Biblio

Continuously growing amount of research experiments using High Performance Computing (HPC) leads to the questions of research data management and in particular how to preserve a scientific experiment including all related data for long term for its future reproduction. This paper covers some challenges and possible solutions related to the preservation of scientific experiments on HPC systems and represents a concept of the preservation system for HPC computations. Storage of the experiment itself with some related data is not only enough for its future reproduction, especially in the long term. For that case preservation of the whole experiment's environment (operating system, used libraries, environment variables, input data, etc.) via containerization technology (e.g. using Docker, Singularity) is proposed. This approach allows to preserve the entire environment, but is not always possible on every HPC system because of security issues. And it also leaves a question, how to deal with commercial software that was used within the experiment. As a possible solution we propose to run a preservation process outside of the computing system on the web-server and to replace all commercial software inside the created experiment's image with open source analogues that should allow future reproduction of the experiment without any legal issues. The prototype of such a system was developed, the paper provides the scheme of the system, its main features and describes the first experimental results and further research steps.

The ability to independently regenerate published computational claims is widely recognized as a key component of scientific reproducibility. In this article we take a narrow interpretation of this goal, and attempt to regenerate published claims from author-supplied information, including data, code, inputs, and other provided specifications, on a different computational system than that used by the original authors. We are motivated by Claerbout and Donoho's exhortation of the importance of providing complete information for reproducibility of the published claim. We chose the Elsevier journal, the Journal of Computational Physics, which has stated author guidelines that encourage the availability of computational digital artifacts that support scholarly findings. In an IRB approved study at the University of Illinois at Urbana-Champaign (IRB \#17329) we gathered artifacts from a sample of authors who published in this journal in 2016 and 2017. We then used the ICERM criteria generated at the 2012 ICERM workshop "Reproducibility in Computational and Experimental Mathematics" to evaluate the sufficiency of the information provided in the publications and the ease with which the digital artifacts afforded computational reproducibility. We find that, for the articles for which we obtained computational artifacts, we could not easily regenerate the findings for 67% of them, and we were unable to easily regenerate all the findings for any of the articles. We then evaluated the artifacts we did obtain (55 of 306 articles) and find that the main barriers to computational reproducibility are inadequate documentation of code, data, and workflow information (70.9%), missing code function and setting information, and missing licensing information (75%). We recommend improvements based on these findings, including the deposit of supporting digital artifacts for reproducibility as a condition of publication, and verification of computational findings via re-execution of the code when possible.