Enhancing speed and scalability of the ParFlow simulation code

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

Survey and Analysis of Production Distributed Computing Infrastructures

This report has two objectives. First, we describe a set of the production distributed infrastructures currently available, so that the reader has a basic understanding of them. This includes explaining why each infrastructure was created and made available and how it has succeeded and failed. The set is not complete, but we believe it is representative. Second, we describe the infrastructures in terms of their use, which is a combination of how they were designed to be used and how users have found ways to use them. Applications are often designed and created with specific infrastructures in mind, with both an appreciation of the existing capabilities provided by those infrastructures and an anticipation of their future capabilities. Here, the infrastructures we discuss were often designed and created with specific applications in mind, or at least specific types of applications. The reader should understand how the interplay between the infrastructure providers and the users leads to such usages, which we call usage modalities. These usage modalities are really abstractions that exist between the infrastructures and the applications; they influence the infrastructures by representing the applications, and they influence the ap- plications by representing the infrastructures

Status and projections of the NAS program

NASA's Numerical Aerodynamic Simulation (NAS) Program has completed development of the initial operating configuration of the NAS Processing System Network (NPSN). This is the first milestone in the continuing and pathfinding effort to provide state-of-the-art supercomputing for aeronautics research and development. The NPSN, available to a nation-wide community of remote users, provides a uniform UNIX environment over a network of host computers ranging from the Cray-2 supercomputer to advanced scientific workstations. This system, coupled with a vendor-independent base of common user interface and network software, presents a new paradigm for supercomputing environments. Background leading to the NAS program, its programmatic goals and strategies, technical goals and objectives, and the development activities leading to the current NPSN configuration are presented. Program status, near-term plans, and plans for the next major milestone, the extended operating configuration, are also discussed

A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor

Workshop proceedings: Information Systems for Space Astrophysics in the 21st Century, volume 1

The Astrophysical Information Systems Workshop was one of the three Integrated Technology Planning workshops. Its objectives were to develop an understanding of future mission requirements for information systems, the potential role of technology in meeting these requirements, and the areas in which NASA investment might have the greatest impact. Workshop participants were briefed on the astrophysical mission set with an emphasis on those missions that drive information systems technology, the existing NASA space-science operations infrastructure, and the ongoing and planned NASA information systems technology programs. Program plans and recommendations were prepared in five technical areas: Mission Planning and Operations; Space-Borne Data Processing; Space-to-Earth Communications; Science Data Systems; and Data Analysis, Integration, and Visualization

ALOJA: A benchmarking and predictive platform for big data performance analysis

The main goals of the ALOJA research project from BSC-MSR, are to explore and automate the characterization of cost-effectivenessof Big Data deployments. The development of the project over its first year, has resulted in a open source benchmarking platform, an online public repository of results with over 42,000 Hadoop job runs, and web-based analytic tools to gather insights about system's cost-performance1. This article describes the evolution of the project's focus and research lines from over a year of continuously benchmarking Hadoop under dif- ferent configuration and deployments options, presents results, and dis cusses the motivation both technical and market-based of such changes. During this time, ALOJA's target has evolved from a previous low-level profiling of Hadoop runtime, passing through extensive benchmarking and evaluation of a large body of results via aggregation, to currently leveraging Predictive Analytics (PA) techniques. Modeling benchmark executions allow us to estimate the results of new or untested configu- rations or hardware set-ups automatically, by learning techniques from past observations saving in benchmarking time and costs.This work is partially supported the BSC-Microsoft Research Centre, the Span- ish Ministry of Education (TIN2012-34557), the MINECO Severo Ochoa Research program (SEV-2011-0067) and the Generalitat de Catalunya (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

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

dReDBox: Materializing a full-stack rack-scale system prototype of a next-generation disaggregated datacenter

Current datacenters are based on server machines, whose mainboard and hardware components form the baseline, monolithic building block that the rest of the system software, middleware and application stack are built upon. This leads to the following limitations: (a) resource proportionality of a multi-tray system is bounded by the basic building block (mainboard), (b) resource allocation to processes or virtual machines (VMs) is bounded by the available resources within the boundary of the mainboard, leading to spare resource fragmentation and inefficiencies, and (c) upgrades must be applied to each and every server even when only a specific component needs to be upgraded. The dRedBox project (Disaggregated Recursive Datacentre-in-a-Box) addresses the above limitations, and proposes the next generation, low-power, across form-factor datacenters, departing from the paradigm of the mainboard-as-a-unit and enabling the creation of function-block-as-a-unit. Hardware-level disaggregation and software-defined wiring of resources is supported by a full-fledged Type-1 hypervisor that can execute commodity virtual machines, which communicate over a low-latency and high-throughput software-defined optical network. To evaluate its novel approach, dRedBox will demonstrate application execution in the domains of network functions virtualization, infrastructure analytics, and real-time video surveillance.This work has been supported in part by EU H2020 ICTproject dRedBox, contract #687632.Peer ReviewedPostprint (author's final draft