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At least 1,153 records · Page 64

DeepDiagnostics: A Software Package for Streamlined Posterior Evaluation

Automated prediction techniques like simulation-based inference (SBI) are important tasks for science experiments that produce large amounts of complex, raw data. However, their development remains in its early stages because the uncertainties of these techniques lack sufficient trustworthiness and interpretability. Packages for SBI provide a growing set of diagnostics; however, the software requirements are substantial, as they are tied to the inference technology itself, and the APIs lack adaptability. We introduce the DeepDiagnostics package for diagnosing posteriors from analytic likelihood-based methods and SBI methods, such as neural posterior estimation. DeepDiagnostics produces a comprehensive set of high-quality visualizations and metrics in a highly accessible, easy-to-use, and flexible package. We address all of these goals by providing a command-line inference tool and a Python API that is controlled through a configuration file. The package includes common diagnostics, such as parity plots, corner (covariance) plots, simulation-based calibration (SBC) diagnostics (including posterior coverage and rank histograms), Lemos et al. s PQMass and TARP, Masserano et al. s WALDO, Linhart et al. s LC2ST, as well as credible region diagnostics developed by our group.

Voetberg, Maggie [Fermilab]↗

The Benefits and Weaknesses of Containerizing Software for HPC

Containerization technology has emerged as a transformative tool for software engineers, offering consistent development and deployment environments, simplifying dependency management, and enhancing scalability and portability across diverse systems. However, its application in High-Performance Computing (HPC) presents unique challenges, including the management of virtualization overhead, the need for efficient resource allocation, and the maintenance of optimal performance for compute-intensiv

Ho, Eric Victor [Sandia National Laboratories (SNL↗

Software Defined Architectures for Portability and Performance

The Software Defined Architectures for Portability and Performance (SODAPOP) project developed a co-design framework to partition and map converged applications on specialized heterogeneous architectures. We started from key domain applications that combine scientific simulation with data analytics and machine learning as drivers to integrate our framework. The framework includes high-level compilers that interfaces with high-level programming frameworks, domain-specific optimization passes, and hardware-oriented optimizations. The framework leverages hardware generators to enable specialization and facilitate exploration of custom system designs.

97 MATHEMATICS AND COMPUTING↗

Identifying geochemical hot moments and their controls on a contaminated river floodplain system using wavelet and entropy approaches, Environmental modelling & software: Dataset

We used entropy and wavelet techniques to identify temporal variability in geochemical constituents and their controls along three transects within a contaminated floodplain system near Rifle CO. The objectives of this study were to: (1) identify hot moments of conservative and redox sensitive species as short time-periods with disproportionally high levels of concentration, and (ii) associate the transport and/or biogeochemical factors controlling this temporal variability. This data package includes tables from Arora et al. 2016a: Identifying geochemical hot moments and their controls on a contaminated river floodplain system using wavelet and entropy approaches, Environmental modelling & software, 85, 27-41. In particular, files include sampling frequency for geochemical data at the Rifle site, and results of entropy analysis.

54 ENVIRONMENTAL SCIENCES↗

Experimental Data Curation at Large Instrument Facilities with Open Source Software

The National Synchrotron Light Source II operating at Brookhaven National Laboratory since 2014 for the US Department of Energy is one of the newest and brightest storage-ring synchrotron facility in the world. NSLS-II, like other facilities, provides pre-processing of the raw data and some analysis capabilities to its users. We describe the research collaborations and open source infrastructure developed at large instrument facilities such as NSLS-II for the purpose of curating high value scientific data along the early stages of the data lifecycle. Data acquisition and curation tasks include storing experiment configuration, detector metadata, raw data acquisition with infrastructure that converts proprietary instrument formats to industry standards. In addition, we describe a specific effort for discovering sample information at NSLS-II and tracing the provenance of analysis performed on acquired images. We show that curation tasks must be embedded into software along the data life cycle for effectiveness and ease of use, and that loosely defined collaborations evolve around shared open source tools. Finally we discuss best practices for experimental metadata capture in such facilities, data access and the new challenges of scale and complexity posed by AI-based discovery for the synthesis of new materials.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Mitiq: A software package for error mitigation on noisy quantum computers

We introduce Mitiq, a Python package for error mitigation on noisy quantum computers. Error mitigation techniques can reduce the impact of noise on near-term quantum computers with minimal overhead in quantum resources by relying on a mixture of quantum sampling and classical post-processing techniques. Mitiq is an extensible toolkit of different error mitigation methods, including zero-noise extrapolation, probabilistic error cancellation, and Clifford data regression. The library is designed to be compatible with generic backends and interfaces with different quantum software frameworks. We describe Mitiq using code snippets to demonstrate usage and discuss features and contribution guidelines. We present several examples demonstrating error mitigation on IBM and Rigetti superconducting quantum processors as well as on noisy simulators.

97 MATHEMATICS AND COMPUTING↗

Social Network Analysis in R: A Software Review

In education research, social network analysis is being widely used to study different interactions and their overall implications. Recently, there has also been a surge in the development of software tools to implement social network analysis. In this article, we review two popular R packages, igraph and statnet suite, in the context of network summarization and modeling. We discuss different aspects of these packages and demonstrate some of their functionalities by analyzing a friendship network of lawyers. Finally, we end with recommendations for using these packages along with pointers to additional resources for network analysis in R.

97 MATHEMATICS AND COMPUTING↗

Combining On-Line Characterization Tools with Modern Software Environments for Optimal Operation of Polymerization Processes

Here, this paper discusses the initial steps towards the formulation and implementation of a generic and flexible model centric framework for integrated simulation, estimation, optimization and feedback control of polymerization processes. For the first time it combines the powerful capabilities of the automatic continuous on-line monitoring of polymerization system (ACOMP), with a modern simulation, estimation and optimization software environment towards an integrated scheme for the optimal operation of polymeric processes. An initial validation of the framework was performed for modelling and optimization using literature data, illustrating the flexibility of the method to apply under different systems and conditions. Subsequently, off-line capabilities of the system were fully tested experimentally for model validations, parameter estimation and process optimization using ACOMP data. Experimental results are provided for free radical solution polymerization of methyl methacrylate.

42 ENGINEERING↗

Atmospheric Transmission Spectroscopy of Hot Jupiter KELT-10b using Synthetic Telluric Correction Software

High-resolution spectroscopic visible data were obtained with the Ultraviolet and Visible Echelle Spectrograph on the Very Large Telescope. Our goal was to analyze the data in an effort to detect the presence of sodium in the atmosphere of hot Jupiter exoplanet KELT-10b, as well as characterize the orbit of the planet via the Rossiter-McLaughlin effect. Eighty spectra were collected during a single transit of KELT-10b. After standard spectroscopic calibration using ESO-Reflex, the synthetic telluric modeling software molecfit was applied to remove terrestrial atmospheric effects, and to refine the wavelength calibration. Sodium is recognized by its characteristic absorption doublet located at 5895.924 and 5889.951 Å, which can be seen in the planet atmosphere transmission spectrum and through excess absorption during the transit. The radial velocity of the host star was analyzed by measuring the average shift of absorption features from spectrum to spectrum. Our results indicate a sodium detection in the planet transmission spectrum with a line contrast of 0.66% and 0.43% ± 0.09% for the sodium DII and DI lines, respectively. Excess absorption measurements agree to within one half combined standard deviation between the planet transmission spectrum (0.143% ± 0.020%, a 7σ detection) and during the time series (0.124% ± 0.034%, a 3.6σ detection) in a band 1.25 Å wide. The wavelength grid corrections provided by molecfit were insufficient to determine radial velocities and measure the Rossiter-McLaughlin effect.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Heat Pump Retrofits for Central Plant Hydronic Heating Systems: A Software Toolkit for Screening and Design

Retrofitting existing central plants with high-efficiency heat pump technologies can play a crucial role in achieving long-term planning goals. Modern heat pump technologies are able to use waste heat recovery to meet a building's heating demand, but there is a lack of accessible tools designed for non-HVAC experts, such as building owners, to quickly and easily conduct what-if analysis, e.g., estimating retrofit costs and payback period for their partial or full equipment replacement. This paper introduces an open-source software toolkit designed to facilitate the initial screening and decision-making of heat pump retrofits in existing central plants using a building's yearly load profile from metered or utility bill data. The toolkit evaluates the technical and economic viability of replacing traditional central plant equipment with various options including water-to-water or air-to-water heat pumps, which can provide efficient and lower-cost heating and cooling. It allows users to compare current central plant configurations with retrofit scenarios, assessing energy consumption, life-cycle costs, and environmental impact. The toolkit offers (1) a web-based tool designed for user-friendly access by a broad audience and (2) Python-based source code for researchers and engineers conducting parametric studies and design parameter optimization. The toolkit compares a typical central plant configuration to a configuration that uses a heat pump to supply hydronic heating and cooling. The output metrics include energy consumption and output of each equipment, life-cycle cost analyses and metrics, and environmental impact of the system.

Excell, L↗

PlantCV v2: Image analysis software for high-throughput plant phenotyping

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring MDSplus data-acquisition software and custom devices

MDSplus is a software tool designed for data acquisition, storage, and analysis of complex scientific experiments. Over the years, MDSplus has primarily been used for data management for fusion experiments. This paper demonstrates that MDSplus can be used for a much wider variety of systems and experiments. We present a step-by-step tutorial describing how to create a simple experiment, manage the data, and analyze it using MDSplus and Python. To this end, a custom example device was developed to be used as the data source. This device was built on an opensource electronic hardware platform, and it consists of a microcontroller and two sensors. We read data from these sensors, store it in MDSplus, and use JupyterLab to visualize and process it. This project and code demo are available on the GitHub site at this URL: https://github.com/santorofer/MDSplusAndCustomeDevices

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NO$\nu$A Data Acquisition Software System

NO{nu}A is an accelerator-based neutrino oscillation experiment which has a great potential to measure the last unknown mixing angle {theta}{sub 13}, the neutrino mass hierarchy, and the CP-violation phase in lepton sector with (1) 700 kW beam, (2) 14 mrad off the beam axis, (3) 810 km long baseline. The Near Detector on the Surface is fully functioning and taking both NuMI and Booster beam data. The far detector building achieved beneficial occupancy on April 13. This proceeding will focus on the DAQ software system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Software Development for a CompactRIO-Based Wire Scanner Control and Data Acquisition SYstem

The Beam Diagnostics and Instrumentation Team at the Los Alamos Neutron Science Center is developing a wire scanner data acquisition and control system with a National Instrument's compactRIO at its core. For this application, the compactRIO controller not only requires programming the FPGA and RT computer internal to the compactRIO, but also requires programming a client computer and a touch panel display. This article will summarize the hardware interfaces and describe the software design approach utilized for programming and interfacing the four systems together in order to fulfill the design requirements and promote reliable interoperability.

42 ENGINEERING↗

A Tunable, Software-based DRAM Error Detection and Correction Library for HPC

Proposed exascale systems will present a number of considerable resiliency challenges. In particular, DRAM soft-errors, or bit-flips, are expected to greatly increase due to the increased memory density of these systems. Current hardware-based fault-tolerance methods will be unsuitable for addressing the expected soft error frequency rate. As a result, additional software will be needed to address this challenge. In this paper we introduce LIBSDC, a tunable, transparent silent data corruption detection and correction library for HPC applications. LIBSDC provides comprehensive SDC protection for program memory by implementing on-demand page integrity verification. Experimental benchmarks with Mantevo HPCCG show that once tuned, LIBSDC is able to achieve SDC protection with 50\% overhead of resources, less than the 100\% needed for double modular redundancy.

99 GENERAL AND MISCELLANEOUS↗

Decision-Support Software for Grid Operators: Transmission Topology Control for Infrastructure Resilience to the Integration of Renewable Generation

GENI Project: The CRA team is developing control technology to help grid operators more actively manage power flows and integrate renewables by optimally turning on and off entire power lines in coordination with traditional control of generation and load resources. The control technology being developed would provide grid operators with tools to help manage transmission congestion by identifying the facilities whose on/off status must change to lower generation costs, increase utilization of renewable resources and improve system reliability. The technology is based on fast optimization algorithms for the near to real-time change in the on/off status of transmission facilities and their software implementation.

ARPA-E↗