Say Hello to the New ADIOS

By Gregory Scott Jones

September 12, 2010

Updated I/O performance library improves ease of use and achieves even better performance

Big machines are one thing. Taking advantage of their full potential is quite another. Application performance has long been trailing hardware as supercomputers have sought, entered, and now surpassed petaflop performance.

One of the factors commonly affecting application performance is input/output (I/O). Researchers regularly find themselves having to choose between the performance of their applications and the amount and quality of the data they write.

It’s a problem familiar to the Oak Ridge Leadership Computing Facility’s (OLCF’s) Scott Klasky from his early years as a researcher with a team from Princeton Plasma Physics Laboratory using the Gyrokinetic Toroidal Code.

“We looked at the performance of how often we would like to write, and we were spending over 30 percent of the time writing the analysis files in a very popular file format. Thirty percent of all your computational time writing data to files is too much,” said Klasky. “The scientists eventually decided that unless it was a run that we definitely wanted to get some visualization out of, we weren’t going to write those because we were wasting our valuable computing time doing this.”

Klasky, along with a team of researchers (Qing Liu, Norbert Podhorszki, Jay Lofstead, Hasan Abbasi, Ron Oldfield, Matt Wolf, Fang Zheng, Ciprian Docan, Manish Parashar, Weikuan Yu, Yuan Tian, Nagiza Samatova, Sriram Lakshminarasimh, Todd Kordenbrock, and others) from Georgia Tech, the OLCF, Rutgers University, and Sandia National Laboratories are the developers of ADIOS, an open-source middleware with the primary goal of making the process of getting information in and out of a supercomputer easier and more effective.

Last week the team released ADIOS 1.2, the latest incarnation of one of computational science’s most effective I/O tools. So far ADIOS has helped researchers make huge strides in fusion, astrophysics and combustion. The new version features some interesting improvements that will doubtless aid researchers in taking full advantage of leading supercomputing platforms.

For starters, previous versions of ADIOS had users construct an external XML file that allowed them to organize their simulation variables into distinct groups and add important metadata to their output. With the new application programming interface (API), which allows for interaction between different software packages, users can now place the APIs directly into their code and interactively construct new variables during run time. This was especially important for adaptive mesh refinement (AMR) codes, such as Chombo, that can alter the variables placed on disk during run time. This new API makes ADIOS much more flexible and allows researchers to choose between defining the output in an external file for maximum flexibility or in their codes.

ADIOS also features a custom I/O method that writes data to subfiles and aggregates it into larger pieces for maximum performance on the leadership-class systems. This method has been shown to get near peak I/O performance for many codes, particularly S3D, on the Cray XT5 and Cray XT4 at the OLCF and Lawrence Berkeley National Laboratory’s National Energy Research Scientific Computing Center.

“We are now able to speed up applications such as S3D to near-peak I/O bandwidth through simple and easy-to-use ADIOS APIs,” said Qing Liu, a member of the ADIOS team at the OLCF. “We are also able to speed up S3D by a factor of more than 15. This is achieved by intelligently aggregating and writing data to storage targets in ADIOS.”

Now users who run on large systems can switch from running on P-processors and writing to P-files — or one file or M-files, transparently. ADIOS users can switch to the best method for individual systems, including the IBM Blue Gene/P at Argonne National Laboratory, where PhD student Yuan Tian, along with her advisor Weikuan Yu at Auburn University, has created a custom method to write more efficiently with ADIOS.

Version 1.2 also features further support for self-describing data in the output. Users can now write more statistics into their data and have more flexibility in their output. For example, users can automatically retrieve the average value, minimum, maximum, and standard deviation for all arrays at negligible computational cost. This feature allows users to take large files (terabytes) and automatically determine these parameters in less than 2 seconds when listing the contents of the data. Furthermore, users can get these statistics for each independent time step in the output.

Finally, version 1.2 features some new asynchronous transport methods, allowing even faster I/O. The trick is scheduling. I/O uses the network bandwidth, and by taking advantage of the downtime during communication between processors, researchers “can essentially get I/O for free,” said Klasky.

For example, both the DataTap and the Network Scalable Service Interface (NSSI) methods, from Georgia Tech and Sandia Labs respectively, send data to a user defined set of nodes (a staging area) and writes the data from these nodes, reducing the performance linkage between the file system and the application. Furthermore, the DataSpace method from Rutgers creates a PGAS environment in the staging area so that independently compiled codes with ADIOS can be used as services to efficiently couple them together.

“The focus for this release is broader compatibility and user convenience. The introduction of the API calls to replace the XML file addresses long-standing requests from a small but vocal part of our user community,” said team member Jay Lofstead. “The AMR-focused enhancements broaden the classes of application that can use ADIOS while maintaining 100 percent backward compatibility. Some additional changes smooth the user experience.”

Taken separately, all of ADIOS’s individual improvements represent significant advances toward more efficient simulations. Taken together, they embody a major innovation in the way computational science will be conducted.

“Working with Scott Klasky and his team has moved our research and our software, such as DataTap and Data Staging, from being interesting research prototypes to becoming artifacts that address the real needs of petascale simulations,” said Georgia Tech team member Karsten Schwan. “By then also interacting with the fusion, astrophysics and combustion modeling communities, we have not only found ways to alleviate their problems with I/O at scale, but we have also gained valuable information about ways to better organize data and quickly analyze it to help scientists understand the behavior of their petascale codes and gain the scientific insights they seek.”

There are few foreseeable limits to ADIOS’s potential. As it is expanded to additional platforms, simulating big science will become correspondingly simpler, allowing researchers to concentrate more on their results than the technical aspects of their simulations. And as high-performance computing becomes an increasingly powerful research tool, there will be no shortage of grateful scientists.

For more information on ADIOS and/or to download the source, check out the project’s Web page.

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!

CMU’s Latest “Card Shark” – Libratus – is Beating the Poker Pros (Again)

January 20, 2017

It’s starting to look like Carnegie Mellon University has a gambling problem – can’t stay away from the poker table. Read more…

By John Russell

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

Weekly Twitter Roundup (Jan. 19, 2017)

January 19, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

France’s CEA and Japan’s RIKEN to Partner on ARM and Exascale

January 19, 2017

France’s CEA and Japan’s RIKEN institute announced a multi-faceted five-year collaboration to advance HPC generally and prepare for exascale computing. Among the particulars are efforts to: build out the ARM ecosystem; work on code development and code sharing on the existing and future platforms; share expertise in specific application areas (material and seismic sciences for example); improve techniques for using numerical simulation with big data; and expand HPC workforce training. It seems to be a very full agenda. Read more…

By Nishi Katsuya and John Russell

HPE Extreme Performance Solutions

Remote Visualization: An Integral Technology for Upstream Oil & Gas

As the exploration and production (E&P) of natural resources evolves into an even more complex and vital task, visualization technology has become integral for the upstream oil and gas industry. Read more…

ARM Waving: Attention, Deployments, and Development

January 18, 2017

It’s been a heady two weeks for the ARM HPC advocacy camp. At this week’s Mont-Blanc Project meeting held at the Barcelona Supercomputer Center, Cray announced plans to build an ARM-based supercomputer in the U.K. while Mont-Blanc selected Cavium’s ThunderX2 ARM chip for its third phase of development. Last week, France’s CEA and Japan’s Riken announced a deep collaboration aimed largely at fostering the ARM ecosystem. This activity follows a busy 2016 when SoftBank acquired ARM, OpenHPC announced ARM support, ARM released its SVE spec, Fujistu chose ARM for the post K machine, and ARM acquired HPC tool provider Allinea in December. Read more…

By John Russell

Women Coders from Russia, Italy, and Poland Top Study

January 17, 2017

According to a study posted on HackerRank today the best women coders as judged by performance on HackerRank challenges come from Russia, Italy, and Poland. Read more…

By John Russell

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

Weekly Twitter Roundup (Jan. 12, 2017)

January 12, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

France’s CEA and Japan’s RIKEN to Partner on ARM and Exascale

January 19, 2017

France’s CEA and Japan’s RIKEN institute announced a multi-faceted five-year collaboration to advance HPC generally and prepare for exascale computing. Among the particulars are efforts to: build out the ARM ecosystem; work on code development and code sharing on the existing and future platforms; share expertise in specific application areas (material and seismic sciences for example); improve techniques for using numerical simulation with big data; and expand HPC workforce training. It seems to be a very full agenda. Read more…

By Nishi Katsuya and John Russell

ARM Waving: Attention, Deployments, and Development

January 18, 2017

It’s been a heady two weeks for the ARM HPC advocacy camp. At this week’s Mont-Blanc Project meeting held at the Barcelona Supercomputer Center, Cray announced plans to build an ARM-based supercomputer in the U.K. while Mont-Blanc selected Cavium’s ThunderX2 ARM chip for its third phase of development. Last week, France’s CEA and Japan’s Riken announced a deep collaboration aimed largely at fostering the ARM ecosystem. This activity follows a busy 2016 when SoftBank acquired ARM, OpenHPC announced ARM support, ARM released its SVE spec, Fujistu chose ARM for the post K machine, and ARM acquired HPC tool provider Allinea in December. Read more…

By John Russell

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

UberCloud Cites Progress in HPC Cloud Computing

January 10, 2017

200 HPC cloud experiments, 80 case studies, and a ton of hands-on experience gained, that’s the harvest of four years of UberCloud HPC Experiments. Read more…

By Wolfgang Gentzsch and Burak Yenier

A Conversation with Women in HPC Director Toni Collis

January 6, 2017

In this SC16 video interview, HPCwire Managing Editor Tiffany Trader sits down with Toni Collis, the director and founder of the Women in HPC (WHPC) network, to discuss the strides made since the organization’s debut in 2014. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

AWS Beats Azure to K80 General Availability

September 30, 2016

Amazon Web Services has seeded its cloud with Nvidia Tesla K80 GPUs to meet the growing demand for accelerated computing across an increasingly-diverse range of workloads. The P2 instance family is a welcome addition for compute- and data-focused users who were growing frustrated with the performance limitations of Amazon's G2 instances, which are backed by three-year-old Nvidia GRID K520 graphics cards. Read more…

By Tiffany Trader

US, China Vie for Supercomputing Supremacy

November 14, 2016

The 48th edition of the TOP500 list is fresh off the presses and while there is no new number one system, as previously teased by China, there are a number of notable entrants from the US and around the world and significant trends to report on. Read more…

By Tiffany Trader

Vectors: How the Old Became New Again in Supercomputing

September 26, 2016

Vector instructions, once a powerful performance innovation of supercomputing in the 1970s and 1980s became an obsolete technology in the 1990s. But like the mythical phoenix bird, vector instructions have arisen from the ashes. Here is the history of a technology that went from new to old then back to new. Read more…

By Lynd Stringer

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

Container App ‘Singularity’ Eases Scientific Computing

October 20, 2016

HPC container platform Singularity is just six months out from its 1.0 release but already is making inroads across the HPC research landscape. It's in use at Lawrence Berkeley National Laboratory (LBNL), where Singularity founder Gregory Kurtzer has worked in the High Performance Computing Services (HPCS) group for 16 years. Read more…

By Tiffany Trader

Dell EMC Engineers Strategy to Democratize HPC

September 29, 2016

The freshly minted Dell EMC division of Dell Technologies is on a mission to take HPC mainstream with a strategy that hinges on engineered solutions, beginning with a focus on three industry verticals: manufacturing, research and life sciences. "Unlike traditional HPC where everybody bought parts, assembled parts and ran the workloads and did iterative engineering, we want folks to focus on time to innovation and let us worry about the infrastructure," said Jim Ganthier, senior vice president, validated solutions organization at Dell EMC Converged Platforms Solution Division. Read more…

By Tiffany Trader

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. Read more…

By John Russell

Leading Solution Providers

D-Wave SC16 Update: What’s Bo Ewald Saying These Days

November 18, 2016

Tucked in a back section of the SC16 exhibit hall, quantum computing pioneer D-Wave has been talking up its new 2000-qubit processor announced in September. Forget for a moment the criticism sometimes aimed at D-Wave. This small Canadian company has sold several machines including, for example, ones to Lockheed and NASA, and has worked with Google on mapping machine learning problems to quantum computing. In July Los Alamos National Laboratory took possession of a 1000-quibit D-Wave 2X system that LANL ordered a year ago around the time of SC15. Read more…

By John Russell

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

Beyond von Neumann, Neuromorphic Computing Steadily Advances

March 21, 2016

Neuromorphic computing – brain inspired computing – has long been a tantalizing goal. The human brain does with around 20 watts what supercomputers do with megawatts. And power consumption isn’t the only difference. Fundamentally, brains ‘think differently’ than the von Neumann architecture-based computers. While neuromorphic computing progress has been intriguing, it has still not proven very practical. Read more…

By John Russell

The Exascale Computing Project Awards $39.8M to 22 Projects

September 7, 2016

The Department of Energy’s Exascale Computing Project (ECP) hit an important milestone today with the announcement of its first round of funding, moving the nation closer to its goal of reaching capable exascale computing by 2023. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

Dell Knights Landing Machine Sets New STAC Records

November 2, 2016

The Securities Technology Analysis Center, commonly known as STAC, has released a new report characterizing the performance of the Knight Landing-based Dell PowerEdge C6320p server on the STAC-A2 benchmarking suite, widely used by the financial services industry to test and evaluate computing platforms. The Dell machine has set new records for both the baseline Greeks benchmark and the large Greeks benchmark. Read more…

By Tiffany Trader

What Knights Landing Is Not

June 18, 2016

As we get ready to launch the newest member of the Intel Xeon Phi family, code named Knights Landing, it is natural that there be some questions and potentially some confusion. Read more…

By James Reinders, Intel

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