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At least 883 records · Page 49

A Distributed Python HPC Framework: ODIN, PyTrilinos, & Seamless

Under this grant, three significant software packages were developed or improved, all with the goal of improving the ease-of-use of HPC libraries. The first component is a Python package, named DistArray (originally named Odin), that provides a high-level interface to distributed array computing. This interface is based on the popular and widely used NumPy package and is integrated with the IPython project for enhanced interactive parallel distributed computing. The second Python package is the Distributed Array Protocol (DAP) that enables separate distributed array libraries to share arrays efficiently without copying or sending messages. If a distributed array library supports the DAP, it is then automatically able to communicate with any other library that also supports the protocol. This protocol allows DistArray to communicate with the Trilinos library via PyTrilinos, which was also enhanced during this project. A third package, PyTrilinos, was extended to support distributed structured arrays (in addition to the unstructured arrays of its original design), allow more flexible distributed arrays (i.e., the restriction to double precision data was lifted), and implement the DAP. DAP support includes both exporting the protocol so that external packages can use distributed Trilinos data structures, and importing the protocol so that PyTrilinos can work with distributed data from external packages.

97 MATHEMATICS AND COMPUTING↗

Chain of Custody Item Monitor Message Viewer v.1.0 Beta

The CoCIM Message Viewer software allows users to connect to and download messages from a Chain of Custody Item Monitor (CoCIM) connected to a serial port on the user’s computer. The downloaded messages are authenticated and displayed in a Graphical User Interface that allows the user a limited degree of sorting and filtering of the downloaded messages as well as the ability to save downloaded files or to open previously downloaded message history files.

Schwartz, Steven Robert↗

Studying Performance Portability of LAMMPS across Diverse GPU-based Platforms

The molecular dynamics simulation software, LAMMPS, utilizes the Kokkos acceleration library to port computation to a diverse set of architectures including those based on GPU accelerators. In addition to Kokkos, LAMMPS contains a vast code base that leverages the CUDA application programming interface using library functions such as cuFFT, CUDA’s fast-fourier transform (FFT) library, and, more recently, also support for AMD’s Heterogeneous Interface for Portability (HIP) that is rapidly growing. While preparing LAMMPS tests for the AMD GPU-based test system precursors to Frontier, we investigated several strategies for accelerating LAMMPS on AMD GPUs, using the AMD Instinct MI100 and MI250X. In this work, we integrated the HIP FFT library, hipFFT, into the particle-particle particle-mesh (PPPM) long-range solver, which allowed the porting of PPPM calculations to the GPUs. Kokkos behavior on the MI100 and MI250X was also investigated through the package kokkos command of LAMMPS, targeting com- munication, memory usage, and particle grid decomposition. The Tersoff, Reax, Lennard-Jones (LJ), EAM, Granular, and PPPM potentials were investigated in this effort, and results from these experiments are provided. The selected potentials were run on Spock (AMD Instinct MI100), Crusher (AMD Instinct MI250X), AFW HPC11 (NVIDIA A100) and Summit (NVIDIA V100), for comparison. Operational roofline models were constructed and analyzed for the Tersoff, Reax, and Lennard-Jones potentials on Crusher and Summit.

Hagerty, Nick↗

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗

VERAIO Software Management Plan

VERAIO is a set of utility codes used to provide a common set of inputs and outputs to the Virtual Environment for Reactor Applications (VERA). VERA is a collection of several different computer codes that all have a common input and output. This prevents the need to manage input and output from each individual code, allowing for ease of use and reducing errors associated with code operability. The VERAIO utilities include VERAIn, VERAView, and VERARun. Each of these utilities is described below. VERAIn is an input processor that reads an ASCII input file generated by users, parses the file, performs some error checking, and writes an XML file to be read by other VERA codes. The main purpose of VERAIn is to provide a common input to all of the VERA codes, so users only need to learn one input. VERAIn is written in Perl and uses YAML configuration files to provide flexibility. VERAView is a graphical user interface (GUI) that reads a VERA hierarchical data format (HDF) output file and allows users to visualize results. VERAView is written in Python. VERARun is a script that drives the VERA execution in a high performance computing (HPC) environment. Work performed at the code level supports the quality assurance program plan (QAPP) (VERA-QA-001) and the VERA Software Quality Assurance Plan (VERA-QA-002).

97 MATHEMATICS AND COMPUTING↗

Novel Serpentine Robot Combinations for Inspection in Hard-to-Reach Areas of Damaged or Decommissioned Structures - 17335

U.S. government agencies, particularly the Dept. of Energy, need robotic tools to handle and inspect high-consequence materials - materials for which mishandling would result in great risk to both application operators and the general public. The remediation and documentation of nuclear waste has become a problem of national significance and it cannot be addressed without robotic tools. The use of robots bypasses the danger and decreases the preparation time to handle harmful materials. In the 1980's and 90's, the US Dept. of Energy (DOE) invested heavily in robotic technologies as part of a comprehensive program of research and development aimed at enabling safer and more efficient cleanup of nuclear waste sites. For the next generation of harder, more complex clean-up problems, there is a clear need for more R and D. There is a clear need for flexible, quickly deployable robotic technologies that can be configured to respond to unforeseen situations -- or can be purpose-built for planned activities -- while keeping human workers safe, yet effective. Modularity and inter-operability are core capabilities for inspection tasks in contaminated facilities with a large variety of inspection problems. With any tool, familiarity breeds ingenuity, and ingenuity leads to new innovations in efficiency, effectiveness, safety, and performance. For example, the simple screwdriver can be held fourteen different ways by an experienced machinist who knows exactly what he or she wants to accomplish at any given moment. As a tool, robots are no different. To maximize the efficiency, effectiveness, safety and performance, redeployment and reuse of familiar tools is essential. Modularity can assist with re-deployment and modularity manifests itself in both hardware and software. In some applications of inspection of high-consequence materials, a common concern has been the simplicity of the tool -- often correlated with cost (which is not always accurate) -- in case it becomes unrecoverable. In the case of robots, which have complex user interfaces and complex dynamics of interaction, the lack of familiarity can lead to clumsy operations and reduced accumulation of knowledge. As a result, while incremental successes may be achieved with sequential uses of different robots, there often is little knowledge gain that is generalizable across multiple uses. Total cost often goes down when a more sophisticated, but more familiar tool, can be used more frequently.An example is the inspection of the H-Canyon Exhaust Air Tunnel at the Savannah River Site nuclear waste facility in the United States [1]. This is a particularly nasty environment, due to the acidic gases, large amounts of erosion and debris, and wet, mucky puddles. Over the past twelve years, six inspections have been attempted with five different robotic vehicles. In fact, these inspections have been successful with their limited, but progressively increasing objectives, although most robots have been abandoned in the tunnel. While each vehicle has cost less than $75,000 (the sacrificial part), the total costs of development have been much higher. The robots used to investigate changed much from iteration to iteration and it is not clear a strong body of generalizable expertise was built up across trials. The authors of this study demonstrated the combination of two types of modular, serpentine, re-configurable robots for locomotion over complex terrains and the inspection of hard-to-reach areas. The MOTHERSHIP is a tread/limb/serpentine hybrid robot design for locomotion over complex terrains, while the CMU snake robot provides highly articulated inspection of highly confined spaces. The demonstration at the Portsmouth Gaseous Diffusion Plant involves a combination of the two whereby gross locomotion is achieved with the MOTHERSHIP and the CMU Snake deploys a sensor package to gather data from behind and under obstacles. Although statically configured in its present state, the combined robot is built of individual modules for which reconfiguration has been demonstrated in both labs at Purdue and CMU. In future work, much higher degrees of reconfiguration and re-purposing of both software and hardware are easily achievable with these unique platforms. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

SMATool: Strength of materials analysis toolkit

The study of the strength of materials is a cornerstone in material science and engineering, playing a critical role in shaping the progress and application of materials in diverse industrial sectors. The strength of a material is meticulously examined to understand the behavior of the material under different stress conditions and environments, thereby guiding material selection and structural design. Herein, we introduce the SMATool, a computational toolkit for the efficient calculation and analysis of material strength at both zero and finite temperatures for 3D, 2D, 1D, and tubular 2D-based nanostructures and nanotubes, as well as 1D nanoribbons. The toolkit is capable of calculating tensile, shear, ultimate, yield, and indentation (Vickers' hardness) strengths in various dimensions, as well as the energy storage capacity. We conducted several calculations both at zero and finite temperatures to validate the accuracy and reliability of the developed software. Here, the results show that the SMATool package provides accurate predictions that align with existing data on material strength. SMATool integrates seamlessly with widely used electronic structure codes like VASP and Quantum Espresso, providing a user-friendly interface catering to academic researchers and industry professionals.

36 MATERIALS SCIENCE↗

Adaptive smart simulator for characterization and MPPT construction of PV array

Partial shading conditions are among the most important problems in large photovoltaic array. Many works of literature are interested in modeling, control and optimization of photovoltaic conversion of solar energy under partial shading conditions, The aim of this study is to build a software simulator similar to hard simulator and to produce a shading pattern of the proposed photovoltaic array in order to use the delivered information to obtain an optimal configuration of the PV array and construct MPPT algorithm. Graphical user interfaces (Matlab GUI) are built using a developed script, this tool is easy to use, simple, and has a rapid of responsiveness, the simulator supports large array simulations that can be interfaced with MPPT and power electronic converters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

RuleBuilder

RuleBuilder is a tool for drawing graphs represented by the BioNetGen rule-based modeling language (BNGL), a domain-specific language used to formulate mathematical models of biochemical interaction networks. This framework provides an intuitive plain-text representation of such networks using a graph-based formalism. The interactions between the model's components are graph-rewriting rules that denote the minimum context needed for the interaction to occur. In some cases the context required for reactions to occur can grow quite large, and the lengthy textual description of the interaction can be difficult to interpret or debug. RuleBuilder is designed to make this process simpler through visualization of individual rule or pattern strings. The software assists in the reading of existing models by converting the BNGL strings of interest into a graph-based representation composed of nodes and edges. RuleBuilder also enables the user to build the visual representation directly from its interface, composing the BNGL string as components and operators are added to the graphical object.

Fricke, Matthew↗

PyPWA: A Partial-Wave/Amplitude Analysis Software Framework

The PyPWA project aims to develop a software framework for Partial Wave and Amplitude Analysis of data; providing the user with software tools to identify resonances from multi-particle final states in photoproduction. Most of the code is written in Python. The software is divided into two main branches: one general-shell where amplitude's parameters (or any parametric model) are to be estimated from the data. This branch also includes software to produce simulated data-sets using the fitted amplitudes. A second branch contains a specific realization of the isobar model (with room to include Deck-type and other isobar model extensions) to perform PWA with an interface into the computer resources at Jefferson Lab. We are currently implementing parallelism and vectorization using the Intel's Xeon Phi family of coprocessors.

Salgado, Carlos↗

A Model for Lean Corporate/ Startup Interfaces: Unlocking Resources of Midcap Corporations Providing a Pathway to Advanced Energy Technologies

Commercializing energy technologies through traditional market pathways is challenging for early-stage energy innovators. Development cycles in energy are long and expensive, and adoption is difficult, making energy technologies of limited interest to venture capital relative to industries with faster growth and shorter product life cycles such as life sciences and software. As such, partnerships with established corporations are one of the most promising, and in some cases only, go-to-market pathways for energy technologies. Startups often seek to work with, large well-known Fortune 500 (and similar) companies. However, the size and risk aversion of those firms often makes partnering challenging. It can take well over 12 months for a large corporation to agree to commercial terms and get internal board / management approval to move forward with a binding agreement with a startup for even a simple starting partnership. This timeline is prohibitive for most early-stage companies who are both time and money constrained, and often working in highly competitive commodity sectors. Mid-cap corporations ($\$ $100M to $\$ $10B) are a promising but untapped resource for partnering with technology developers because they are often nimbler, tend to be fiercely competitive, and are looking for new revenue or cost-saving opportunities. These factors make them both more receptive to disruptive technologies, and more capable of integrating them. However, while Fortune 500 companies often have venturing groups that facilitate the initial connection process, most midcap incumbents do not have the resources to create standalone corporate venture groups. As a result, although they could help each other significantly (startup technologies make midcaps more competitive; midcaps offer a faster commercialization pathway to startups), midcap companies and startups rarely work together. In 2017, ADL Ventures (ADL) received Award #DE-EE0008111 from DOE EERE’s Innovative Pathways program to unlock the domain expertise and material resources of midcap companies. The goal of the award was to support energy technology commercialization via an innovation platform for startups to interface with midcap corporations. During the grant period, we have developed a novel open innovation platform that allows financially conservative incumbents to efficiently engage with energy innovators and startups, thereby unlocking the incumbents’ domain expertise, strategic capital, R&D facilities, supply chain, and pathways to market. We have executed full-scale open innovation challenges for three clients, exceeding the initial proposed goal of two. We also built a diversified opportunity pipeline which resulted in four projects contracted for 2020, meeting the goals of the proposal, with others pending.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Tower Illuminance Model (TIM): Interactive Real-Time Flyover Simulation Tool to Evaluate Glare and Avian-Flux Hazards

Solar glare reflections and avian solar-flux hazards are an important concern for concentrating solar installations. Reflected sunlight from 'standby' heliostats has been noted by pilots as potentially hazardous, and reports of birds being singed by concentrated sunlight has created concern. This paper presents the Tower Illuminance Model ('TIM'), a software application developed to investigate glare and avian-flux hazards at concentrating solar power towers in a convenient and interactive manner. TIM simulates a field of heliostats in standby mode, wherein sunlight is not reflected toward the central receiver but at some location in the airspace around the receiver. The user can select a range of aiming strategies and field configurations and can navigate the simulated airspace above the heliostat field in real-time using an interactive 3D interface. As the user 'flies' through the airspace, TIM calculates the irradiance, glare hazard, and potential avian flux hazard. TIM is currently undergoing validation and industry testing.

14 SOLAR ENERGY↗

Machine Intelligence-Centered System for Automated Characterization of Functional Materials and Interfaces

Classic design of experiment relies on a time-intensive workflow that requires planning, data interpretation, and hypothesis building by experienced researchers. Here, in this paper, we describe an integrated, machine-intelligent experimental system which enables simultaneous dynamic tests of electrical, optical, gravimetric, and viscoelastic properties of materials under a programmable dynamic environment. Specially designed software controls the experiment and performs on-the-fly extensive data analysis and dynamic modeling, real-time iterative feedback for dynamic control of experimental conditions, and rapid visualization of experimental results. The system operates with minimal human intervention and enables time-efficient characterization of complex dynamic multifunctional environmental responses of materials with simultaneous data processing and analytics. The system provides a viable platform for artificial intelligence (AI)-centered material characterization, which, when coupled with an AI-controlled synthesis system, could lead to accelerated discovery of multifunctional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Multi-Agent System Concept for Rapid Energy Storage Development

Many energy storage systems that use technologies such as batteries are composed of power electronics conditioning systems and battery management systems. These are often produced by multiple manufacturers and require hardware and software integration for full grid functionality. This paper proposes an agent-based framework to support the development of an energy storage system with standardized communications. This framework can be utilized with different power conversion systems with an appropriate hardware interface.

Starke, Michael↗

Design and Analysis of High Heat Flux Plasma-Facing Components for NSTX Upgrade

The National Spherical Tokamak Experiment (NSTX) upgrade (NSTX-U) requirements lead to enhanced heat loads on plasma-facing components (PFCs) especially in the divertor regions, where normal heat flux density can reach up to 8 MW/m 2 . For these high heat flux (HHF) regions, the PFCs were redesigned, to use castellations which relieved the thermal stresses associated with high incident heat flux. Another design feature of HHF PFCs is the absence of front face mounting holes which create localized areas of high temperature and thermal stress concentrations. Optimized shaping of the front face of the HHF PFCs eliminates regions where the front face is perpendicular to the heat flux direction during normal helicity operation and spreads the heat load. A unique mechanism was designed to connect PFC tiles to the NSTX-U center stack casing using locking features accessible from the low heat flux regions. Isotropic graphite was selected as the HHF PFC tile material. Initial tile design parameters were accessed using analytical expressions for pulsed heat flux loading. A working prototype of the locking mechanism was created during the initial stages of the design to prove the concept performance. This article presents an overview of the divertor HHF PFC design and the results of the thermal and structural analyses performed using ANSYS software. The results of the analyses cover normal operating conditions and disruptions which impose electromagnetic (EM) loads from eddy and halo currents. The 3-D, transient, nonlinear analyses took into account the temperature-dependent properties of the materials, friction interfaces between the parts, and variable electric properties of the parts and interfaces. The results confirm that the HHF PFC tiles remain within the allowable limits for the loads defined by the NSTX-U Recovery Project. In addition, tolerance stack up analyses were performed to ensure tile performance in the worst possible assembly configuration. Finally, the design process was completed successfully, and the NSTX HHF PFC tiles are currently in the production phase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

LIQUID

LIQUID is a software tool for identifying lipids in LC-MS/MS-based lipidomics data. It is described in publication LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data (doi: 10.1093/bioinformatics/btx046). LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.

Payne, Sam↗

nSnare™

nSnare™ analyses and categorizes log messages generated by various and customizable third party software packages using a custom multi-tiered rules engine. Each log message is either determined to be a false positive, or it is assigned a score based on the severity of the potential attack and confidence that the activity described by the log message is not a false positive. Log messages are then assigned to an event, which is a collection of log messages related to a single potential attack. Meta-analysis rules run on the collection of all logs within an event to correlate multiple related logs into a single known attack signature. When the sum of the scores of all logs within an event exceeds a pre-defined threshold, the event is labelled as an attack and an automated response is generated to block the attacker from connecting to any protected resources, called quarantining within the application, for a variable length of time. The length of time that the quarantine lasts for is based on the severity and frequency of the attack, along with historical information on the attacker and any third party provided threat intelligence data that the system has gathered. An additional random length of time is added to each quarantine so the algorithm cannot easily be learned and bypassed by a persistent attacker. A confidence score is generated based on a proprietary algorithm that determines the likelihood that the data which lead to the attacker getting quarantined was a false positive. A threat intelligence record is created for each detected attack, with details on the attacker, a summary of what triggered the quarantine, the severity of the attack and the confidence the system has that the attack is not the result of false data, which can then be shared with external entities so that they can also protect themselves from a related attack. The software also includes a web based front end for analyzing the current quarantined attacks, removing a quarantine in the case of a false positive, viewing previously quarantined attacks, and tracking suspicious activity that the system is currently evaluating. The web interface also allows the creation and modification of rules used by the rules engine, and the maintenance of a whitelist of known good systems that should never be automatically quarantined.

Hoying, Andrew↗