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Primeur weekly 2017-02-27

Focus

Square Kilometre Array data crunching will require compute power beyond Moore's Law ...

Exascale supercomputing

ADIOS Version 1.11 moves I/O framework from research to production ...

Focus on Europe

Microsoft researcher tapped for opening keynote at ISC 2017 ...

Atos acquires zData, a premier consulting firm with unparalleled expertise in Big Data solutions ...

HPC5 consortium now registered as official Digital Hub with I4MS ...

Middleware

HPE and Red Hat join forces to give customers greater choice for NFV deployments ...

Hardware

Tokyo Tech supercomputer TSUBAME3.0 scheduled to start operating in summer 2017 ...

NASA saves energy and water with new modular supercomputing facility ...

Mellanox sets new DPDK performance record with ConnectX-5 ...

Mellanox introduces world-leading 6WIND-based router and IPsec Indigo platform at unmatched price/performance ...

Mellanox and ECI smash virtual CPE performance barriers with Indigo-based platform ...

ORNL director moving to new post at Battelle ...

DDN ranks no. 1 as HPC storage market leader and top supplier ...

National Science Foundation funds supercomputer cluster at Penn State ...

Applications

Watson Health Medical Imaging Collaborative expands to 24 members; IBM debuts Watson Imaging Clinical Review, the first cognitive imaging offering ...

3D-e-Chem team develops Virtual Machine for computer-aided drug discovery ...

IBM Research is training Watson to identify eye retina abnormalities ...

Lorentz-eScience competition 2018 to issue Call for Applications ...

Learning how to fine-tune nanofabrication ...

Deep Learning predicts hematopoietic stem cell development ...

New algorithm identifies gene transfers between different bacterial species ...

Artificial intelligence in quantum systems, too ...

ExxonMobil sets record on NCSA's Blue Waters supercomputer ...

The Cloud

eww ITandTEL implements high-performance Platform-as-a-Service environment with Red Hat technologies ...

ADIOS Version 1.11 moves I/O framework from research to production


A visualization using Finite Time Lyapunov Exponents (FTLE) of the bulk velocity field derived from particles in an XGC1 fusion simulation. The bulk velocity field was computed and visualized in situ using the ADIOS staging transport method. Image courtesy of James Kress and David Pugmire.
23 Feb 2017 Oak Ridge - The Department of Energy's Oak Ridge National Laboratory (ORNL) has issued the latest release of its Adaptable I/O System (ADIOS), a middleware that speeds up scientific simulations on parallel computing resources such as the laboratory's Titan supercomputer by making input/output operations more efficient.

While ADIOS has long been used by researchers to streamline file reading and writing in their applications, the production of data in scientific computing is growing faster than I/O can handle. Reducing data "on the fly" is critical to keep I/O up to speed with today's largest scientific simulations and realize the full potential of resources such as Titan to make real-world scientific breakthroughs. And it's also a key feature in the latest ADIOS release.

"As we approach the exascale, there are many challenges for ADIOS and I/O in general", stated Scott Klasky, scientific data group leader in ORNL's Computer Science and Mathematics Division. "We must reduce the amount of data being processed and program for new architectures. We also must make our I/O frameworks interoperable with one another, and version 1.11 is the first step in that direction."

The upgrade boasts a number of new improvements aimed at ensuring these challenges are met, including

  • a simplified write application programming interface (API) that reduces complexity via introduction of a novel buffering technique;
  • lossy compression with ZFP, a software from Peter Lindstrom at Lawrence Livermore National Laboratory, that reduces the size of data on storage;
  • a query API with multiple indexing/query methods, from John Wu at Lawrence Berkeley National Laboratory and Nagiza Samatova of North Carolina State University;
  • a "bprecover" utility for resilience that exploits the ADIOS file format’s multiple copies of metadata;
  • in-memory time aggregation for file-based output, allowing for efficient I/O with difficult write patterns;
  • novel Titan-scale-supported staging from Manish Parashar at Rutgers University; and
  • a laundry list of various other performance improvements.

These modifications represent the latest evolution in ADIOS’s journey from research to production, as version 1.11 now makes it easier to move data from one code to another. ADIOS's user base has gone from just a single code to hundreds of parallel applications spread across dozens of domain areas.

"ADIOS has been a vital part of our large-scale XGC fusion code", stated Choong-Seock Chang, head of the Center for Edge Physics Simulation at Princeton Plasma Physics Laboratory. "With the continuous version updates, the performance of XGC keeps getting better; during one of our most recent ITER runs, we were able to further accelerate the I/O, which enabled new insights into our scientific results."

ADIOS's success in the scientific community has led to its adoption among several industrial applications seeking more efficient I/O. Demand for ADIOS has grown sufficiently so that the development team is now partnering with Kitware, a world expert in data visualization infrastructure, to construct a data framework for the scientific community that will further the efficient location and reduction of data plaguing parallel scientific computing and likely further grow ADIOS's user base.

Throughout its evolution, ADIOS's development team has ensured that the middleware remains fast, concurrent, scalable, portable, and perhaps most of all, resilient - the bprecover feature in 1.11 that allows for the recovery of uncorrupted data. According to Scott Klasky, being part of the DOE national lab system was critical to ensuring the scalability of the ever-growing platform, an asset that will remain critical as ORNL moves towards the exascale.

Because exascale hardware is widely expected to be disruptive, particularly in terms of incredibly fast nodes that will make it difficult for networks and I/O to keep up, researchers are preparing now for the daunting I/O challenge to come.

ADIOS was one of four ORNL-led software development projects to receive funding from the Exascale Computing Project, a collaborative effort between the DOE's Office of Science and the National Nuclear Security Administration to develop a capable exascale ecosystem, encompassing applications, system software, hardware technologies and architectures, and workforce to meet the scientific and national security mission needs of DOE in the mid-2020 timeframe.

The award is a testament to ADIOS's ability in making newer technologies sustainable, usable, fast, and interoperable - so that they will all be able to read from and possibly write to other important file formats.

As the journey to exascale continues, ADIOS's unique I/O capabilities will be necessary to ensure that the world's most powerful computers, and the applications they host, can continue to facilitate scientific breakthroughs impossible through experimentation alone.

"With ADIOS we saw a 20-fold increase in I/O performance compared to our best previous solution", stated Michael Bussmann, a junior group leader in computational radiation physics at Helmholtz-Zentrum Dresden-Rossendorf. "This made it possible to take full snapshots of the simulation, enabling us to study our laser-driven particle accelerator from the single-particle level to the full system. It is a game changer, going from 20 minutes to below one minute for a snapshot."
Source: Oak Ridge National Laboratory - ORNL

Back to Table of contents

Primeur weekly 2017-02-27

Focus

Square Kilometre Array data crunching will require compute power beyond Moore's Law ...

Exascale supercomputing

ADIOS Version 1.11 moves I/O framework from research to production ...

Focus on Europe

Microsoft researcher tapped for opening keynote at ISC 2017 ...

Atos acquires zData, a premier consulting firm with unparalleled expertise in Big Data solutions ...

HPC5 consortium now registered as official Digital Hub with I4MS ...

Middleware

HPE and Red Hat join forces to give customers greater choice for NFV deployments ...

Hardware

Tokyo Tech supercomputer TSUBAME3.0 scheduled to start operating in summer 2017 ...

NASA saves energy and water with new modular supercomputing facility ...

Mellanox sets new DPDK performance record with ConnectX-5 ...

Mellanox introduces world-leading 6WIND-based router and IPsec Indigo platform at unmatched price/performance ...

Mellanox and ECI smash virtual CPE performance barriers with Indigo-based platform ...

ORNL director moving to new post at Battelle ...

DDN ranks no. 1 as HPC storage market leader and top supplier ...

National Science Foundation funds supercomputer cluster at Penn State ...

Applications

Watson Health Medical Imaging Collaborative expands to 24 members; IBM debuts Watson Imaging Clinical Review, the first cognitive imaging offering ...

3D-e-Chem team develops Virtual Machine for computer-aided drug discovery ...

IBM Research is training Watson to identify eye retina abnormalities ...

Lorentz-eScience competition 2018 to issue Call for Applications ...

Learning how to fine-tune nanofabrication ...

Deep Learning predicts hematopoietic stem cell development ...

New algorithm identifies gene transfers between different bacterial species ...

Artificial intelligence in quantum systems, too ...

ExxonMobil sets record on NCSA's Blue Waters supercomputer ...

The Cloud

eww ITandTEL implements high-performance Platform-as-a-Service environment with Red Hat technologies ...