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At least 793 records · Page 44

Applying the FAIR Principles to computational workflows

Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative’s FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows. We present recommendations with commentary that reflects our discussions and justifies our choices and adaptations. These are offered to workflow users and authors, workflow management system developers, and providers of workflow services as guidelines for adoption and fodder for discussion. The FAIR recommendations for workflows that we propose in this paper will maximize their value as research assets and facilitate their adoption by the wider community.

97 MATHEMATICS AND COMPUTING↗

An FPGA-Based Neuromorphic Processor with All-to-All Connectivity

Neuromorphic computing is a promising paradigm for future energy-efficient computing. At present, however, it is in its nascent stages—most hardware implementations are research-grade, commercial products are not available, and the software tools are not production-ready. The lack of hardware and software tools makes neuromorphic computing inaccessible to researchers around the globe. To this extent, we intend to build a low-cost, open-source, FPGA-based digital neuromorphic processor that can be used by researchers worldwide. In this paper, we present a preliminary implementation of the processor on a Xilinx Artix-7 FPGA using SystemVerilog. Our implementation supports the integrate-and-fire neuron with two parameters each for neurons and synapses. It also features all-to-all connectivity among neurons on the hardware. We test our implementation on four cases: bars and stripes datasets, shortest path algorithm, logic gates, and 8-3 encoder. We also perform a scalability study to understand the resource utilization of the FPGA as the number of all-to-all connected neurons increases. With our implementation, the Artix- 7 supports 65 neurons with all-to-all connectivity. Moreover, all the test cases mentioned above achieve 100% accuracy.

Maheshwari, Disha↗

Electric Drive Technologies Research: ELT223 Component Modeling, Co-Optimization, and Trade-Space Evaluation Annual Report

This project is intended to support the development of new traction drive systems that meet the targets of 100 kW/L for power electronics and 50 kW/L for electric machines with reliable operation to 300,000 miles. To meet these goals, new designs must be identified that make use of state-of-the-art and next-generation electronic materials and design methods. Designs must exploit synergies between components, for example converters designed for high-frequency switching using wide band gap (WBG) devices and ceramic capacitors. This project included: (1) a survey of available technologies; (2) investigating new technologies, that for example, reduce volume of thermal management or magnetic components; (3) the development of computer aided design tools that consider the converter volume, reliability, and electrical performance; (4) exercising the design software to evaluate performance gaps and predict the impact of certain technologies and design approaches, i.e. GaN semiconductors, ceramic capacitors, ceramic thermal management components, and select topologies; (5) building and testing hardware prototypes to validate models and concepts. The design tools enable co-optimization of the power module and passive elements and provide some design guidance. At the end of the project, new advanced computing methods, such as machine learning approaches, were considered.

33 ADVANCED PROPULSION SYSTEMS↗

A Study on Computational Cost Reduction of Simulations of Phase-Change Material (PCM) Embedded Heat Exchangers

Thermal storage can be implemented using Phase-Change Materials (PCM), which absorb significant latent heat with a relatively small temperature change. PCM phase-change processes are transient and are driven by thermal diffusion and natural convection – the latter, especially for melting process. Modeling and simulation of PCM heat exchangers (HX’s) is typically computationally intensive due to the relatively complex time-dependent physics. Most of the PCM modeling work in the literature uses high-order modeling tools such as Computational Fluid Dynamics (CFD) and Lattice-Boltzmann Method (LBM). For design purposes, the existing PCM modeling approaches are not practical, limiting researchers in their ability to investigate new ideas and different PCM’s with faster turnarounds. This paper presents a study investigating the reduction of computational cost of PCM embedded HX’s CFD models by evaluating the feasibility of spatial reduction without losing accuracy. The analysis consists of comparing full and partial domain under full melting conditions. The subject of this study is a single straight tube with circular transverse fins in the vertical orientation, using PCM’s with 35oC nominal melting temperature. Different tube and fin dimensions are investigated. Results indicate that the reduced domain reproduces - in half the run time - the same behavior as the full domain since the buoyancy effects are localized and patterned. The outputs from the partial domain simulation were used to build a non-general correlation for the PCM heat transfer characteristics and demonstrated how it can be implemented in a Finite Control Volume Reduced Order Model (ROM). The ROM can accurately reproduce the CFD simulations at 4 to 5 orders of magnitude faster.

25 ENERGY STORAGE↗

Ensemble Simulations on Leadership Computing Systems

Scientific productivity can be enhanced through workflow management tools, relieving large High Performance Computing (HPC) system users from the tedious tasks of scheduling and designing the complex computational execution of scientific applications. This paper presents a study on the usage of ensemble workflow tools to accelerate science using the Summit and Frontier supercomputing systems. The research aims to connect science domain simulations using Oak Ridge Leadership Computing Facility (OLCF) supercomputing platforms with ensemble workflow methods in order to accelerate HPC-enabled discovery and boost scientific impact. We present the coupling, porting and optimization of Radical-Cybertools on three applications: Chroma, NAMD and LAMMPS. The tools augment traditional HPC monolithic runs with a pilot scheduler. Lessons-learned are discussed for physics, biology and materials science applications. We discuss intrinsic limitations of coupling and porting ensemble workflow tools to applications that run on large HPC systems. The origins of technical challenges and their solutions developed during the implementation process are discussed. Data management strategies, OLCF’s policies for ensembles, and natively supported workflow tools are also summarized.

Georgiadou, Antigoni [ORNL] (ORCID:000000020977631↗

Atomic-precision advanced manufacturing for Si quantum computing

Abstract A materials synthesis method that we call atomic-precision advanced manufacturing (APAM), which is the only known route to tailor silicon nanoelectronics with full 3D atomic precision, is making an impact as a powerful prototyping tool for quantum computing. Quantum computing schemes using atomic ( 31 P) spin qubits are compelling for future scale-up owing to long dephasing times, one- and two-qubit gates nearing high-fidelity thresholds for fault-tolerant quantum error correction, and emerging routes to manufacturing via proven Si foundry techniques. Multiqubit devices are challenging to fabricate by conventional means owing to tight interqubit pitches forced by short-range spin interactions, and APAM offers the required (Å-scale) precision to systematically investigate solutions. However, applying APAM to fabricate circuitry with increasing numbers of qubits will require significant technique development. Here, we provide a tutorial on APAM techniques and materials and highlight its impacts in quantum computing research. Finally, we describe challenges on the path to multiqubit architectures and opportunities for APAM technique development. Graphic Abstract

36 MATERIALS SCIENCE↗

WAVES [Slides]

WAVES (LANL code C23004) is a computational engineering workflow tool that integrates parametric studies with traditional software build systems.

42 ENGINEERING↗

Multi-fidelity information fusion and resource allocation

This project created and demonstrated a framework for the efficient and accurate prediction of complex systems with only a limited amount of highly trusted data. These next generation computational multi-fidelity tools fuse multiple information sources of varying cost and accuracy to reduce the computational and experimental resources needed for designing and assessing complex multi-physics/scale/component systems. These tools have already been used to substantially improve the computational efficiency of simulation aided modeling activities from assessing thermal battery performance to predicting material deformation. This report summarizes the work carried out during a two year LDRD project. Specifically we present our technical accomplishments; project outputs such as publications, presentations and professional leadership activities; and the project’s legacy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

In Search of Optimum Fresh-Cut Raw Material: Using Computer Vision Systems as a Sensory Screening Tool for Browning-Resistant Romaine Lettuce Accessions

The popularity of ready-to-eat (RTE) salads has prompted novel technology to prolong the shelf life of their ingredients. Fresh-cut romaine lettuce is widely used in RTE salads; however, its tendency to quickly discolor continues to be a challenge for the industry. Selecting the ideal lettuce accessions for use in RTE salads is essential to ensure maximum shelf life, and it is critical to have a practical way to assess and compare the quality of multiple lettuce accessions that are being considered for use in fresh-cut applications. Thus, in this work we aimed to determine whether a computer vision system (CVS) composed of image acquisition, processing, and analysis could be effective to detect visual quality differences among 16 accessions of fresh-cut romaine lettuce during postharvest storage. The CVS involved a post-capturing color correction, effective image segmentation, and calculation of a browning index, which was tested as a predictor of quality and shelf life of fresh-cut romaine lettuce. The results demonstrated that machine vision software can be implemented to replace or supplement the scoring of a trained panel and instrumental quality measurements. Overall visual quality, a key sensory parameter that determines food preferences and consumer behavior, was highly correlated with the browning index, with a Pearson correlation coefficient of −0.85. Other important sensory decision parameters were also strongly or moderately correlated with the browning index, with Pearson correlation coefficients of −0.84 for freshness, 0.79 for off odor, and 0.57 for browning. The ranking of the accessions according to quality acceptability from the sensory evaluation produced a similar pattern to those obtained with the CVS. This study revealed that multiple lettuce accessions can be effectively benchmarked for their performance as fresh-cut sources via a CVS-based method. Future opportunities and challenges in using machine vision image processing to predict consumer preferences for RTE salad greens is also discussed.

Agriculture↗

The ISO 50001 Impact Estimator Tool (IET 50001 V1.1.4) - User Guide and Introduction to the ISO 50001 Impacts Methodology

ISO 50001-Energy management systems – Requirements with guidance for use, is an internationally developed standard that provides organizations with a flexible framework for implementing an energy management system (EnMS) with the goal of continual energy performance improvement. The ISO 50001 standard was first published in 2011 and has since seen growth in the number of certificates issued around the world, primarily in the industrial (agriculture, manufacturing, and mining) and service (commercial) sectors. Policy makers in many regions and countries are looking to or are already using ISO 50001 as a basis for energy efficiency, carbon reduction, and other energy performance improvement schemes. The Impact Estimator Tool 50001 (IET 50001 Tool) is a computational model developed to assist researchers and policy makers determine the potential impact of ISO 50001 implementation in the industrial and service (commercial) sectors for a given region or country. The IET 50001 Tool is based upon a methodology initially developed by the Lawrence Berkeley National Laboratory that has been improved upon and vetted by a group of international researchers. By using a commonly accepted and transparent methodology, users of the IET 50001 Tool can easily and clearly communicate the potential impact of ISO 50001 for a region or country.

97 MATHEMATICS AND COMPUTING↗

Classification and computation of extreme events in turbulent combustion

In the design of practical combustion systems, ensuring safety and reliability is an important requirement. For instance, reliably avoiding lean blowout, flame flashback or inlet unstart is critical for ensuring safe operation. Currently, the science of predicting such events is based on prior experience, limited modeling or diagnostic tools and purely statistical approaches. Even though computational and experimental tools for studying combustion devices have vastly advanced in the last three decades, the analysis of such failure events has not been pursued widely. While the use of data for model development and calibration is being widely accepted, the extension to failure events introduces numerous challenges. In particular, the focus here is on so-called data-poor problems, where the cost of generating data is extremely high and is not easily amenable to existing computational and experimental approaches. Data-poor problems are particularly relevant when related to extreme events (also called anomalous events) that can lead to catastrophic failure of the system. It is argued that transient events that describe such failure can have different causal mechanisms. To develop the scientific inference process, a classification of such problems is used to determine specific modeling paths as well as computational tools needed. Research opportunities in the emerging field of extreme event prediction are highlighted in order to identify critical and immediate needs.

97 MATHEMATICS AND COMPUTING↗

Extension of the Advanced Test Reactor Operating Envelope Via Enhanced Reactor Physics Validation Techniques

The Korea Atomic Energy Research Institute is currently in the process of qualifying a low-enriched-uranium fuel element design for the new Ki-Jang Research Reactor (KJRR). As part of this effort, a prototype KJRR fuel element was irradiated in this paper for several operating cycles in the northeast flux trap of the Advanced Test Reactor (ATR) at the Idaho National Laboratory. The KJRR fuel element contained a very large quantity of fissile material (618 g 235 U) in comparison with historical ATR experiment standards (<1 g 235 U), and its presence in the ATR flux trap was expected to create a neutronic configuration that would be well outside of the approved validation envelope for the reactor physics analysis methods used to support ATR operations. Accordingly, it was necessary to conduct an extensive set of new low-power physics measurements in the ATR Critical Facility (ATRC), a companion facility to the ATR, located in an immediately adjacent building and sharing the same fuel storage canal. The new measurements included fission power distributions, reactivity, and measurements related to the calibration of the in-core online instrumentation. The effort was focused on the objective of expanding the validation envelope for the computational reactor physics tools used to support ATR operations and safety analysis to include the planned KJRR irradiation in the ATR and similar experiments that are anticipated in the future. The computational and experimental results have demonstrated that the neutronic behavior of the KJRR fuel element in the ATRC is well understood in terms of its general effects on ATRC core reactivity and fission power distributions and its effects on the calibration of the ATR Lobe Power Calculation and Indication System, as well as in terms of its own internal fission rate distribution and total fission power per unit ATRC core power. Finally, taken as a whole, these results have significantly extended the ATR physics validation envelope, thereby enabling an entire new class of irradiation experiments.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Validation of High-Fidelity Reactor Physics Models for Support of the KJRR Experimental Campaign in the Advanced Test Reactor

The Korea Atomic Energy Research Institute is currently in the process of qualifying a Low-Enriched Uranium fuel element design for the new Ki-Jang Research Reactor (KJRR). As part of this effort, a prototype KJRR fuel element was irradiated for several operating cycles in the Northeast Flux Trap of the Advanced Test Reactor (ATR) at the Idaho National Laboratory. The KJRR fuel element contained a very large quantity of fissile material (618g 235U) in comparison with historical ATR experiment standards (<1g 235U), and its presence in the ATR flux trap was expected to create a neutronic configuration that would be well outside of the approved validation envelope for the reactor physics analysis methods used to support ATR operations. Accordingly it was necessary, prior to high-power irradiation of the KJRR fuel element in the ATR, to conduct an extensive set of new low-power physics measurements with the KJRR fuel element installed in the ATR Critical Facility (ATRC), a companion facility to the ATR that is located in an immediately adjacent building, sharing the same fuel handling and storage canal. The new measurements had the objective of expanding the validation envelope for the computational reactor physics tools used to support ATR operations and safety analysis to include the planned KJRR irradiation in the ATR and similar experiments that are anticipated in the future. The computational and experimental results demonstrated that the neutronic behavior of the KJRR fuel element in the ATRC is well-understood, both in terms of its general effects on core excess reactivity and fission power distributions, its effects on the calibration of the core lobe power measurement system, as well as in terms of its own internal fission rate distribution and total fission power per unit ATRC core power. Taken as a whole, these results have significantly extended the ATR physics validation envelope, thereby enabling an entire new class of irradiation experiments.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

Prediction of Thermal Conditions of DED With FEA Metal Additive Simulation

This paper presents the integration of wire-arc additive manufacturing (WAAM) using Gas Metal Arc Welding (GMAW) into a machine tool to create a retrofit hybrid computer numeric control (CNC) machine tool. GMAW, along with other direct energy deposition systems, has the capacity to deposit material faster than the excess thermal energy can dissipate. This results in the need to allow the part to cool between consecutive layers, which is the most time-consuming part of the additive process. Finite element analysis (FEA) was used in conjunction with monitored build plate surface temperatures during deposition samples to improve adequate dwell time prediction and to develop a cooling system. A deposition was completed where no dwell time was used and the build plate along with the machine table temperatures were monitored. A second deposition was completed where only one bead was deposited and the traverse speed was increased. The GMAW welder was mounted on a 3-axis CNC machine where two square deposition samples were completed. A FEA model was designed and verified using the monitored samples. The model will be used to determine improved depositions speeds and whether forced cooling would allow for an increased deposition rate without structural failure. It was determined the FEA software can be used to accurately model and predict the thermal response of WAAM AM components.

Heinrich, Lauren↗

Can Cooling and Heating Functions Be Modeled with Homogeneous Radiation Fields?

Abstract Cooling and heating functions describe how radiative processes impact the thermal state of a gas as a function of its temperature and other physical properties. In a most general case the functions depend on the detailed distributions of ionic species and on the radiation spectrum. Hence, these functions may vary on a very wide range of spatial and temporal scales. In this paper, we explore cooling and heating functions between 5 ≤ z ≤ 10 in simulated galaxies from the Cosmic Reionization On Computers project. We compare three functions: (1) the actual cooling and heating rates of hydrodynamic cells as a function of cell temperature, (2) the median cooling and heating functions computed using median interstellar medium (ISM) properties (median ISM), and (3) the median of the cooling and heating functions of all gas cells (instantaneous). We find that the median ISM and instantaneous approaches to finding a median cooling and heating function give identical results within the spread due to cell-to-cell variation. However, the actual cooling (heating) rates experienced by the gas at different temperatures in the simulations do not correspond to either summarized cooling (heating) functions. In other words, the thermodynamics of the gas in the simulations cannot be described by a single set of a cooling plus a heating function with a spatially constant radiation field that could be computed with common tools, such as CLOUDY.

79 ASTRONOMY AND ASTROPHYSICS↗

Performance Analysis of PIConGPU: Particle-in-Cell on GPUs using NVIDIA’s NSight Systems and NSight Compute

PIConGPU, Particle In Cell on GPUs, is an open source simulations framework for plasma and laser-plasma physics used to develop advanced particle accelerators for radiation therapy of cancer, high energy physics and photon science. While PIConGPU has been optimized for at least 5 years to run well on NVIDIA GPU-based clusters, there has been limited exploration by the development team of potential scalability bottlenecks using recently updated and new tools including NVIDIA’s NVProf tool and the brand-new NVIDIA NSight Suite (Systems and Compute) tools. PIConGPU is a highly optimized application that runs production jobs at scale on a system Oak Ridge Leadership Facility’s (OLCF) Summit supercomputer (using the full machine at 4600 nodes; at 98% of GPU utilization on all ~28000 NVIDIA Volta GPUs). PIConGPU has been selected as one of the the eight applications for OLCF’s coveted Center for Accelerated Application Readiness (CAAR) program aimed at the facility’s Frontier supercomputer (OLCF’s first exascale system to launch in 2021), to partner with our vendors (primary vendors: AMD and Cray/HPE) ensuring that Frontier will be able to perform large-scale science when it opens to users in 2022. To this effect, performance engineers on the PIConGPU team wanted to dive deep into the application to understand at the finest granularity, which portions of the code could be further optimized to exploit the hardware on Summit at it’s maximum potential and also to elucidate which key kernels should be tracked and optimized for the CAAR effort to port this code to Frontier. Any bottlenecks that are observed via performance profiling on Summit are likely to also impact scalability on the Frontier-dev system and the Frontier Early Access (EA) system. Additionally, the engineers wanted to take a closer look at the newest NVIDIA profiling tools which allows us to identify the most useful features on these tools and will provide an opportunity to compare it to new AMD and Cray’s performance analysis tool releases and provide feedback to our vendor partners on what features are most important and mission critical for CAAR efforts. The primary goal of this report is to focus on the evaluation of PIConGPU’s most time-intensive kernels using NVProf and NSight Suite. Three kernels, Current Deposition (also known as Compute Current), Particle Push (Move and Mark), and Shift Particles are known to be some of the most time-consuming kernels in PIConGPU. The Current xi Deposition kernel and Particle Push kernel both set up the particle attributes for running any physics simulation with PIConGPU, so it is crucial to improve the performance of these two kernels. In this report, we measure single GPU metrics for the three kernels, offer high level takeaways from the conducted analysis, and compare the profiling data from NSight Compute to that of NVProf. This analysis was performed using a grid size of 240 x 272 x 224, and 10 time steps with the Mid-November Figure of Merit (FOM) run setup. The Traveling Wave Electron Acceleration (TWEAC) science case used in this run is a representative science case for PIConGPU. This execution can also be used for baseline analysis on AMD MI50/ MI60 systems. As of the time of writing, the PIConGPU application has limited use for features of NSight Systems, so this report will mainly focus on insights garnered from NSight Compute. For this analysis, we run the “full” metric set available in NSight Compute version 2020.1.2 and use NSight Systems version 2020.3.1 to generate the application timeline.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Computer-aided classification of suspicious pigmented lesions using wide-field images

Early identification of melanoma is conducted through whole-body visual examinations to detect suspicious pigmented lesions, a situation that fluctuates in accuracy depending on the experience and time of the examiner. Computer-aided diagnosis tools for skin lesions are typically trained using pre-selected single-lesion images, taken under controlled conditions, which limits their use in wide-field scenes. Here, we propose a computer-aided classifier system with such input conditions to aid in the rapid identification of suspicious pigmented lesions at the primary care level. 133 patients with a multitude of skin lesions were recruited for this study. All lesions were examined by a board-certified dermatologist and classified into “suspicious” and “non-suspicious”. A new clinical database was acquired and created by taking Wide-Field images of all major body parts with a consumer-grade camera under natural illumination condition and with a consistent source of image variability. 3–8 images were acquired per patient on different sites of the body, and a total of 1759 pigmented lesions were extracted. A machine learning classifier was optimized and build into a computer aided classification system to binary classify each lesion using a suspiciousness score. In a testing set, our computer-aided classification system achieved a sensitivity of 100% for suspicious pigmented lesions that were later confirmed by dermoscopy examination (“SPL_A”) and 83.2% for suspicious pigmented lesions that were not confirmed after examination (“SPL_B”). Sensitivity for non-suspicious lesions was 72.1%, and accuracy was 75.9%. With these results we defined a suspiciousness score that is aligned with common macro-screening (naked eye) practices. This work demonstrates that wide-field photography combined with computer-aided classification systems can distinguish suspicious from non-suspicious pigmented lesions, and might be effective to assess the severity of a suspicious pigmented lesions. We believe this approach could be useful to support skin screenings at a population-level.

60 APPLIED LIFE SCIENCES↗