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Primeur weekly 2019-04-23

Quantum computing

Quantum computing start-up Zapata Computing raises $21 million in Series A financing ...

World-record quantum computing result for Sydney teams ...

Improving quantum computers ...

Focus on Europe

ISC STEM Student Day now open for sign-up ...

Dr. Debora Sijacki wins the 2019 PRACE Ada Lovelace Award for HPC ...

Middleware

Japan-based Core Micro Systems becomes a Bright Advanced Reseller ...

2019 DOE Performance Portability Meeting breaks new ground ...

Hardware

Mellanox delivers record revenue for the first quarter of 2019 ...

Intel acquires Omnitek and strengthens FPGA video and vision offering ...

Spectra Logic and Arcitecta debut joint genomics data management solution at Bio-IT World Conference & Expo '19 ...

World-class data science server to amplify Clemson's supercomputer ...

Cadence collaborates with TSMC to accelerate 5nm FinFET innovation, enabling next-generation SoC production design ...

Applications

Researchers gather at Ohio Supercomputer Center for spring Statewide Users Group conference ...

Blue Waters user Claire Porter wins NOAA David Johnson Award for ArcticDEM ...

Helping research reach new heights with AI ...

U.S. Department of Energy's INCITE Programme seeks proposals for 2020 ...

AT&T leverages Argonne's climate modeling and infrastructure resilience expertise to benefit Southeastern U.S. ...

Searching for photocathodes that convert CO2 into fuels ...

ECMWF to present second edition of the Summer of Weather Code (ESoWC) 2019 ...

HPC supports first black hole image ...

Research using TACC supercomputers studies bioelectric effects of cells to develop new anti-cancer strategies ...

TACC enhances computational reproducibility ...

The Cloud

Creating a cloak for grid data in the Cloud ...

TACC enhances computational reproducibility


19 Apr 2019 Austin - Trust, but verify. The well-known proverb speaks to the heart of the scientific method, which builds on the results of others but requires that data be collected in a way that can be repeated with the same results. Scientific reproducibility extends beyond just recreating the conditions of a physical experiment. The computational analysis of data also factors into the reproducibility equation.

"Computational reproducibility is a subset of the broader and even harder topic of scientific reproducibility", stated Dan Stanzione, TACC's executive director.

Computational reproducibility can be difficult to achieve. Even working with the same data, one analysis might yield small differences from another. Dan Stanzione explained that a computer's hardware and software systems can change a lot over time, partially because of software upgrades such as security patches. Changes in scientific software libraries, operating system components, and computer hardware upgrades can slightly alter results.

"If we can't get the exact same answer bit-for-bit, then what's close enough? What's a scientifically valid way to represent that? That's what we're after", Dan Stanzione stated.

"Reproducibility means many things to many people, because it is in fact many things, and it has many aspects", stated Doug James, former deputy director for High Performance Computing at TACC. Doug James cited a definition for reproducibility by Lorena Barba, associate professor of mechanical and aerospace engineering at George Washington University. "She describes reproducibility as conducting your research as if someone might want to do it again. That means traceability, automation, and transparency. It means the ability to survive inspection by one's peers, to give them the confidence that if they needed or wanted to do this again, they could", Doug James stated.

Researchers can control the software configuration of their workstations, but not on the systems at TACC and other supercomputing centres. But Doug James explained that TACC has developed tools for researchers to control their software environments. One example is the Lmod module system, written and maintained by TACC's manager of HPC Software Tools, Robert McLay.

"The module system has commands that offer insight into what you can load and have loaded. It allows you to save, preserve, and quickly recover your favorite collections of software so that you can come to the table tomorrow with the same software that you had today. And in particular, it's designed to make managing and controlling the software environment easy and repeatable for the individual user. That's the kind of thing that TACC does in the supercomputing environment to promote and enhance reproducibility", Doug James stated.

Other tools developed at TACC to enhance reproducibility include XALT, which keeps track of the software packages, libraries, and versions used to execute essentially any job, workflow or command on the system; and TACC Stats, which leverages XALT metadata to gauge how efficiently the software uses its resources.

TACC also enhances reproducibility through the expanded use of containers, added Dan Stanzione. "Containers are a very lightweight technology for virtualization. We can store not only the code that you used, but also the environment around it, the operating system, and the libraries. That way we can go back and get the same software environment and store the whole thing", he stated. Docker, an open source container platform, is one of the main tools used for this purpose.

Another opportunity for TACC to enhance reproducibility comes from the increasing use of science gateways and web services, which provide a portal for TACC systems without users having to build and compile their own code. Software versions, workflows, and other metadata can be stored for later use. "If we can preserve the data and then build a container to preserve the software environment, we have a lot of pieces that help make science more reproducible", Dan Stanzione stated. "Our strategy is to keep pushing those technologies forward and expose our users to the best practices for enhancing computational reproducibility."
Source: University of Texas at Austin, Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2019-04-23

Quantum computing

Quantum computing start-up Zapata Computing raises $21 million in Series A financing ...

World-record quantum computing result for Sydney teams ...

Improving quantum computers ...

Focus on Europe

ISC STEM Student Day now open for sign-up ...

Dr. Debora Sijacki wins the 2019 PRACE Ada Lovelace Award for HPC ...

Middleware

Japan-based Core Micro Systems becomes a Bright Advanced Reseller ...

2019 DOE Performance Portability Meeting breaks new ground ...

Hardware

Mellanox delivers record revenue for the first quarter of 2019 ...

Intel acquires Omnitek and strengthens FPGA video and vision offering ...

Spectra Logic and Arcitecta debut joint genomics data management solution at Bio-IT World Conference & Expo '19 ...

World-class data science server to amplify Clemson's supercomputer ...

Cadence collaborates with TSMC to accelerate 5nm FinFET innovation, enabling next-generation SoC production design ...

Applications

Researchers gather at Ohio Supercomputer Center for spring Statewide Users Group conference ...

Blue Waters user Claire Porter wins NOAA David Johnson Award for ArcticDEM ...

Helping research reach new heights with AI ...

U.S. Department of Energy's INCITE Programme seeks proposals for 2020 ...

AT&T leverages Argonne's climate modeling and infrastructure resilience expertise to benefit Southeastern U.S. ...

Searching for photocathodes that convert CO2 into fuels ...

ECMWF to present second edition of the Summer of Weather Code (ESoWC) 2019 ...

HPC supports first black hole image ...

Research using TACC supercomputers studies bioelectric effects of cells to develop new anti-cancer strategies ...

TACC enhances computational reproducibility ...

The Cloud

Creating a cloak for grid data in the Cloud ...