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.”

Recommendations

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!

Google Cloud Makes Good on Promise to Add Nvidia P100 GPUs

September 21, 2017

Google has taken down the notice on its cloud platform website that says Nvidia Tesla P100s are “coming soon.” That's because the search giant has announced the beta launch of the high-end P100 Nvidia Tesla GPUs on t Read more…

By George Leopold

Cray Wins $48M Supercomputer Contract from KISTI

September 21, 2017

It was a good day for Cray which won a $48 million contract from the Korea Institute of Science and Technology Information (KISTI) for a 128-rack CS500 cluster supercomputer. The new system, equipped with Intel Xeon Scal Read more…

By John Russell

Adolfy Hoisie to Lead Brookhaven’s Computing for National Security Effort

September 21, 2017

Brookhaven National Laboratory announced today that Adolfy Hoisie will chair its newly formed Computing for National Security department, which is part of Brookhaven’s new Computational Science Initiative (CSI). Read more…

By John Russell

HPE Extreme Performance Solutions

HPE Prepares Customers for Success with the HPC Software Portfolio

High performance computing (HPC) software is key to harnessing the full power of HPC environments. Development and management tools enable IT departments to streamline installation and maintenance of their systems as well as create, optimize, and run their HPC applications. Read more…

PNNL’s Center for Advanced Tech Evaluation Seeks Wider HPC Community Ties

September 21, 2017

Two years ago the Department of Energy established the Center for Advanced Technology Evaluation (CENATE) at Pacific Northwest National Laboratory (PNNL). CENATE’s ambitious mission was to be a proving ground for near- Read more…

By John Russell

Stanford University and UberCloud Achieve Breakthrough in Living Heart Simulations

September 21, 2017

Cardiac arrhythmia can be an undesirable and potentially lethal side effect of drugs. During this condition, the electrical activity of the heart turns chaotic, Read more…

By Wolfgang Gentzsch, UberCloud, and Francisco Sahli, Stanford University

PNNL’s Center for Advanced Tech Evaluation Seeks Wider HPC Community Ties

September 21, 2017

Two years ago the Department of Energy established the Center for Advanced Technology Evaluation (CENATE) at Pacific Northwest National Laboratory (PNNL). CENAT Read more…

By John Russell

Exascale Computing Project Names Doug Kothe as Director

September 20, 2017

The Department of Energy’s Exascale Computing Project (ECP) has named Doug Kothe as its new director effective October 1. He replaces Paul Messina, who is stepping down after two years to return to Argonne National Laboratory. Kothe is a 32-year veteran of DOE’s National Laboratory System. Read more…

Takeaways from the Milwaukee HPC User Forum

September 19, 2017

Milwaukee’s elegant Pfister Hotel hosted approximately 100 attendees for the 66th HPC User Forum (September 5-7, 2017). In the original home city of Pabst Blu Read more…

By Merle Giles

Kathy Yelick Charts the Promise and Progress of Exascale Science

September 15, 2017

On Friday, Sept. 8, Kathy Yelick of Lawrence Berkeley National Laboratory and the University of California, Berkeley, delivered the keynote address on “Breakthrough Science at the Exascale” at the ACM Europe Conference in Barcelona. In conjunction with her presentation, Yelick agreed to a short Q&A discussion with HPCwire. Read more…

By Tiffany Trader

DARPA Pledges Another $300 Million for Post-Moore’s Readiness

September 14, 2017

The Defense Advanced Research Projects Agency (DARPA) launched a giant funding effort to ensure the United States can sustain the pace of electronic innovation vital to both a flourishing economy and a secure military. Under the banner of the Electronics Resurgence Initiative (ERI), some $500-$800 million will be invested in post-Moore’s Law technologies. Read more…

By Tiffany Trader

IBM Breaks Ground for Complex Quantum Chemistry

September 14, 2017

IBM has reported the use of a novel algorithm to simulate BeH2 (beryllium-hydride) on a quantum computer. This is the largest molecule so far simulated on a quantum computer. The technique, which used six qubits of a seven-qubit system, is an important step forward and may suggest an approach to simulating ever larger molecules. Read more…

By John Russell

Cubes, Culture, and a New Challenge: Trish Damkroger Talks about Life at Intel—and Why HPC Matters More Than Ever

September 13, 2017

Trish Damkroger wasn’t looking to change jobs when she attended SC15 in Austin, Texas. Capping a 15-year career within Department of Energy (DOE) laboratories, she was acting Associate Director for Computation at Lawrence Livermore National Laboratory (LLNL). Her mission was to equip the lab’s scientists and research partners with resources that would advance their cutting-edge work... Read more…

By Jan Rowell

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

Six Exascale PathForward Vendors Selected; DoE Providing $258M

June 15, 2017

The much-anticipated PathForward awards for hardware R&D in support of the Exascale Computing Project were announced today with six vendors selected – AMD Read more…

By John Russell

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

Top500 Results: Latest List Trends and What’s in Store

June 19, 2017

Greetings from Frankfurt and the 2017 International Supercomputing Conference where the latest Top500 list has just been revealed. Although there were no major Read more…

By Tiffany Trader

Leading Solution Providers

IBM Clears Path to 5nm with Silicon Nanosheets

June 5, 2017

Two years since announcing the industry’s first 7nm node test chip, IBM and its research alliance partners GlobalFoundries and Samsung have developed a proces 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

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

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