Luca Cinquini

The Earth System Grid Federation: An open infrastructure for access to distributed geospatial data

Abstract The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration that aims at developing the software infrastructure needed to facilitate and empower the study of climate change on a global scale. The ESGF’s architecture employs a system of geographically distributed peer nodes, which are independently administered yet united by the adoption of common federation protocols and application programming interfaces (APIs). The cornerstones of its interoperability are the peer-to-peer messaging that is continuously exchanged among all nodes in the federation; a shared architecture and API for search and discovery; and a security infrastructure based on industry standards (OpenID, SSL, GSI and SAML). The ESGF software stack integrates custom components (for data publishing, searching, user interface, security and messaging), developed collaboratively by the team, with popular application engines (Tomcat, Solr) available from the open source community. The full ESGF infrastructure has now been adopted by multiple Earth science projects and allows access to petabytes of geophysical data, including the entire Fifth Coupled Model Intercomparison Project (CMIP5) output used by the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5) and a suite of satellite observations (obs4MIPs) and reanalysis data sets (ANA4MIPs). This paper presents ESGF as a successful example of integration of disparate open source technologies into a cohesive, wide functional system, and describes our experience in building and operating a distributed and federated infrastructure to serve the needs of the global climate science community.

Evaluating cloud computing in the NASA DESDynI ground data system

The proposed NASA Deformation, Ecosystem Structure and Dynamics of Ice (DESDynI) mission would be a first-of-breed endeavor that would fundamentally change the paradigm by which Earth Science data systems at NASA are built. DESDynI is evaluating a distributed architecture where expert science nodes around the country all engage in some form of mission processing and data archiving. This is compared to the traditional NASA Earth Science missions where the science processing is typically centralized. Whats more, DESDynI is poised to profoundly increase the amount of data collection and processing well into the 5 terabyte/day and tens of thousands of job range, both of which comprise a tremendous challenge to DESDynIs proposed distributed data system architecture. In this paper, we report on a set of architectural trade studies and benchmarks meant to inform the DESDynI mission and the broader community of the impacts of these unprecedented requirements. In particular, we evaluate the benefits of cloud computing and its integration with our existing NASA ground data system software called Apache Object Oriented Data Technology (OODT). The preliminary conclusions of our study suggest that the use of the cloud and OODT together synergistically form an effective, efficient and extensible combination that could meet the challenges of NASA science missions requiring DESDynI-like data collection and processing volumes at reduced costs.

Architecting Data-Intensive Software Systems

Data-intensive software is increasingly prominent in today’s world, where the collection, processing, and dissemination of ever-larger volumes of data has become a driving force behind innovation in the early twenty-first century. The trend towards massive data manipulation is broad-based, and case studies can be examined in domains from politics, to intelligence gathering, to scientific and medical research. The scientific domain in particular provides a rich array of case studies that offer ready insight into many of the modern software engineering, and software architecture challenges associated with data-intensive systems.

Big Data Challenges in Climate Science: Improving the next-generation cyberinfrastructure

The knowledge we gain from research in climate science depends on the generation, dissemination, and analysis of high-quality data. This work comprises technical practice as well as social practice, both of which are distinguished by their massive scale and global reach. As a result, the amount of data involved in climate research is growing at an unprecedented rate. Some examples of the types of activities that increasingly require an improved cyberinfrastructure for dealing with large amounts of critical scientific data are climate model intercomparison (CMIP) experiments; the integration of observational data and climate reanalysis data with climate model outputs, as seen in the Observations for Model Intercomparison Projects (Obs4MIPs), Analysis for Model Intercomparison Projects (Ana4MIPs), and Collaborative Reanalysis Technical Environment-Intercomparison Project (CREATE-IP) activities; and the collaborative work of the Intergovernmental Panel on Climate Change (IPCC). This article provides an overview of some of climate sciences big data problems and the technical solutions being developed to advance data publication, climate analytics as a service, and interoperability within the Earth System Grid Federation (ESGF), which is the primary cyberinfrastructure currently supporting global climate research activities.

Radio Array of Portable Interferometric Detectors (RAPID): Development of a deployable multiple application radio array

The Radio Array of Portable Interferometric Detectors (RAPID) is an advanced radio designed for multi-role applications. The system implements a spatially diverse sparse array technology and can be deployed and reconfigured easily. Data are captured at the raw voltage level using the system in the field and processed post-experiment. Signal processing for the system is software defined and uses a scalable Cloud computing architecture. The system builds upon the Square Kilometer Array Low Frequency Aperture antenna (SKALA) in combination with custom hardware for data acquisition on a per antenna basis. The instrument uses physically disconnected elements, a high performance direct digitization receiver, hot swap solid state storage, solar and battery power, and wireless control for interconnection. Schedule based operation can also be used in radio quiet locations or to enable minimally attended operation. RAPID is intended for application as both an Astronomical radio telescope and a Geospace imaging radar system. The high degree of mobility a orded by the system enables a wide variety of interferometric configurations and allows deployment of the instrument at locations which are optimal for specific scientific goals.

Summarizing performance for genome scale measurement of miRNA: reference samples and metrics

BackgroundThe potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measurement assurance are critical components of genome-scale measurements. Here, we evaluated the utility of a set of total RNA samples, designed with between-sample differences in the relative abundance of miRNAs, as process controls.ResultsThree pure total human RNA samples (brain, liver, and placenta) and two different mixtures of these components were evaluated as measurement assurance control samples on multiple measurement systems at multiple sites and over multiple rounds. In silico modeling of mixtures provided benchmark values for comparison with physical mixtures. Biomarker development laboratories using next-generation sequencing (NGS) or genome-scale hybridization assays participated in the study and returned data from the samples using their routine workflows. Multiplexed and single assay reverse-transcription PCR (RT-PCR) was used to confirm in silico predicted sample differences. Data visualizations and summary metrics for genome-scale miRNA profiling assessment were developed using this dataset, and a range of performance was observed. These metrics have been incorporated into an online data analysis pipeline and provide a convenient dashboard view of results from experiments following the described design. The website also serves as a repository for the accumulation of performance values providing new participants in the project an opportunity to learn what may be achievable with similar measurement processes.ConclusionsThe set of reference samples used in this study provides benchmark values suitable for assessing genome-scale miRNA profiling processes. Incorporation of these metrics into an online resource allows laboratories to periodically evaluate their performance and assess any changes introduced into their measurement process.

A topical evaluation and discussion of data movement technologies for data-intensive scientific applications

Transferring large volumes of information from one location to potentially many others that are geographically distributed and across varying networks is still prevalent in modern scientific data systems. This is despite the movement to push computation to the data and to reduce data movement needed to compute answers to challenging scientific problems, to disseminate information to the scientific community, and to acquire data for curation and enrichment. Because of this, it is imperative that decisions made regarding data movement systems and architectures be backed by both analytical rigor, and also by empirical evidence and measurement. The purpose of this study is to expand on the work performed by our research team over the last decade and to take a fresh look at the evaluation of multiple topical data transfer technologies in use cases derived from data-intensive scientific systems and applications in the areas of Earth science. We report on the evaluation of a set of data movement technologies against a set of empirically derived comparison dimensions. Based on this evaluation, we make recommendations towards the selection of appropriate data movement technologies in scientific applications and scenarios.

Optimization of system architecture for Big Data analysis in climate science

In this paper, we describe an emergent tool called DAWN (short for Distributed Analytics, Workflows and Numeric) which is a model for simulating, analyzing and optimizing system architectures for executing arbitrary data processing pipelines. As an example, we will apply DAWN to the investigation of a real-life Big Data use case in climate science: the evaluation of simulated rainfall characteristics using high-resolution observational data. We will show how DAWN can help in determining the optimal architecture, and science algorithms, to execute this case study analyzing distributed datasets, as a tradeoff between the overall time cost and the uncertainty of calculated metrics for model evaluation. We will also show how DAWN can guide architectural decisions for future research, specifically impacting how data should be generated and analyzed to cope with future projected data volumes.

Architecting Scientific Data Systems in the Cloud

Scientists, educators, decision makers, students, and many others utilize scientific data produced by science instruments. They study our universe, make new discoveries in areas such as weather forecasting and cancer research, and shape policy decisions that impact nations fiscally, socially, economically, and in many other ways. Over the past 20 years or so, the data produced by these scientific instruments have increased in volume, complexity, and resolution, causing traditional computing infrastructures to have difficulties in scaling up to deal with them. This reality has led us, and others, to investigate the applicability of cloud computing to address the scalability challenges. NASA’s Jet Propulsion Laboratory (JPL) is at the forefront of transitioning its science applications to the cloud environment. Through the Apache Object Oriented Data Technology (OODT) framework, for NASA’s first software released at the open-source Apache Software Foundation (ASF), engineers at JPL have been able to scale the storage and computational aspects of their scientific data systems to the cloud – thus achieving reduced costs and improved performance. In this chapter, we report on the use of Apache OODT for cloud computing, citing several examples in a number of scientific domains. Experience, specific performance, and numbers are also reported. Directions for future work in the area are also suggested.

SciDAC's Earth System Grid Center for Enabling Technologies Semi-Annual Progress Report for the Period October 1, 2009 through March 31, 2010

This report summarizes work carried out by the ESG-CET during the period October 1, 2009 through March 31, 2009. It includes discussion of highlights, overall progress, period goals, collaborations, papers, and presentations. To learn more about our project, and to find previous reports, please visit the Earth System Grid Center for Enabling Technologies (ESG-CET) website. This report will be forwarded to the DOE SciDAC program management, the Office of Biological and Environmental Research (OBER) program management, national and international collaborators and stakeholders (e.g., the Community Climate System Model (CCSM), the Intergovernmental Panel on Climate Change (IPCC) 5th Assessment Report (AR5), the Climate Science Computational End Station (CCES), the SciDAC II: A Scalable and Extensible Earth System Model for Climate Change Science, the North American Regional Climate Change Assessment Program (NARCCAP), and other wide-ranging climate model evaluation activities).