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. 2017 May 11;12(5):e0177459.
doi: 10.1371/journal.pone.0177459. eCollection 2017.

Singularity: Scientific containers for mobility of compute

Gregory M Kurtzer  1 , Vanessa Sochat  2 , Michael W Bauer  1   3   4
Affiliations

Singularity: Scientific containers for mobility of compute

Gregory M Kurtzer et al. PLoS One. .

Abstract

Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity is an open source initiative that harnesses the expertise of system and software engineers and researchers alike, and integrates seamlessly into common workflows for both of these groups. As its primary use case, Singularity brings mobility of computing to both users and HPC centers, providing a secure means to capture and distribute software and compute environments. This ability to create and deploy reproducible environments across these centers, a previously unmet need, makes Singularity a game changing development for computational science.

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Conflict of interest statement

Competing Interests: Authors VS and MWB have declared that no competing interests exist. GMK briefly worked with the company Ontropos as a consultant to help them use Singularity containers in their infrastructure. This relationship did not play a role in the development of Singularity, study design, decision to publish, or preparation of the manuscript. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Singularity usage workflow.
The standard Singularity Usage Workflow involves a working endpoint (left) where the user has root, and a container can be created, modified and updated, and then transferred to a shared computational resource (right) to be executed at scale.
See this image and copyright information in PMC

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Grants and funding

Author VS is supported by Stanford Research Computing (IT) and the Stanford School of Medicine, and author MWB is supported by the Frankfurt Institute of Advanced Studies (FIAS). Author GMK is an employee of Lawrence Berkeley National Lab, the Department of Energy, and UC Regents. This manuscript has been authored by an author (GMK) at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231 with the U.S. Department of Energy. The U.S. Government retains, and the publisher, by accepting the article for publication, acknowledges, that the U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. Government purposes. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.