Deploying Jupyter Notebooks at scale on XSEDE resources for Science Gateways and workshops

Jupyter Notebooks have become a mainstream tool for interactive computing in every field of science. Jupyter Notebooks are suitable as companion applications for Science Gateways, providing more flexibility and post-processing capability to the users. Moreover they are often used in training events and workshops to provide immediate access to a pre-configured interactive computing environment. The Jupyter team released the JupyterHub web application to provide a platform where multiple users can login and access a Jupyter Notebook environment. When the number of users and memory requirements are low, it is easy to setup JupyterHub on a single server. However, setup becomes more complicated when we need to serve Jupyter Notebooks at scale to tens or hundreds of users. In this paper we will present three strategies for deploying JupyterHub at scale on XSEDE resources. All options share the deployment of JupyterHub on a Virtual Machine on XSEDE Jetstream. In the first scenario, JupyterHub connects to a supercomputer and launches a single node job on behalf of each user and proxies back the Notebook from the computing node back to the user's browser. In the second scenario, implemented in the context of a XSEDE consultation for the IRIS consortium for Seismology, we deploy Docker in Swarm mode to coordinate many XSEDE Jetstream virtual machines to provide Notebooks with persistent storage and quota. In the last scenario we install the Kubernetes containers orchestration framework on Jetstream to provide a fault-tolerant JupyterHub deployment with a distributed filesystem and capability to scale to thousands of users. In the conclusion section we provide a link to step-by-step tutorials complete with all the necessary commands and configuration files to replicate these deployments.Comment: 7 pages, 3 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications

Many scientific problems require multiple distinct computational tasks to be executed in order to achieve a desired solution. We introduce the Ensemble Toolkit (EnTK) to address the challenges of scale, diversity and reliability they pose. We describe the design and implementation of EnTK, characterize its performance and integrate it with two distinct exemplar use cases: seismic inversion and adaptive analog ensembles. We perform nine experiments, characterizing EnTK overheads, strong and weak scalability, and the performance of two use case implementations, at scale and on production infrastructures. We show how EnTK meets the following general requirements: (i) implementing dedicated abstractions to support the description and execution of ensemble applications; (ii) support for execution on heterogeneous computing infrastructures; (iii) efficient scalability up to O(10^4) tasks; and (iv) fault tolerance. We discuss novel computational capabilities that EnTK enables and the scientific advantages arising thereof. We propose EnTK as an important addition to the suite of tools in support of production scientific computing

Data Access for LIGO on the OSG

During 2015 and 2016, the Laser Interferometer Gravitational-Wave Observatory (LIGO) conducted a three-month observing campaign. These observations delivered the first direct detection of gravitational waves from binary black hole mergers. To search for these signals, the LIGO Scientific Collaboration uses the PyCBC search pipeline. To deliver science results in a timely manner, LIGO collaborated with the Open Science Grid (OSG) to distribute the required computation across a series of dedicated, opportunistic, and allocated resources. To deliver the petabytes necessary for such a large-scale computation, our team deployed a distributed data access infrastructure based on the XRootD server suite and the CernVM File System (CVMFS). This data access strategy grew from simply accessing remote storage to a POSIX-based interface underpinned by distributed, secure caches across the OSG.Comment: 6 pages, 3 figures, submitted to PEARC1

Educational Technology as Seen Through the Eyes of the Readers

In this paper, I present the evaluation of a novel knowledge domain visualization of educational technology. The interactive visualization is based on readership patterns in the online reference management system Mendeley. It comprises of 13 topic areas, spanning psychological, pedagogical, and methodological foundations, learning methods and technologies, and social and technological developments. The visualization was evaluated with (1) a qualitative comparison to knowledge domain visualizations based on citations, and (2) expert interviews. The results show that the co-readership visualization is a recent representation of pedagogical and psychological research in educational technology. Furthermore, the co-readership analysis covers more areas than comparable visualizations based on co-citation patterns. Areas related to computer science, however, are missing from the co-readership visualization and more research is needed to explore the interpretations of size and placement of research areas on the map.Comment: Forthcoming article in the International Journal of Technology Enhanced Learnin

A Taxonomy for Management and Optimization of Multiple Resources in Edge Computing

Edge computing is promoted to meet increasing performance needs of data-driven services using computational and storage resources close to the end devices, at the edge of the current network. To achieve higher performance in this new paradigm one has to consider how to combine the efficiency of resource usage at all three layers of architecture: end devices, edge devices, and the cloud. While cloud capacity is elastically extendable, end devices and edge devices are to various degrees resource-constrained. Hence, an efficient resource management is essential to make edge computing a reality. In this work, we first present terminology and architectures to characterize current works within the field of edge computing. Then, we review a wide range of recent articles and categorize relevant aspects in terms of 4 perspectives: resource type, resource management objective, resource location, and resource use. This taxonomy and the ensuing analysis is used to identify some gaps in the existing research. Among several research gaps, we found that research is less prevalent on data, storage, and energy as a resource, and less extensive towards the estimation, discovery and sharing objectives. As for resource types, the most well-studied resources are computation and communication resources. Our analysis shows that resource management at the edge requires a deeper understanding of how methods applied at different levels and geared towards different resource types interact. Specifically, the impact of mobility and collaboration schemes requiring incentives are expected to be different in edge architectures compared to the classic cloud solutions. Finally, we find that fewer works are dedicated to the study of non-functional properties or to quantifying the footprint of resource management techniques, including edge-specific means of migrating data and services.Comment: Accepted in the Special Issue Mobile Edge Computing of the Wireless Communications and Mobile Computing journa

Jetstream: A self-provisoned, scalable science and engineering cloud environment

The paper describes the motivation behind Jetstream, its functions, hardware configuration, software environment, user interface, design, use cases, relationships with other projects such as Wrangler and iPlant, and challenges in implementation.Funded by the National Science Foundation Award #ACI - 144560