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Computer scientist Arjun Shankar is director of the Compute and Data Environment for Science (CADES), ORNL’s multidisciplinary big data computing center. CADES offers computing, networking and data analytics to facilitate workflows for both ORNL and external research projects.
Year after year, network traffic keeps reaching newhighs as unprecedented volumes of data flow between an ever-increasing number of sources and destinations. As part of the Analysis on the Wire project, we aim to develop a network-centric approach for streaming data processing to facilitate scientific data analysis and reduce the overhead in sending big data to a data center. This work discusses our design for programmable network devices to augment network capabilities for streaming data processing, including efforts in progress at Brookhaven National Laboratory and the challenges faced to date.
The ushering in of the big-data era, ably supported by exponential advances in computation, has provided new impetus to data-driven control in several engineering sectors. This topic's rapid and deep expansion has precipitated the need to showcase the highlights of data-driven approaches. There has been a rich history of contributions from the control systems community in data-driven control. At the same time, several new concepts and research directions have also been introduced in recent years. Many of these contributions and concepts have started to transition from theory to practical applications. This paper will overview the historical contributions and highlight recent concepts and research directions.
Cloud computing offers the promise of being able to analyze Big Data earth Observations at scale, by allowing scientists to deploy many nodes at once to analyze the data. However, in order to take full advantage of cloud scalability, it is often necessary to reorganize and reformat the data to enable fine-grained, parallel access to the data in Web Object Storage. NASA recently conducted a study of several formats that are optimized for analysis in the cloud: Parquet, zarr, HDF (Hierarchical Data Format) in the Cloud, and Cloud-Optimized GeoTIFF (Tagged Image File Format). They were compared against non-cloud-optimized formats, netCDF (network Common Data Form) and GeoTIFF, with criteria based both on stewardship and analysis performance.
Scientific research data provides unique challenges that are distinct from classic “Big Data” sources. One common element in research data is that the experiment, observations, or simulation were designed, and data were specifically acquired, to shed light on an open scientific question. The data and methods are usually “owned” by the researcher(s) and the data itself might not be viewed to have long-term scientific significance after the results have been published. Often, the data volume was relatively low, with data sometimes easier to reproduce than to catalog and store. Some data and meta-data were not collected in a digital form, or were stored on antiquated or obsolete media. Generally speaking, policies, tools, and management of digital research data have reflected an ad hoc approach that varies domain by domain and research group by research group. This model, which treats research data as disposable, is proving to be a serious limitation as the volume and complexity of research data explodes. Changes are required at every level of scientific research: within the individual groups, and across scientific domains and interdisciplinary collaborations. Enabling researchers to learn about available tools, processes, and procedures should encourage a spirit of cooperation and collaboration, allowing researchers to come together for the common good. In conclusion, these community-oriented efforts provide the potential for targeted projects with high impact.
Scientists overview and identify regions of interest by transforming data into compact information descriptors that characterize simulation results and allow detailed analysis on demand. Among many existing feature descriptors, statistical information derived from data samples is a promising approach to taming the big data avalanche because data distributionscomputed from a population can compactly describe the presence and characteristics of salient data features with minimal data movement. The ability to computationally summarize and process data using distributions also provides an efficient and representative capture of information that can adjust to size and resource constraints, with the added benefit that uncertainty associated with results can be quantified and communicated. In this project, we have developed a distribution-based data analysis and visualization framework for optimizing in situ processing and analysis of extreme-scale scientific data.
Focal Areas: (1) Insight gleaned from complex data (both observed and simulated) using artificial intelligence(AI), big data analytics, and other advanced methods, including explainable AI and physics- or knowledge-guided AI (2) Data acquisition and assimilation enabled by machine learning, AI, and advanced methods including experimental/network design/optimization, unsupervised learning (including deep learning), and hardware-related efforts involving AI (e.g., edge computing).
Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the "FAIRness" of NASA's GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility.
NASA is presented with a number of opportunities and challenges in federating its Earth Science Data Systems in the burgeoning world of cloud computing. Cloud hosting of Earth Science data provides a new way of bringing data together, at least from a virtual location sense, and is one of the main motives for NASA to host data there. However, NASA is also faced with a Big Data Variety challenge, brought on by the variety of the EO datasets in its archives. This diversity requires many diverse science archives to service the different science communities. As a result, nearly every major function in the Earth Observing System Data and Information System (EOSDIS) must also be federated across its data centers. This pattern is repeated with many of the outside agencies and organizations that EOSDIS federates with, such as the Committee for Earth Observing Satellites, leading to pioneering work on "deep federation" in a joint project with the European Space Agency to develop a Multi-Mission Algorithm and Analysis Platform.
Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the “FAIRness” of NASA’s GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility.
The VIIRS instruments onboard the SNPP and NOAA-20 satellites have identical spatial resolutions and the same spectral bands. Similar prelaunch tests and identical on-orbit calibration algorithms established the foundation for their consistent Earth measurements. Calibration assessment and consistency comparisons are useful to maintain their performance and measurement accuracy. Simultaneous nadir overpasses (SNO) between two satellites are commonly used for a direct calibration comparison between sensors. However, there are no SNO between SNPP and NOAA20. Hence, a reference sensor or Earth measurements are normally used to bridge the comparison. As a reference, we focus on the Advanced Baseline Imager (ABI) onboard the GOES-R series spacecraft and its application to the SNPP and NOAA-20 VIIRS comparison. GOES16 and GOES17are the first two satellites of the GOES-R series and were launched on November 19, 2016, and March 12, 2018, respectively. Their operational positions are on the equator with longitudes of 75.2° West over land and 137.2° West over ocean, respectively. The ABI is the primary imaging instrument of these spacecrafts for the Earth’s weather, oceans, and environment, with observations (every 10 minutes) that provide vast data for GEO-Low Earth orbit (LEO)and LEO-LEO comparisons utilizing it as an intermediate reference sensor. VIIRS and ABI have spectrally matched bands and can have simultaneous measurements over any selected site every day. The simultaneous measurements over the same site also have various scan angles. These features provide advantages for a VIIRS-to-ABI comparison. The spectral response function difference between instruments, sites selected, and view angles will have effects on the instrument measurements. Their impacts on the calibration comparison, including the use of double differences, will be discussed. By collecting VIIRS measurements over a large range of view angles, the view angle effect will also be investigated. The collection of an ample amount of data provides an advantage for statistical analyses and potential big data applications to sensor calibration assessments. This method can also be applied to other sensor calibration comparison and performance assessments, such as GOES16 and GOES17 ABI, and Terra and Aqua MODIS.
The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases of inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.
Wide-area data transfers in high-performance computing infrastructures and big data applications are increasingly carried over dynamically provisioned dedicated network connections, which provide high capacities with no competing traffic. Throughput of TCP and UDT over wide-area connections depends, often in a complex non-linear way, on the congestion control mechanism, buffer sizes, and the number of parallel streams. In addition, our extensive TCP and UDT throughput measurements and time traces over a suite of physical and emulated 10 Gbps connections with 0-366 ms round-trip times (RTTs) show significant statistical and temporal variations. Consequently, parameter selection and optimization for transport methods require data analytics to complement analytical throughput models. We present analytics based on the concavity-convexity of throughput profiles which provide insights into peak throughput and superior/inferior trend compared to linear interpolations based on RTT. In particular, we propose the utilization-concavity coefficient, a scalar metric that incorporates both utilization and concavity profile to characterize the overall performance of a transport protocol. These measurements-based anaytics enable us to select a transport protocol and its parameters for a given host and connection configuration to achieve high throughput with statistical guarantees.
Discovering the underlying structure of a high-dimensional signal or big data has always been a challenging topic, and has become harder to tackle especially when the observations are exposed to arbitrary sparse perturbations. Here in this paper, built on the model of a union of subspaces (UoS) with sparse outliers and inspired by a basis pursuit strategy, we exploit the fundamental structure of a Grassmann manifold, and propose a new technique of pursuing the subspaces systematically by solving a non-convex optimization problem using the alternating direction method of multipliers. This problem as noted is further complicated by non-convex constraints on the Grassmann manifold, as well as the bilinearity in the penalty caused by the subspace bases and coefficients. Nevertheless, numerical experiments verify that the proposed algorithm, which provides elegant solutions to the sub-problems in each step, is able to de-couple the subspaces and pursue each of them under time-efficient parallel computation.
While future terabit networks hold the promise of signifi- cantly improving big-data motion among geographically distributed data centers, significant challenges must be overcome even on today s 100 gigabit networks to real- ize end-to-end performance. Multiple bottlenecks exist along the end-to-end path from source to sink. Data stor- age infrastructure at both the source and sink and its in- terplay with the wide-area network are increasingly the bottleneck to achieving high performance. In this paper, we identify the issues that lead to congestion on the path of an end-to-end data transfer in the terabit network en- vironment, and we present a new bulk data movement framework called LADS for terabit networks. LADS ex- ploits the underlying storage layout at each endpoint to maximize throughput without negatively impacting the performance of shared storage resources for other users. LADS also uses the Common Communication Interface (CCI) in lieu of the sockets interface to use zero-copy, OS-bypass hardware when available. It can further im- prove data transfer performance under congestion on the end systems using buffering at the source using flash storage. With our evaluations, we show that LADS can avoid congested storage elements within the shared stor- age resource, improving I/O bandwidth, and data transfer rates across the high speed networks.
Objective We describe use cases and an institutional reference architecture for maintaining high-capacity, data-intensive network flows (e.g., 10, 40, 100 Gbpsþ) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods High-end networking, packet filter firewalls, network intrusion detection systems. Results We describe a “Medical Science DMZ” concept as an option for secure, high-volume transport of large, sensitive data sets between research institutions over national research networks. Discussion The exponentially increasing amounts of “omics” data, the rapid increase of high-quality imaging, and other rapidly growing clinical data sets have resulted in the rise of biomedical research “big data.” The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large data sets. Maintaining data-intensive flows that comply with HIPAA and other regulations presents a new challenge for biomedical research. Recognizing this, we describe a strategy that marries performance and security by borrowing from and redefining the concept of a “Science DMZ”—a framework that is used in physical sciences and engineering research to manage high-capacity data flows. Conclusion By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and meeting regulatory requirements.
The massive data generated by scientists daily serve as both a major catalyst for new discoveries and innovations, as well as a significant roadblock that restricts access to the data. Here, our paper introduces a new approach to removing Big Data barriers and democratizing access to petascale data for the broader scientific community. Our novel data fabric abstraction layer allows user-friendly querying of scientific information while hiding the complexities of dealing with file systems or cloud services. We enable FAIR (Findable, Accessible, Interoperable, and Reusable) access to datasets such as NASA’s petascale climate datasets. Our paper presents an approach to managing, visualizing, and analyzing petabytes of data within a browser on equipment ranging from the top NASA supercomputer to commodity hardware like a laptop. Our novel data fabric abstraction utilizes state-of-the art progressive compression algorithms and machine-learning insights to power scalable visualization dashboards for petascale data. The result provides users with the ability to identify extreme events or trends dynamically, expanding access to scientific data and further enabling discoveries. We validate our approach by improving the ability of climate scientists to visually explore their data via three fully interactive dashboards. We further validate our approach by deploying the dashboards and simplified training materials in the classroom at a minority-serving institution. These dashboards, released in simplified form to the general public, contribute significantly to a broader push to democratize the access and use of climate data.
The rollout of smart meters in the last several years has opened up new forms of previously unavailable energy data. Many utilities are now able in real-time to capture granular, household level interval usage data at very high-frequency levels for a large proportion of their residential and small commercial customer population. This can be linked to other time and locationspecific information, providing vast, constantly growing streams of rich data (sometimes referred to by the recently popular buzz word, “big data”). Within the energy industry there is increasing interest in tapping into the opportunities that these data can provide.