Computational micromagnetics has become an essential tool in academia and industry to support fundamental research and the design and development of devices. Consequently, computational micromagnetics is widely used in the community, and the fraction of time researchers spend performing computational studies is growing. We focus on reducing this time by improving the interface between the numerical simulation and the researcher. We have designed and developed a human-centred research environment called Ubermag. With Ubermag, scientists can control an existing micromagnetic simulation package, such as OOMMF, from Jupyter notebooks. The complete simulation workflow, including definition, execution, and data analysis of simulation runs, can be performed within the same notebook environment. Numerical libraries, co-developed by the computational and data science community, can immediately be used for micromagnetic data analysis within this Python-based environment. By design, it is possible to extend Ubermag to drive other micromagnetic packages from the same environment.

Ubermag: Towards more effective micromagnetic workflows

More than ninety percent of published Jupyter notebooks do not state dependencies on external packages. This makes them non-executable and thus hinders reproducibility of scientific results. We present SnifferDog, an approach that 1) collects the APIs of Python packages and versions, creating a database of APIs; 2) analyzes notebooks to determine candidates for required packages and versions; and 3) checks which packages are required to make the notebook executable (and ideally, reproduce its stored results). In its evaluation, we show that SnifferDog precisely restores execution environments for the largest majority of notebooks, making them immediately executable for end users.

pdf/restoring-execution-environments-of-jupyter-notebooks-388807ergw.pdf

Restoring Execution Environments of Jupyter Notebooks

Abstract. With the increase in computational power, ocean models with kilometer-scale resolution have emerged over the last decade. These models have been used for quantifying the energetic exchanges between spatial scales, informing the design of eddy parametrizations, and preparing observing networks. The increase in resolution, however, has drastically increased the size of model outputs, making it difficult to transfer and analyze the data. It remains, nonetheless, of primary importance to assess more systematically the realism of these models.
Here, we showcase a cloud-based analysis framework proposed by the Pangeo project that aims to tackle such distribution and analysis challenges. We analyze the output of eight submesoscale-permitting simulations, all on the cloud, for a crossover region of the upcoming Surface Water and Ocean Topography (SWOT) altimeter mission near the Gulf Stream separation.
The cloud-based analysis framework (i) minimizes the cost of duplicating and storing ghost copies of data and (ii) allows for seamless sharing of analysis results amongst collaborators. We describe the framework and provide example analyses (e.g., sea-surface height variability, submesoscale vertical buoyancy fluxes, and comparison to predictions from the mixed-layer instability parametrization). Basin- to global-scale, submesoscale-permitting models are still at their early stage of development; their cost and carbon footprints are also rather large. It would, therefore, benefit the community to document the different model configurations for future best practices. We also argue that an emphasis on data analysis strategies would be crucial for improving the models themselves.


Cloud-based framework for inter-comparing submesoscale-permitting realistic ocean models

Software development for data reduction and analysis at large research facilities is increasingly professionalized, and internationally coordinated. To foster software quality and sustainability, and to facilitate collaboration, representatives from software groups of European neutron and muon facilities have agreed on a set of guidelines for development practices, infrastructure, and functional and non-functional product properties. These guidelines have been derived from actual practices in software projects from the EU funded consortium ‘Science and Innovation with Neutrons in Europe in 2020’ (SINE2020), and have been enriched through extensive literature review. Besides guiding the work of the professional software engineers in our computing groups, we hope to influence scientists who are willing to contribute their own data treatment software to our community. Moreover, this work may also provide inspiration to scientific software development beyond the neutron and muon field.

Guidelines for collaborative development of sustainable data treatment software

Abstract. With the increase in computational power, ocean models with kilometer-scale resolution have emerged over the last decade. These models have been used for quantifying the energetic exchanges between spatial scales, informing the design of eddy parametrizations and preparing observing networks. The increase in resolution, however, has drastically increased the size of model outputs, making it difficult to transfer and analyze the data. Nonetheless, it is of primary importance to assess more systematically the realism of these models. Here, we showcase a cloud-based analysis framework proposed by the Pangeo Project that aims to tackle such distribution and analysis challenges. We analyze the output of eight submesoscale-permitting simulations, all on the cloud, for a crossover region of the upcoming Surface Water and Ocean Topography (SWOT) altimeter mission near the Gulf Stream separation. The models used in this study are run with the NEMO, CROCO, MITgcm, HYCOM, FESOM and FIO-COM code bases. The cloud-based analysis framework: i) minimizes the cost of duplicating and storing ghost copies of data, and ii) allows for seamless sharing of analysis results amongst collaborators. We describe the framework and provide example analyses (e.g., sea-surface height variability, submesoscale vertical buoyancy fluxes, and comparison to predictions from the mixed-layer instability parametrization). Basin-to-global scale, submesoscale-permitting models are still at their early stage of development; their cost and carbon footprints are also rather large. It would, therefore, benefit the community to document the different model configurations for future best practices. We also argue that an emphasis on data analysis strategies would be crucial for improving the models themselves. 

/pdf/cloud-based-framework-for-inter-comparing-submesoscale-1jufasde.pdf

Cloud-based framework for inter-comparing submesoscale permitting realistic ocean models

Jupyter notebooks are executable documents that are displayed in a web browser. The notebook elements consist of human-authored contextual elements and computer code, and computer-generated output from executing the computer code. Such outputs can include tables and plots. The notebook elements can be executed interactively, and the whole notebook can be saved, re-loaded and re-executed, or converted to read-only formats such as HTML, LaTeX and PDF. Exploiting these characteristics, Jupyter notebooks can be used to improve the effectiveness of computational and data exploration, documentation, communication, reproducibility and re-usability of scientific research results. They also serve as building blocks of remote data access and analysis as is required for facilities hosting large data sets and initiatives such as the European Open Science Cloud (EOSC). In this contribution we report from our experience of using Jupyter notebooks for data analysis at research facilities, and outline opportunities and future plans.

/pdf/data-exploration-and-analysis-with-jupyter-notebooks-5fmd07metf.pdf

Data Exploration and Analysis with Jupyter Notebooks

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Data Exploration and Analysis with Jupyter Notebooks