron spin control: Levitated nanodiamond is research gem ...

The Scripps Research Institute leverages powerful end-to-end DDN storage to help reveal secrets to new medical treatments ...

Applications

MSC Software partners with Italian Campania Region Technological Aerospace District for the development of aeronautical programmes ...

Deloitte Advisory Cyber Risk Services and Cray offer advanced Cyber Reconnaissance and Analytics services ...

Strathclyde mathematician wins prize for research into speeding up stroke diagnosis ...

Underlying molecular networks suggest new targets to combat brain cancer ...

An accelerated pipeline to open materials research ...

Rice wins interdisciplinary Big Data grant ...

Study uses text-mining to improve market intelligence on startups ...

The Cloud

The HNSciCloud Pre-Commercial Procurement tender is out: you can bid now ...

CSC and IBM expand strategic alliance with collaboration utilizing IBM Cloud for z to enable clients' move to Cloud ...