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At least 649 records · Page 36

SpectraCodec: A Hilbert curve-based method for encoding metadata in mass spectra for machine learning applications (SpectraCodec) v1

Machine learning approaches to mass spectrometry (MS) data analysis require structured metadata for optimal performance. However, current MS file formats necessitate external metadata sources, creating integration challenges that impede analytical workflows. Here, we present a novel approach for encoding metadata directly within mzML files using one-hot encoding of ASCII characters mapped via Hilbert space-filling curves. This strategy embeds metadata in the first spectrum's m/z-intensity space, ensuring persistence with the primary data, eliminating the need for external metadata files, and maintaining compatibility with existing MS software. We demonstrate that the Hilbert curve mapping efficiently utilizes the two-dimensional spectral space while maintaining robust data recovery. This method offers a practical solution for machine learning applications in mass spectrometry by ensuring metadata and spectral data remain unified through all stages of analysis.

Bowen, Benjamin [Lawrence Berkeley National Labora↗

Pumpchart v1.0.0

Pumpchart is a graphical tool that plots the state of a hydraulic system overlayed on a pump curve and system curve. It assists with determining the optimal performance of the system. One advantage of Pumpchart over other softwares is that it is integrated with the Grafana dashboarding software, so that data can be plotted in real-time for instant operator feedback. It is intended to be used at NERSC to monitor the performance of our cooling water pumps.

Venture, Nicholas [Lawrence Berkeley National Labo↗

Evaluating Multi-core Architectures through Accelerating the Three-Dimensional Lax–Wendroff Correction

Wave propagation forward modeling is a widely used computational method in oil and gas exploration. The iterative stencil loops in such problems have broad applications in scientific computing. However, executing such loops can be highly time time-consuming, which greatly limits application’s performance and power efficiency. In this paper, we accelerate the forward modeling technique on the latest multi-core and many-core architectures such as Intel Sandy Bridge CPUs, NVIDIA Fermi C2070 GPU, NVIDIA Kepler K20x GPU, and the Intel Xeon Phi Co-processor. For the GPU platforms, we propose two parallel strategies to explore the performance optimization opportunities for our stencil kernels. For Sandy Bridge CPUs and MIC, we also employ various optimization techniques in order to achieve the best.

3D Wave Forward Modeling↗

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community

BACKGROUND:Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community-bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. RESULTS:The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. CONCLUSION:The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.

59 BASIC BIOLOGICAL SCIENCES↗

Pycheron: A Python-Based Seismic Waveform Data Quality Control Software Package

Supplementing an existing high-quality seismic monitoring network with openly available station data could improve coverage and decrease magnitudes of completeness; however, this can present challenges when varying levels of data quality exist. Without discerning the quality of openly available data, using it poses significant data management, analysis, and interpretation issues. Incorporating additional stations without properly identifying and mitigating data quality problems can degrade overall monitoring capability. If openly available stations are to be used routinely, a robust, automated data quality assessment for a wide range of quality control (QC) issues is essential. To meet this need, we developed Pycheron, a Python-based library for QC of seismic waveform data. Pycheron was initially based on the Incorporated Research Institutions for Seismology’s Modular Utility for STAtistical kNowledge Gathering but has been expanded to include more functionality. Pycheron can be implemented at the beginning of a data processing pipeline or can process stand-alone data sets. Its objectives are to (1) identify specific QC issues; (2) automatically assess data quality and instrumentation health; (3) serve as a basic service that all data processing builds on by alerting downstream processing algorithms to any quality degradation; and (4) improve our ability to process orders of magnitudes more data through performance optimizations. This article provides an overview of Pycheron, its features, basic workflow, and an example application using a synthetic QC data set.

58 GEOSCIENCES↗

STATUS OF THE SECOND INTERACTION REGION DESIGN FOR ELECTRON-ION COLLIDER

Provisions are being made in the Electron Ion Collider (EIC) design for future installation of a second Interaction Region (IR), in addition to the day-one primary IR. The envisioned location for the second IR is the existing experi- mental hall at RHIC IP8. It is designed to work with the same beam energy combinations as the first IR, covering a full range of the center-of-mass energy of ?20 GeV to ?140 GeV. The goal of the second IR is to complement the first IR, and to improve the detection of scattered particles with magnetic rigidities similar to those of the ion beam. To achieve this, the second IR hadron beamline features a secondary focus in the forward ion direction. The design of the second IR is still evolving. This paper reports the current status of its pa- rameters, magnet layout, and beam dynamics and discusses the ongoing improvements being made to ensure its optimal performance.

Gamage, B.↗

BOPTest As a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.

Paul, Lazlo↗

Semantic Interoperability to Enable Smart, Grid-Interactive Efficient Buildings

Achieving a widespread transition to grid-interactive, efficient buildings (GEBs) depends critically on there being sufficient interoperability among connected building systems. While many critical elements already exist at the technical interoperability level (TCP/IP, BACnet, etc.), a lack of interoperability in the semantic level hinders streamlined integration of interdependent applications. Semantics refers to expressing information about “things” in a way that can be consistently understood by applications. Key components of formalized semantics include identifying what a “thing” is (its “type”), defining general information about that “thing” (its characteristics or properties), and defining the appropriate relationships of that “thing” to other “things” (its function or role in a larger system). Although this might seem initially trivial, the success of smart building applications is highly dependent on maintaining consistent self-descriptive notions of the “things”. Without semantic interoperability, it is technically difficult, labor-intensive, and cost-prohibitive to enable three key objectives of GEBs: optimizing performance, automatically identifying and diagnosing faults, and delivering grid services. Industry, academia, and standards bodies have invested effort in developing information models to facilitate semantic interoperability, however, they have not been widely adopted across the U.S. commercial building portfolio. This paper will present a pathway to drive semantic interoperability through a three-pronged approach to be led by the DOE Building Technologies Office in partnership with NIST and multiple national laboratories comprising: 1) industry engagement and coordination across existing efforts; 2) a semantic interoperability standard that empowers building owners to identify and require interoperable attributes when procuring equipment and applications; 3) tools to assist in implementation and a test framework to verify compliance of products with semantic interoperability specifications. This approach is designed to accelerate the timeline for adoption of semantic interoperability specifications. The intent is to reduce soft costs associated with implementing advanced controls, fault detection and diagnostics, and other smart building technologies and use cases as a necessary step in achieving an energy efficient smart grid future.

Bergmann, Harry↗

Example Work Domain Analysis for a Reference Sodium Fast Reactor

The nuclear industry is currently designing and building a new generation of reactors that will include different structural, functional, and environmental aspects, all of which are likely to have a significant impact on the way these plants are operated. In order to meet economic and safety objectives, these new reactors will all use advanced technologies to some extent, including new materials and advanced digital instrumentation and control systems. New technologies will affect not only operational strategies, but will also require a new approach to how functions are allocated to humans or machines to ensure optimal performance. Uncertainty about the effect of large scale changes in plant design will remain until sound technical bases are developed for new operational concepts and strategies. Up-to-date models and guidance are required for the development of operational concepts for complex socio-technical systems. This report describes how the classical Work Domain Analysis method was adapted to develop operational concept frameworks for new plants. This adaptation of the method is better able to deal with the uncertainty and incomplete information typical of first-of-a-kind designs. Practical examples are provided of the systematic application of the method in the operational analysis of sodium-cooled reactors. Insights from this application and its utility are reviewed and arguments for the formal adoption of Work Domain Analysis as a value-added part of the Systems Engineering process are presented.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling of the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.

97 MATHEMATICS AND COMPUTING↗

Direct Drive Wave Energy Buoy

This Project aims to satisfy objectives of the DOE’s Water Power Program by completing a system detailed design (SDD) and other important activities in the first phase of a utility-scale grid-connected ocean wave energy demonstration. In early 2012, Columbia Power (CPwr) had determined that further cost and performance optimization was necessary in order to commercialize its StingRAY wave energy converter (WEC). CPwr’s progress toward commercialization, and the requisite technology development path, were focused on transitioning toward a commercial-scale demonstration. This path required significant investment to be successful, and the justification for this investment required improved annual energy production (AEP) and lower capital costs. Engineering solutions were developed to address these technical and cost challenges, incorporated into a proposal to the US Department of Energy (DOE), and then adapted to form the technical content and statement of project objectives of the resulting Project (DE-EE0005930). Through Project cost-sharing and technical collaboration between DOE and CPwr, and technical collaboration with Oregon State University (OSU), National Renewable Energy Lab (NREL) and other Project partners, we have demonstrated experimentally that these conceptual improvements have merit and made significant progress towards a certified WEC system design at a selected and contracted deployment site at the Wave Energy Test Site (WETS) at the Marine Corps Base in Oahu, HI (MCBH).

16 TIDAL AND WAVE POWER↗

Parallel File System I/O Performance Testing On LANL Clusters

These are slides from a presentation on parallel file system I/O performance testing on LANL clusters. I/O is a known bottleneck for HPC applications. Performance optimization of I/O is often required. This summer project entailed integrating IOR under Pavilion and automating the results analysis. The slides cover the following topics: scope of the work, tools utilized, IOR-Pavilion test workflow, build script, IOR parameters, how parameters are passed to IOR, *run_ior: functionality, Python IOR-Output Parser, Splunk data format, Splunk dashboard and features, and future work.

97 MATHEMATICS AND COMPUTING↗

Residential Indoor Temperature Study

In this study, we are adding to the body of knowledge around answering the question: What are good assumptions for HVAC set points in U.S. homes? We collected and analyzed indoor temperature data from US homes using funding from the U.S. Department of Energy's Building America (BA) program, due to the program's reliance on accurate energy simulation of homes. Simulations are used to set Building America goals, predict the impact of new building techniques and technologies, inform research objectives, evaluate home performance, optimize efficiency packages to meet savings goals, customize savings approaches to specific climate zones, and myriad other uses.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Metal Hydride Compression

Conventional hydrogen compressors often contribute over half of the cost of hydrogen stations, have poor reliability, and have insufficient flow rates for a mature FCEV market. Fatigue associated with their moving parts including cracking of diaphragms and failure of seal leads to failure in conventional compressors, which is exacerbated by the repeated starts and stops expected at fueling stations. Furthermore, the conventional lubrication of these compressors with oil is generally unacceptable at fueling stations due to potential fuel contamination. Metal hydride (MH) technology offers a very good alternative to both conventional (mechanical) and newly developed (electrochemical, ionic liquid pistons) methods of hydrogen compression. Advantages of MH compression include simplicity in design and operation, absence of moving parts, compactness, safety and reliability, and the possibility to utilize waste industrial heat to power the compressor. Beyond conventional H2 supplies of pipelines or tanker trucks, another attractive scenario is the on-site generating, pressuring and delivering pure H 2 at pressure (≥ 875 bar) for refueling vehicles at electrolysis, wind, or solar generating production facilities in distributed locations that are too remote or widely distributed for cost effective bulk transport. MH hydrogen compression utilizes a reversible heat-driven interaction of a hydride-forming metal alloy with hydrogen gas to form the MH phase and is a promising process for hydrogen energy applications [1,2]. To deliver hydrogen continuously, each stage of the compressor must consist of multiple MH beds with synchronized hydrogenation & dehydrogenation cycles. Multistage pressurization allows achievement of greater compression ratios using reduced temperature swings compared to single stage compressors. The objectives of this project are to investigate and demonstrate on a laboratory scale a two-stage MH hydrogen (H 2 ) gas compressor with a feed pressure of >50 bar and a delivery pressure ≥ 875 bar of high purity H 2 gas using the scheme shown in Figure 1. Progress to date includes the selection of two candidate metal hydrides for each compressor stage, supplier engagement and synthesis of small samples, and the beginning of in-depth characterization of their thermodynamics, kinetics, and hydrogen capacities for optimal performance with respect to energy requirements and efficiency. Additionally, bed design trade studies are underway and will be finalized in FY18. Subsequently, the prototype two-stage compressor will be fabricated, assembled and experimentally evaluated in FY19.

08 HYDROGEN↗

Retrieving Historical Electrorefining Data

Pyrochemical Operations began at Los Alamos National Laboratory (LANL) during 1962 (1). Electrorefining (ER) has been implemented as a routine process since the 1980’s. The process data that went through the ER operation was recorded but had never been logged in an online database. Without a database new staff members are hindered in their work by the lack of information. To combat the issue a database in Access was created to collect the historical data. The years from 2000 onward were entered and queries were created to analyze trends. These trends will aid engineering and operations staff to reach optimal performance for the startup of the new lines.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Staghorn: An Automated Large-Scale Distributed System Analysis Platform

Conducting experiments on large-scale distributed computing systems is becoming significantly easier with the assistance of emulation. Researchers can now create a model of a distributed computing environment and then generate a virtual, laboratory copy of the entire system composed of potentially thousands of virtual machines, switches, and software. The use of real software, running at clock rate in full virtual machines, allows experiments to produce meaningful results without necessitating a full understanding of all model components. However, the ability to inspect and modify elements within these models is bound by the limitation that such modifications must compete with the model, either running in or alongside it. This inhibits entire classes of analyses from being conducted upon these models. We developed a mechanism to snapshot an entire emulation-based model as it is running. This allows us to \freeze time" and subsequently fork execution, replay execution, modify arbitrary parts of the model, or deeply explore the model. This snapshot includes capturing packets in transit and other input/output state along with the running virtual machines. We were able to build this system in Linux using Open vSwitch and Kernel Virtual Machines on top of Sandia's emulation platform Firewheel. This primitive opens the door to numerous subsequent analyses on models, including state space exploration, debugging distributed systems, performance optimizations, improved training environments, and improved experiment repeatability.

97 MATHEMATICS AND COMPUTING↗

AToM (Advanced Tokamak Modeling)

This final report for the AToM project documents the contributions from General Atomics over the period 1 September 2014 to 31 August 2017. This includes significant progress on the development of tokamak integrated modeling frameworks (OMFIT and IPS), and development of new workflows for computing plasma profile (temperature, density, etc) evolution. Significant effort was also carried out in the high-performance computing arena, by adding the COGENT edge-simulation code to the AToM portfolio, and performing optimization of the CGYRO plasma turbulence code. Issues of data management and user outreach are also documented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SLEEC: Semantics-Rich Libraries for Effective Exascale Computation. Final Technical Report

SLEEC (Semantics-rich Libraries for Effective Exascale Computation) was a project funded by the Department of Energy X-Stack Program, award number DE-SC0008629. The initial project period was September 2012–August 2015. The project was renewed for an additional year, expiring August 2016. Finally, the project received a no-cost extension, leading to a final expiry date of August 2017. Modern applications, especially those intended to run at exascale, are not written from scratch. Instead, they are built by stitching together various carefully-written, hand-tuned libraries. Correctly composing these libraries is difficult, but traditional compilers are unable to effectively analyze and transform across abstraction layers. Domain specific compilers integrate semantic knowledge into compilers, allowing them to transform applications that use particular domain-specific languages, or domain libraries. But they do not help when new domains are developed, or applications span multiple domains. SLEEC aims to fix these problems. To do so, we are building generic compiler and runtime infrastructures that are semantics-aware but not domain-specific. By performing optimizations related to the semantics of a domain library, the same infrastructure can be made generic and apply across multiple domains.

97 MATHEMATICS AND COMPUTING↗