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At least 649 records · Page 36

Transformation of OODT CAS to Perform Larger Tasks

A computer program denoted OODT CAS has been transformed to enable performance of larger tasks that involve greatly increased data volumes and increasingly intensive processing of data on heterogeneous, geographically dispersed computers. Prior to the transformation, OODT CAS (also alternatively denoted, simply, 'CAS') [wherein 'OODT' signifies 'Object-Oriented Data Technology' and 'CAS' signifies 'Catalog and Archive Service'] was a proven software component used to manage scientific data from spaceflight missions. In the transformation, CAS was split into two separate components representing its canonical capabilities: file management and workflow management. In addition, CAS was augmented by addition of a resource-management component. This third component enables CAS to manage heterogeneous computing by use of diverse resources, including high-performance clusters of computers, commodity computing hardware, and grid computing infrastructures. CAS is now more easily maintainable, evolvable, and reusable. These components can be used separately or, taking advantage of synergies, can be used together. Other elements of the transformation included addition of a separate Web presentation layer that supports distribution of data products via Really Simple Syndication (RSS) feeds, and provision for full Resource Description Framework (RDF) exports of metadata.

Mattmann, Chris↗

Boosting RDataFrame performance with transparent bulk event processing

RDataFrame is ROOT’s high-level interface for Python and C++ data analysis. Since it first became available, RDataFrame adoption has grown steadily and it is now poised to be a major component of analysis software pipelines for LHC Run 3 and beyond. Thanks to its design inspired by declarative programming principles, RDataFrame enables the development of highperformance, highly parallel analyses without requiring expert knowledge of multi-threading and I/O: user logic is expressed in terms of self-contained, small computation kernels tied together by a high-level API. This design completely decouples analysis logic from its actual execution, and opens several interesting avenues for workflow optimization. In particular, in this work we explore the benefits of moving internal data processing from an event-by-event to a bulkby-bulk loop. This refactoring dramatically reduces the framework’s runtime overheads; in collaboration with the I/O layer it improves data access patterns; it exposes information that optimizing compilers might use to auto-vectorize the invocation of user-defined computations; finally, while existing user-facing interfaces remain unaffected, it becomes possible to additionally offer interfaces that explicitly expose bulks of events, useful e.g. for the injection of GPU kernels into the analysis workflow. In order to inform similar future R&D, design challenges will be presented, as well as an investigation of the relevant timememory trade-off backed by novel performance benchmarks.

Guiraud, Enrico↗

Streaming Large-Scale Microscopy Data to a Supercomputing Facility

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy generates data at a nominal rate of 480 Gbit s -1 (87,000 frames s -1 ⁠), producing a 700 GB dataset in 15 s. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera’s data acquisition system to supercomputing nodes at the National Energy Research Scientific Computing Center, bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a postmortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.

4D-STEM↗

STNS01-21 BEE - FY21 P6-2: Archive, clone, and re-run workflows [Slide]

BEE will give ECP a tool that great simplifies the deployment of containerized workflows on the next generation of pre-exascale and exascale systems, as well as public and private clouds. BEE allows scientists to describe their workflow using the Common Workflow Language and then deploy that workflow across the entire spectrum of systems without having to learn the specifics of each container runtime, HPC resource manager, or cloud API. BEE also streamlines the curation and sharing of common workflows among the scientific community.

97 MATHEMATICS AND COMPUTING↗

Bridging Equipment Reliability Data and Risk Informed Decisions in a Plant Operation Context

Industry equipment reliability and asset management programs are essential elements that help ensure the safe and economical operation of nuclear power plants. The effectiveness of these programs is addressed in several industry-developed and regulatory programs. The Risk-Informed Asset Management (RIAM) project is tasked to develop tools in support of the equipment reliability and asset management programs at nuclear power plants. These tools are designed to create a direct bridge between component health/lifecycle data and decision making (e.g., maintenance scheduling and project prioritization). The goal of this article is to provide a guide for specific use cases that the RIAM project is targeting. We have grouped uses cases into three main areas. The first area focuses on the analysis of equipment reliability data with a particular emphasis on condition-based data, such as test/surveillance reports and component monitoring data. The second area focuses on the integration of equipment reliability into system/plant reliability models to determine system/plant health and identify the components that are critical to maintain an operational system. Lastly, the third area manages plant resources, such as maintenance activities and replacement scheduling using optimization methods. Here the primary focus is on supporting typical system engineer decisions regarding maintenance activity scheduling and component aging management. This is performed in a risk-informed context where the term “risk” is broadly constructed to include both plant reliability and economics. This framework combines data analytics tools to analyze equipment reliability data with risk-informed methods designed to support system engineer decisions (e.g., maintenance and replacement schedules, optimal maintenance posture) in a customizable workflow.

97 - MATHEMATICS AND COMPUTING↗

WETO Software Stack Best Practices

Wind energy researchers typically share one key characteristic: a passion for increasing wind energy in the global energy mix. The U.S. Department of Energy (DOE) supports this mission in a number of ways including allocating funding directly to various aspects of wind energy research through the Office of Energy Efficiency and Renewable Energy (EERE) via the Wind Energy Technologies Office (WETO). While the traditional output of research is academic publication, software development efforts are increasingly a major focus. Software tools in the research environment allow researchers to describe an idea and quickly increase the scope and scale as they study it further. As a product of research, these tools represent a direct pipeline from researcher to industry practitioners since they are the implementation of ideas described in academic publications. Given this vital role in wind energy research and commercial development, the broad research software portfolio supported by WETO must maintain a minimum level of quality to support the wind energy field in the growing transition to renewable energy. This report outlines a series o f best practices to be adopted by all WETO-supported software projects, as well as expectations that the communities interacting with these projects should have of the developers and tools themselves. Wind energy research software has a unique standing in the field of scientific software. The stakeholders are varied with a subset being: (1) DOE EERE leadership, (2) DOE WETO leadership and program managers, (3) National lab leadership, (4) Associated project principle investigators, (5) Research software engineers, (6) Wind energy researchers in academia (including graduate students, post docs, and national lab staff), (7) Industry researchers and practitioners, (8) Commercial software developers, and (9) The general public interested in wind energy. These software are typically the end-user of other generic software libraries, so the funding cycles are often tied to applied research rather than the development of the software itself. Since the developers are also wind energy researchers, these tools are typically designed in a way that closely resembles the application in which they're used. Additionally, the expertise and incentives for the developers have a high variability, and often neither are aligned with software engineering or computer science. Given the unique environment in which wind energy research software is produced and consumed, it is critical for model owners to understand the context of their software. A framework for developing this understanding is to answer the following questions of a given software project: What is it's purpose? What is its role in the field of wind energy? What is the profile of the expected users? For how long will it be relevant? What is the expected impact? These questions allow model owners to identify the appropriate methods for the design, development, and long term maintenance of their software. Additionally, the answer provide context for future planners to understand why particular decisions were made and discern the consequences of changing course. The information is aggregated from experience within WETO-supported software development groups as well as external organizations and efforts to define the craft of research software engineering. These best practices aim to make the collaborative development process efficient and effective while improving the model understanding across stakeholders. Additionally, the general adoption of a common framework for software quality ensures that the end users of WETO software can trust these tools and accurately understand the risks to workflow integration.

17 WIND ENERGY↗

Cloud Computing for Mission Design and Operations

The space mission design and operations community already recognizes the value of cloud computing and virtualization. However, natural and valid concerns, like security, privacy, up-time, and vendor lock-in, have prevented a more widespread and expedited adoption into official workflows. In the interest of alleviating these concerns, we propose a series of guidelines for internally deploying a resource-oriented hub of data and algorithms. These guidelines provide a roadmap for implementing an architecture inspired in the cloud computing model: associative, elastic, semantical, interconnected, and adaptive. The architecture can be summarized as exposing data and algorithms as resource-oriented Web services, coordinated via messaging, and running on virtual machines; it is simple, and based on widely adopted standards, protocols, and tools. The architecture may help reduce common sources of complexity intrinsic to data-driven, collaborative interactions and, most importantly, it may provide the means for teams and agencies to evaluate the cloud computing model in their specific context, with minimal infrastructure changes, and before committing to a specific cloud services provider.

cloud computing↗

OpenCHAMI Developer Summit [Slides]

The mission of the OpenCHAMI consortium is to steward the collaborative development and continuous evolution of cloud-like software to manage High Performance Computing capacity regardless of the size or deployment platform. We are guided by the operators and practitioners who use modern tooling and concepts to address the needs of classical HPC applications and the growing AI/ML and Data Science community that wish to leverage HPC capacity within their own workflows, to meet their needs with their own tools.

97 MATHEMATICS AND COMPUTING↗

Science Federation Emulation Testbed: Demonstration of VFSIE Functionalities

The Virtual Federated Science Instrument Environment (VFSIE) is a digital twin of a federated infrastructure of multiple sites with science instruments and computing systems that are geographically dispersed. It emulates the federation using containers and virtual hosts (vhosts) connected over local and wide-area networks for the main purpose of supporting the development and testing of science workflows and software stacks, which will subsequently transition to the physical infrastructure. In this demo, we present VFSIE of a four sites scenario and illustrate the following use cases: (i) execution of federation stack components that expose resources to enable a science user to execute workflows, (ii) execution of remote control commands of beam-line instruments to collect measurements and position the sensor, and (iii) remote execution and access of Jupyter Notebook for tomographic image computations

Al Najjar, Anees↗

Land-use analysis using infrastructure representations and high-resolution flood inundation mapping techniques

In the face of climate change and population growth in coastal regions, land-use analysis efforts are more challenging than ever. Land-use decision-makers in coastal communities are burdened with the difficult choices of where to place new homes versus other assets. While there has been an increased focus on hazard mitigation and disaster resilience in the field of planning, evidence points towards continued development in risk-prone areas including flood zones. Residential development within flood zones specifically continues to be a major issue. To help counter this trend, this study introduces a novel land-use analysis method, coupling topographic flood inundation mapping techniques with digital elevation model (DEM) adaptations. This Topographic Model Scenario Generation workflow can be used by planners early in the land-use decision making process and provides an alternative to high-computational hydraulic models. The analysis also includes the identification of strengths and weaknesses of topographic models' recognition of built infrastructure assets, adding to a limited body of knowledge addressing recommended uses of such models. Levees and canals prove particularly functional in this context while detention ponds less so, likely due to a lack of total water mass accountability. Lastly, we provide a functional demonstration in Southeast Texas to illustrate the workflow's ability to create multiple infrastructure scenarios and visualize their effects across different flood events.

42 ENGINEERING↗

Leveraging Automated Fiber Placement Computer Aided Process Planning Framework for Defect Validation and Dynamic Layup Strategies

Process planning represents an essential stage of the Automated Fiber Placement (AFP) workflow. It develops useful and efficient machine processes based upon the working material, composite design, and manufacturing resources. The current state of process planning requires a high degree of interaction from the process planner and could greatly benefit from increased automation. Therefore, a list of key steps and functions are created to identify the more difficult and time-consuming phases of process planning. Additionally, a set of metrics must exist by which to evaluate the effectiveness of the manufactured laminate from the machine code created during the Process Planning stage. Layup strategies, in addition to dog ears, stagger shifts, steering constraints, and starting points, represented the group of functions labeled as process optimization and ranked the highest in terms of priority for automation. The laminates resulting from the selected parameters are evaluated through the occurrences of principal defect metrics such as fiber gaps, overlaps, angle deviation and steering violations. This document presents an automated software solution to the layup strategy and starting point selection phase of process planning. A series of ply scenarios are generated with variations of these ply parameters and evaluated according to a set of metrics entered by the Process Planner. These metrics are generated through use of the Analytical Hierarchy Process (AHP), where relative importance between each of the fiber features are defined. The ply scenarios are selected which reduce the overall fiber feature scores based on the defects the Process Planner wishes to minimize.

HiCAM↗

Virtual Engineering of Low-Temperature Conversion

In this work, we present the development of an overarching software framework and supporting multiphysics models to simulate the end-to-end process of biomass conversion. This virtual engineering (VE) software is designed with the goal of accelerating research and development and reducing risk for market-relevant biomass conversion processes. We currently support multiple models, computing paradigms, and fidelities representing the steps of feedstock pretreatment, enzymatic hydrolysis, and bioconversion. Although this VE approach was developed to support a biomass workflow, we have designed each component in a way that allows us to easily support new domains, unit models, and feedstocks. We begin by presenting the user-facing aspects of the VE software and highlight how simulated elements are defined and linked by VE functions. We then present an overview of the high-fidelity computational fluid dynamics (CFD) models developed to support our target domain before segueing into our efforts to develop accurate and fast surrogate models, capturing the salient outcomes from the CFD simulations in a significantly less computationally demanding manner. We then present how VE calculations interface with a commercial techno-economic analysis software, Aspen Plus. We conclude by presenting VE case studies that leverage these methods and discuss how our methods can be extended to support a wide variety of accelerated biofuel commercialization pathways in the future.

biofuel↗

A multiphysics coupling framework for exascale simulation of fracture evolution in subsurface energy applications

Predicting the evolution of fractured media is challenging due to coupled thermal, hydrological, chemical and mechanical processes that occur over a broad range of spatial scales, from the microscopic pore scale to field scale. We present a software framework and scientific workflow that couples the pore scale flow and reactive transport simulator Chombo-Crunch with the field scale geomechanics solver in GEOS to simulate fracture evolution in subsurface fluid-rock systems. This new multiphysics coupling capability comprises several novel features. An HDF5 data schema for coupling fracture positions between the two codes is employed and leverages the coarse resolution of the GEOS mechanics solver which limits the size of data coupled, and is, thus, not taxed by data resulting from the high resolution pore scale Chombo-Crunch solver. The coupling framework requires tracking of both before and after coarse nodal positions in GEOS as well as the resolved embedded boundary in Chombo-Crunch. We accomplished this by developing an approach to geometry generation that tracks the fracture interface between the two different methodologies. The GEOS quadrilateral mesh is converted to triangles which are organized into bins and an accessible tree structure; the nodes are then mapped to the Chombo representation using a continuous signed distance function that determines locations inside, on and outside of the fracture boundary. The GEOS positions are retained in memory on the Chombo-Crunch side of the coupling. The time stepping cadence for coupled multiphysics processes of flow, transport, reactions and mechanics is stable and demonstrates temporal reach to experimental time scales. The approach is validated by demonstration of 9 days of simulated time of a core flood experiment with fracture aperture evolution due to invasion of carbonated brine in wellbore-cement and sandstone. We also demonstrate usage of exascale computing resources by simulating a high resolution version of the validation problem on OLCF Frontier.

97 MATHEMATICS AND COMPUTING↗

HTESP (High-throughput electronic structure package): A package for high-throughput ab initio calculations

High-throughput ab initio calculations are the indispensable parts of data-driven discovery of new materials with desirable properties, as reflected in the establishment of several online material databases. The accumulation of extensive theoretical data through computations enables data-driven discovery by constructing machine learning and artificial intelligence models to predict novel compounds and forecast their properties. Efficient usage and extraction of data from these existing online material databases can accelerate the next stage materials discovery that targets different and more advanced properties, such as electron–phonon coupling for phonon-mediated superconductivity. However, extracting data from these databases, generating tailored input files for different ab initio calculations, performing such calculations, and analyzing new results can be demanding tasks. Here, in this work, we introduce a software package named “HTESP” (High-Throughput Electronic Structure Package) written in Python and Bash languages, which automates the entire workflow including data extraction, input file generation, calculation submission, result collection and plotting. Our HTESP will help speed up future computational materials discovery processes.

36 MATERIALS SCIENCE↗

A multi-scale cognitive interaction model of instrument operations at the Linac Coherent Light Source

The Linac Coherent Light Source (LCLS) is the world’s first x-ray free electron laser. It is a scientific user facility operated by the SLAC National Accelerator Laboratory, at Stanford, for the U.S. Department of Energy. As beam time at LCLS is extremely valuable and limited, experimental efficiency—getting the most high quality data in the least time—is critical. Our overall project employs cognitive engineering methodologies with the goal of improving experimental efficiency and increasing scientific productivity at LCLS by refining experimental interfaces and workflows, simplifying tasks, reducing errors, and improving operator safety and stress. Here, in this study, we describe a multi-agent, multi-scale computational cognitive interaction model of instrument operations at LCLS. Our model simulates the aspects of human cognition at multiple cognitive and temporal scales, ranging from seconds to hours, and among agents playing multiple roles, including instrument operator, real time data analyst, and experiment manager. The model can roughly predict impacts stemming from proposed changes to operational interfaces and workflows. Example results demonstrate the model’s potential in guiding modifications to improve operational efficiency. We discuss the implications of our effort for cognitive engineering in complex experimental settings and outline future directions for research. The model is open source, and the videos of the supplementary material provide extensive detail.

47 OTHER INSTRUMENTATION↗

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection.

59 BASIC BIOLOGICAL SCIENCES↗

Information Management Workflow and Tools Enabling Multiscale Modeling Within ICME Paradigm

With the increased emphasis on reducing the cost and time to market of new materials, the need for analytical tools that enable the virtual design and optimization of materials throughout their processing - internal structure - property - performance envelope, along with the capturing and storing of the associated material and model information across its lifecycle, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. Fortunately, material information management systems and physics-based multiscale modeling methods have kept pace with the growing user demands. Herein, recent efforts to establish workflow for and demonstrate a unique set of web application tools for linking NASA GRC's Integrated Computational Materials Engineering (ICME) Granta MI database schema and NASA GRC's Integrated multiscale Micromechanics Analysis Code (ImMAC) software toolset are presented. The goal is to enable seamless coupling between both test data and simulation data, which is captured and tracked automatically within Granta MI®, with full model pedigree information. These tools, and this type of linkage, are foundational to realizing the full potential of ICME, in which materials processing, microstructure, properties, and performance are coupled to enable application-driven design and optimization of materials and structures.

Materials Engineering↗

Unstructured Grid Adaptation and Solver Technology for Turbulent Flows

Unstructured grid adaptation is a tool to control Computational Fluid Dynamics (CFD) discretization error. However, adaptive grid techniques have made limited impact on production analysis workflows where the control of discretization error is critical to obtaining reliable simulation results. Issues that prevent the use of adaptive grid methods are identified by applying unstructured grid adaptation methods to a series of benchmark cases. Once identified, these challenges to existing adaptive workflows can be addressed. Unstructured grid adaptation is evaluated for test cases described on the Turbulence Modeling Resource (TMR) web site, which documents uniform grid refinement of multiple schemes. The cases are turbulent flow over a Hemisphere Cylinder and an ONERA M6Wing. Adaptive grid force and moment trajectories are shown for three integrated grid adaptation processes with Mach interpolation control and output error based metrics. The integrated grid adaptation process with a finite element (FE) discretization produced results consistent with uniform grid refinement of fixed grids. The integrated grid adaptation processes with finite volume schemes were slower to converge to the reference solution than the FE method. Metric conformity is documented on grid/metric snapshots for five grid adaptation mechanics implementations. These tools produce anisotropic boundary conforming grids requested by the adaptation process.

Park, Michael A.↗