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At least 37 records · Page 2

Lessons Learned From Developing A Streaming Data Framework for Scientific Analysis

We describe the development and usage of a streaming data analysis software framework. The framework is used for three different applications: Earth science hyper-spectral imaging analysis, Electromyograph pattern detection, and Electroencephalogram state determination. In each application the framework was used to answer a series of science questions which evolved with each subsequent answer. This evolution is summarized in the form of lessons learned.

Wheeler. Kevin R.↗

Online learning of quadratic manifolds from streaming data for nonlinear dimensionality reduction and nonlinear model reduction

Here, this work introduces an online greedy method for constructing quadratic manifolds from streaming data, designed to enable in situ analysis of numerical simulation data on the Petabyte scale. Unlike traditional batch methods, which require all data to be available upfront and take multiple passes over the data, the proposed online greedy method incrementally updates quadratic manifolds in one pass as data points are received, eliminating the need for expensive disk input/output operations as well as storing and loading data points once they have been processed. A range of numerical examples demonstrate that the online greedy method learns accurate quadratic manifold embeddings while being capable of processing data that far exceed common disk input/output capabilities and volumes as well as main-memory sizes.

97 MATHEMATICS AND COMPUTING↗

The Open Source DataTurbine Initiative: Streaming Data Middleware for Environmental Observing Systems

The Open Source DataTurbine Initiative is an international community of scientists and engineers sharing a common interest in real-time streaming data middleware and applications. The technology base of the OSDT Initiative is the DataTurbine open source middleware. Key applications of DataTurbine include coral reef monitoring, lake monitoring and limnology, biodiversity and animal tracking, structural health monitoring and earthquake engineering, airborne environmental monitoring, and environmental sustainability. DataTurbine software emerged as a commercial product in the 1990 s from collaborations between NASA and private industry. In October 2007, a grant from the USA National Science Foundation (NSF) Office of Cyberinfrastructure allowed us to transition DataTurbine from a proprietary software product into an open source software initiative. This paper describes the DataTurbine software and highlights key applications in environmental monitoring.

Fountain T.↗

Implementation of a Multichannel Serial Data Streaming Algorithm using the Xilinx Serial RapidIO Solution

In the current world of applications that use reconfigurable technology implemented on field programmable gate arrays (FPGAs), there is a need for flexible architectures that can grow as the systems evolve. A project has limited resources and a fixed set of requirements that development efforts are tasked to meet. Designers must develop robust solutions that practically meet the current customer demands and also have the ability to grow for future performance. This paper describes the development of a high speed serial data streaming algorithm that allows for transmission of multiple data channels over a single serial link. The technique has the ability to change to meet new applications developed for future design considerations. This approach uses the Xilinx Serial RapidIO LOGICORE Solution to implement a flexible infrastructure to meet the current project requirements with the ability to adapt future system designs.

RapidIO↗

NREL Stratus - Enabling Workflows to Fuse Data Streams, Modeling, Simulation, and Machine Learning

Integrating cloud services into advanced computing facilities provides significant new capabilities over focusing solely on traditional high performance computing (HPC) workloads. This brings complementary capabilities as well as enabling new focused roles for HPC. They are especially potent for workflows that fuse data streams, modeling and simulation ('modsim') and machine learning. A key challenge to adopting a hybrid edge-cloud-HPC model is to align optimal capability, data, and user intent on the right resources for each step in a workflow.?The NREL Stratus service provides a basis for this: Stratus layers capabilities needed to make?cloud services accessible to a lab-based scientific community on commercial offerings, and; currently supports upwards of 200 projects ranging from IOT integration to traditional modeling and simulation. This provides a real-world inventory of scientific workflow elements. A growing knowledge base enables placing these elements appropriately between the edge, cloud, and traditional HPC. This paper outlines a vision via reference architecture and the application of that architecture in a typical workflow highlighting multiple components: sensor data intake, cleaning and transforming (edge/cloud suitable); generation of synthetic data through modsim, computationally heavy ML training and hyperparameter optimization (HPC suitable), and; inference and deployment (cloud ideal). Every step in such a workflow involves a cost-benefit analysis regarding the data movement, computational efficiency, availability, latency, and resource capabilities. The reference architecture and examples outlined allow for understanding new opportunities in the context of emerging workflows that combine IOT, cloud, and HPC to bolster scientific productivity.

AI↗

28 NREL Stratus - Enabling Workflows to Fuse Data Streams, Modeling, Simulation, and Machine Learning: Preprint

Integrating cloud services into advanced computing facilities provides significant new capabilities over focusing solely on traditional high performance computing (HPC) workloads. This brings complementary capabilities as well as enabling new focused roles for HPC. They are especially potent for workflows that fuse data streams, modeling and simulation ('modsim') and machine learning. A key challenge to adopting a hybrid edge-cloud-HPC model is to align optimal capability, data, and user intent on the right resources for each step in a workflow.?The NREL Stratus service provides a basis for this: Stratus layers capabilities needed to make?cloud services accessible to a lab-based scientific community on commercial offerings, and; currently supports upwards of 200 projects ranging from IOT integration to traditional modeling and simulation. This provides a real-world inventory of scientific workflow elements. A growing knowledge base enables placing these elements appropriately between the edge, cloud, and traditional HPC. This paper outlines a vision via reference architecture and the application of that architecture in a typical workflow highlighting multiple components: sensor data intake, cleaning and transforming (edge/cloud suitable); generation of synthetic data through modsim, computationally heavy ML training and hyperparameter optimization (HPC suitable), and; inference and deployment (cloud ideal). Every step in such a workflow involves a cost-benefit analysis regarding the data movement, computational efficiency, availability, latency, and resource capabilities. The reference architecture and examples outlined allow for understanding new opportunities in the context of emerging workflows that combine IOT, cloud, and HPC to bolster scientific productivity.

AI↗

Platform Agnostic Streaming Data Application Performance Models

The mapping of computational needs onto execution resources is, by and large, a manual task, and users are frequently guided simply by intuition and past experiences. We present a queueing theory based performance model for streaming data applications that takes steps towards a better understanding of resource mapping decisions, thereby assisting application developers to make good mapping choices. The performance model (and associated cost model) are agnostic to the specific properties of the compute resource and application, simply characterizing them by their achievable data throughput. We illustrate the model with a pair of applications, one chosen from the field of computational biology and the second is a classic machine learning problem.

Faber, Clayton↗

Streaming Data in HPC Workflows Using ADIOS

The “IO Wall” problem, in which the gap between computation rate and data access rate grows continuously, poses significant problems to scientific workflows which have traditionally relied upon using the filesystem for intermediate storage between workflow stages. One way to avoid this problem in scientific workflows is to stream data directly from producers to consumers and avoiding storage entirely. However, the manner in which this is accomplished is key to both performance and usability. This paper presents the Sustainable Staging Transport, an approach which allows direct streaming between traditional file writers and readers with few application changes. SST is an ADIOS “engine”, accessible via standard ADIOS APIs, and because ADIOS allows engines to be chosen at run-time, many existing file-oriented ADIOS workflows can utilize SST for direct application-to-application communication without any source code changes. This paper describes the design of SST and presents performance results from various applications that use SST, for feeding model training with simulation data with substantially higher bandwidth than the theoretical limits of Frontier’s file system, for strong coupling of separately developed applications for multiphysics multiscale simulation, or for in situ analysis and visualization of data to complete all data processing shortly after the simulation finishes.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗

FIFO Buffer for Asynchronous Data Streams

Variable-rate, asynchronous data signals from up to four measuring instruments or other sources combined in first-in/first-out (FIFO) buffer for transmission on single channel. Constructed in complementary metal-oxide-semiconductor (CMOS) logic, buffer consumes low power (only 125 mW at 5V) and conforms to aerospace standards of reliability and maintainability.

Bascle, K. P.↗

Open Source Initiative Powers Real-Time Data Streams

Under an SBIR contract with Dryden Flight Research Center, Creare Inc. developed a data collection tool called the Ring Buffered Network Bus. The technology has now been released under an open source license and is hosted by the Open Source DataTurbine Initiative. DataTurbine allows anyone to stream live data from sensors, labs, cameras, ocean buoys, cell phones, and more.

Source record↗

A High-level Design for Bidirectional Data Streaming to High-Performance Computing Systems from External Science Facilities

Cutting-edge science is increasingly data-driven due to the emergence of scientific machine learning models that can guide scientists toward fruitful areas of exploration. Experimental science facilities such as light and neutron sources, particle colliders, and radio astronomy telescopes are also producing raw measurement data at rates that exceed available data storage and computing capacity at those facilities. As a result, scientific workflows are being developed that concurrently couple experiments at science facilities with high-performance computing (HPC) facilities to enable analysis of experimental data while the experiment is ongoing, and where analysis results are potentially fed back to the experiment for use in experimental control and/or steering in a time-sensitive manner. Our goal is to design, prototype, and deploy a new capability for the Oak Ridge Leadership Computing Facility (OLCF) that enables such workflows through support for bidirectional, memory-based streaming of data from external experiments into and out of OLCF HPC systems. This high-level design document describes the related work and motivating use cases that inform our understanding of the technical requirements for this capability, and describes a proposed architectural solution that meets these requirements and our plans for demonstrating the capability.

97 MATHEMATICS AND COMPUTING↗

A tale of two towers: comparing NEON and AmeriFlux data streams at Bartlett Experimental Forest

Long-term ecological data are essential for detecting impacts of climate change and other global change factors, and for making informed predictions about future change. However, long-term measurements are rarely replicated at the site level, which raises questions about their representativeness. We used a multiscale approach to evaluate the agreement of parallel observations from AmeriFlux and NEON (National Ecological Observatory Network) towers at Bartlett Experimental Forest, New Hampshire, USA. The two towers are separated by a horizontal distance of 93 m. Here, we focused our analysis on standard meteorological variables; fluxes of CO 2 , sensible heat, and latent heat measured by eddy covariance; and phenology derived from PhenoCam imagery. Results suggest excellent agreement between AmeriFlux and NEON in meteorology and phenology, and good agreement in fluxes at the half-hourly scale. However, large disagreements in CO 2 and latent heat fluxes occurred at the annual scale, with implications especially for the forest carbon balance. The AmeriFlux tower measurements indicate a site that is close to carbon-neutral (-8 ± 65 g C m -2 y -1 , mean ± 1 SD), whereas the NEON tower measurements indicate a forest that is a carbon sink (-137 ± 10 g C m -2 y -1 ). Causes of this disagreement may include measurement height (26 m vs. 35 m), which resulted in different flux footprints being measured by the two towers, and differences in the flux measurement systems. Our results suggest the need for caution when attempting to merge long-term flux data from two different measurement platforms, and when using measurements from any one measurement platform to inform decision-making on issues related to carbon accounting or natural climate solutions.

Carbon cycle↗

Facilitating Analysis of Multiple Partial Data Streams

Robotic Operations Automation: Mechanisms, Imaging, Navigation report Generation (ROAMING) is a set of computer programs that facilitates and accelerates both tactical and strategic analysis of time-sampled data especially the disparate and often incomplete streams of Mars Explorer Rover (MER) telemetry data described in the immediately preceding article. As used here, tactical refers to the activities over a relatively short time (one Martian day in the original MER application) and strategic refers to a longer time (the entire multi-year MER missions in the original application). Prior to installation, ROAMING must be configured with the types of data of interest, and parsers must be modified to understand the format of the input data (many example parsers are provided, including for general CSV files). Thereafter, new data from multiple disparate sources are automatically resampled into a single common annotated spreadsheet stored in a readable space-separated format, and these data can be processed or plotted at any time scale. Such processing or plotting makes it possible to study not only the details of a particular activity spanning only a few seconds, but also longer-term trends. ROAMING makes it possible to generate mission-wide plots of multiple engineering quantities [e.g., vehicle tilt as in Figure 1(a), motor current, numbers of images] that, heretofore could be found only in thousands of separate files. ROAMING also supports automatic annotation of both images and graphs. In the MER application, labels given to terrain features by rover scientists and engineers are automatically plotted in all received images based on their associated camera models (see Figure 2), times measured in seconds are mapped to Mars local time, and command names or arbitrary time-labeled events can be used to label engineering plots, as in Figure 1(b).

Maimone, Mark W.↗

Managing Multi-Instrument Data Streams in Secure Environments

The capture and curation of all primary instrument data is a potentially valuable source of added insight into experiments or diagnostics in laboratory experiments. The data can, when properly curated, enable analysis beyond the current practice that uses just a subset of the as-measured data. Complete curated data can also be input for machine learning and other data exploration tools. Conveniently storing and accessing instrument data requires that the instruments are connected to databases and users through a networking infrastructure. This infrastructure needs to accommodate a wide array of instruments which can range from single laboratory mounted probes for environment monitoring to computers managing multiple instruments. These resources may also include mobile devices on which researchers record instrument and experiment state related notes. These varied data sources bring with them the challenges of different communications capabilities and protocols as well as the primary data typically being produced in proprietary formats. These challenges are further compounded when the instruments need to operate in secure environments such as required in national laboratories. We will discuss the SmartLab, an ongoing effort to set up a system for instrument and simulation data curation at NASA Langley Research Center. We will outline the challenges faced in managing the data sources required for ongoing research activities and the solutions that are being considered and implemented to address those challenges.

instrument data management↗

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome and flexibly extended for in situ analysis. The openPMD-api is a library for the description of scientific data according to the Open Standard for Particle-Mesh Data (openPMD). Its approach towards recent challenges posed by hardware heterogeneity lies in the decoupling of data description in domain sciences, such as plasma physics simulations, from concrete implementations in hardware and IO. The streaming backend is provided by the ADIOS2 framework, developed at Oak Ridge National Laboratory. This paper surveys two openPMD-based loosely-coupled setups to demonstrate flexible applicability and to evaluate performance. In loose coupling, as opposed to tight coupling, two (or more) applications are executed separately, e.g. in individual MPI contexts, yet cooperate by exchanging data. This way, a streaming-based workflow allows for standalone codes instead of tightly-coupled plugins, using a unified streaming-aware API and leveraging high-speed communication infrastructure available in modern compute clusters for massive data exchange. We determine new challenges in resource allocation and in the need of strategies for a flexible data distribution, demonstrating their influence on efficiency and scaling on the Summit compute system. The presented setups show the potential for a more flexible use of compute resources brought by streaming IO as well as the ability to increase throughput by avoiding filesystem bottlenecks.

Poeschel, Franz↗

EdgeAI: Machine learning via direct attached accelerator for streaming data processing at high shot rate x-ray free-electron lasers

We present a case for low batch-size inference with the potential for adaptive training of a lean encoder model. We do so in the context of a paradigmatic example of machine learning as applied in data acquisition at high data velocity scientific user facilities such as the Linac Coherent Light Source-II x-ray Free-Electron Laser. We discuss how a low-latency inference model operating at the data acquisition edge can capitalize on the naturally stochastic nature of such sources. We simulate the method of attosecond angular streaking to produce representative results whereby simulated input data reproduce high-resolution ground truth probability distributions. By minimizing the mean-squared error between the decoded output of the latent representation and the ground truth distributions, we ensure that the encoding layers and resulting latent representation maintains full fidelity for any downstream task, be it classification or regression. We present throughput results for data-parallel inference of various batch sizes, some with throughput exceeding 100 k images per second. We also show in situ training below 10 s per epoch for the full encoder–decoder model as would be relevant for streaming and adaptive real-time data production at our nation’s scientific light sources.

97 MATHEMATICS AND COMPUTING↗