XSEDE14 Workshop Wrestles with Reproducibility

By Faith Singer-Villalobos

August 19, 2014

Imagine that you are trying to create a new sauce for a special dish, or the perfect adhesive for a new aircraft, or you’re flying a helicopter looking for victims of a natural disaster — and you succeed at each of these. This is wonderful news for your dinner guests, or the company that will use the new adhesive, and especially for the victims of the natural disaster. But the question is — Could you do it again and get the same results? Or, did you just get lucky the first time?

At the XSEDE14 conference in Atlanta, a roomful of computational veterans from inside and outside the NSF Extreme Science and Engineering Discovery Environment (XSEDE) participated in a full-day workshop on the topic of reproducibility, and clearly, there is a lot at stake.

“There is a growing awareness in the computational research community that this question of ‘can we do it again’ is becoming important for us in new ways, and the stakes are high — computational research is helping to save lives, answering policy questions, and making an impact on the world,” said Doug James, an HPC researcher at the Texas Advanced Computing Center, in his opening remarks for the workshop.

People have been thinking about reproducibility for a long time – it is one thing to reproduce a small scale lab experiment, or a computation on your desktop, but it is an entirely different matter to reproduce something that the Hubble Space Telescope did over five years at the cost of hundreds of millions of dollars, for example.

So, what is reproducibility? One working definition might resemble this: the ability to repeat an experiment to the degree necessary to assess the correctness and importance of the results. Practices that promote reproducibility include anything that makes a researcher more organized, provides a better audit trail, allows a researcher to track source code, and to know what data sources were used.

Victoria Stodden of Columbia University, who led a roundtable on the topic of reproducibility in 2009 and an ICERM workshop on Reproducibility in Computational and Experimental Mathematics in 2012, gave the keynote address at the XSEDE14 workshop. She raised the issue of a credibility crisis.

“Reproducibility has hit the popular press over the last several months,” Stodden said, citing recent coverage by The Economist (October 2013) and editorials in Nature and Science. Issues around the importance of reproducibility were catalyzed by the clinical trials scandal at Duke University in computational genomics where mistakes in the research were uncovered in 2010 in The Cancer Letter.

“This really goes to the heart of how important reproducibility issues are, and how we need to reconstruct the pipeline of thinking, reasoning and observation that a scientist does, but for the computational aspects, too, where many of these decisions are being manifest.”

Stodden also touched on separate discussions going on regarding different aspects of reproducibility such as statistical reproducibility, which questions the research decisions about the statistics and data analysis, and empirical reproducibility, which focuses on the reporting standards for the physical experiment, but does not focus on the computational steps.

Everyone in the room agreed that computational research is now in a position where complexity and mission criticality take on new import, and the community needs to develop confidence in the results of that research. But what should our priorities be? Training? Better tools? New steps in proposals and submissions?

NCSA Director Ed Seidel shared his view that there are three levels where things have to happen to get momentum moving in right direction: 1) campus level; 2) national level; and 3) publisher level.

Seidel said that local campuses have to think about how they can begin to support local data services, not just repositories, so there is a local structure. “This is a policy issue that vice chancellors for research and provosts need to take seriously…and there are organizations in place like Internet2 and Educause that span the research universities across the country that can help,” Seidel said. “It’s important to frame it not just as data but more around reproducibility; scope the problem beyond data and the data infrastructure.”

In addition, Seidel cited the XSEDE initiative as being a good organization for aiding the reproducibility process. XSEDE was instrumental in starting the National Data Service Consortium, aimed at organizing a number of individual efforts for data services around tools to create data collections to get Digital Object Identifiers or ‘DOIs’ associated with them and to provide linking services to publishers. While typically thought of as pointers to data collections, DOIs can also attach to code. This is a crucial part of reproducibility.

Professional societies and journals can play a part as well. Many are starting to require links to the data referenced in a publication. But reproducible practices must start in the research group.

Victoria Stodden, Assistant Professor, Department of Statistics, Columbia University and Lorena Barba, Assistant Professor, California Institute of Technology
Victoria Stodden, Assistant Professor, Department of Statistics, Columbia University and Lorena Barba, Assistant Professor, California Institute of Technology

Lorena Barba of George Washington University and a leading advocate of reproducible science said, “Conducting research reproducibly doesn’t mean someone else will reproduce the results, but that you are doing it as if someone would do this. By providing full documentation, access to input data and source code, the community will have confidence in your results and will label them as reproducible even if they are, in fact, not reproduced.”

Many other people added to the conversation including Mark Fahey of the National Institute of Computational Sciences. According to Fahey, the centers need to step up and take some responsibility for providing documentation about how users build and run their codes. Fahey said, “Centers can automatically collect information for each code built and each run of the code, and this information can be made available back to the researcher for publications if desired. There are already two prototypes (ALTD and Lariat) at a variety of computing centers around the world that collect a good portion of this information, and a new improved infrastructure is in development called XALT funded by NSF.”


At the outset of the workshop, the group committed to a key deliverable: recommendations in the form of priorities and initiatives for organizations and communities.

“It’s been implicit that ‘Of course, this is what people do, system administrators and researchers check to ensure that codes gets the same results after systems upgrades and when porting to new platforms’ but reproducibility has never been a formal enterprise,” said Nancy Wilkins-Diehr of the San Diego Supercomputer Center, who summarized the workshop and helped facilitate suggestions for moving forward.

“This is a good time to do this. Computational science is a respected contributor of the scientific knowledge base. Important decisions are now based on simulation. While this is gratifying, it has very real implications for our responsibilities as well,” she said.

The participants intend to move forward with humility, however. “The vision for the recommendations is to honor the reality of a diverse set of viewpoints and include ideas that might be outside of the box,” James concluded. Everyone agrees that there is a need to promote confidence-building tools and methodologies that do not adversely affect performance.

Recommendations will be ready in the September 2014 timeframe — please refer to xsede.org/reproducibility to read them. In addition, you can send comments and suggestions to help@xsede.org. The Help Desk will send any and all inquiries to the XSEDE team working on this initiative.

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!

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 scientists the ability to use machine learning to identify e Read more…

By Rob Farber

Mellanox Reacts to Activist Investor Pressures in Letter to Shareholders

March 16, 2018

Activist investor Starboard Value has been exerting pressure on Mellanox Technologies to increase its returns. In response, the high-performance networking company on Monday, March 12, published a letter to shareholders outlining its proposal for a May 2018 extraordinary general meeting (EGM) of shareholders and highlighting its long-term growth strategy and focus on operating margin improvement. Read more…

By Staff

Quantum Computing vs. Our ‘Caveman Newtonian Brain’: Why Quantum Is So Hard

March 15, 2018

Quantum is coming. Maybe not today, maybe not tomorrow, but soon enough. Within 10 to 12 years, we’re told, special-purpose quantum systems will enter the commercial realm. Assuming this happens, we can also assume that quantum will, over extended time, become increasingly general purpose as it delivers mind-blowing power. Read more…

By Doug Black

HPE Extreme Performance Solutions

Achieve Optimal Performance at Scale with High Performance Fabrics for HPC

High Performance Computing (HPC) is unlocking a new era of speed and productivity to fuel business transformation. Rapid advancements in HPC capabilities are helping organizations operate faster and more effectively than ever, but in today’s fast-paced marketplace, a new generation of technologies is required to reach greater scalability and cost-efficiency. Read more…

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 IT in its willingness to outsource computational power. The m Read more…

By Chris Downing

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

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

Stephen Hawking, Legendary Scientist, Dies at 76

March 14, 2018

Stephen Hawking passed away at his home in Cambridge, England, in the early morning of March 14; he was 76. Born on January 8, 1942, Hawking was an English theo Read more…

By Tiffany Trader

Hyperion Tackles Elusive Quantum Computing Landscape

March 13, 2018

Quantum computing - exciting and off-putting all at once - is a kaleidoscope of technology and market questions whose shapes and positions are far from settled. Read more…

By John Russell

Part Two: Navigating Life Sciences Choppy HPC Waters in 2018

March 8, 2018

2017 was not necessarily the best year to build a large HPC system for life sciences say Ari Berman, VP and GM of consulting services, and Aaron Gardner, direct Read more…

By John Russell

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

SciNet Launches Niagara, Canada’s Fastest Supercomputer

March 5, 2018

SciNet and the University of Toronto today unveiled "Niagara," Canada's most-powerful supercomputer, comprising 1,500 dense Lenovo ThinkSystem SD530 high-perfor Read more…

By Tiffany Trader

Part One: Deep Dive into 2018 Trends in Life Sciences HPC

March 1, 2018

Life sciences is an interesting lens through which to see HPC. It is perhaps not an obvious choice, given life sciences’ relative newness as a heavy user of H Read more…

By John Russell

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

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

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

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

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

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

Leading Solution Providers

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

V100 Good but not Great on Select Deep Learning Aps, Says Xcelerit

November 27, 2017

Wringing optimum performance from hardware to accelerate deep learning applications is a challenge that often depends on the specific application in use. A benc Read more…

By John Russell

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

AMD Wins Another: Baidu to Deploy EPYC on Single Socket Servers

December 13, 2017

When AMD introduced its EPYC chip line in June, the company said a portion of the line was specifically designed to re-invigorate a single socket segment in wha Read more…

By John Russell

World Record: Quantum Computer with 46 Qubits Simulated

December 18, 2017

Scientists from the Jülich Supercomputing Centre have set a new world record. Together with researchers from Wuhan University and the University of Groningen, Read more…

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

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