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DOE OSTI2024

Application of performance portability solutions for GPUs and many-core CPUs to track reconstruction kernels

Next generation High-Energy Physics (HEP) experiments are presented with significant computational challenges, both in terms of data volume and processing power. Using compute accelerators, such as GPUs, is one of the promising ways to provide the necessary computational power to meet the challenge. The current programming models for compute accelerators often involve using architecture-specific programming languages promoted by the hardware vendors and hence limit the set of platforms that the code can run on. Developing software with platform restrictions is especially unfeasible for HEP communities as it takes significant effort to convert typical HEP algorithms into ones that are efficient for compute accelerators. Multiple performance portability solutions have recently emerged and provide an alternative path for using compute accelerators, which allow the code to be executed on hardware from different vendors. We apply several portability solutions, such as Kokkos, SYCL, C++17 std::execution::par and Alpaka, on two mini-apps extracted from the mkFit project: p2z and p2r. These apps include basic kernels for a Kalman filter track fit, such as propagation and update of track parameters, for detectors at a fixed z or fixed r position, respectively. The two mini-apps explore different memory layout formats. We report on the development experience with different portability solutions, as well as their performance on GPUs and many-core CPUs, measured as the throughput of the kernels from different GPU and CPU vendors such as NVIDIA, AMD and Intel.

Kwok, Ka Martin↗

DOE OSTI2024

UN-SiC TRISO Post Irradiation Examination Developmental Work

As part of efforts to strengthen INL?s post irradiation analysis capabilities with non-Advanced Gas Reactor (AGR) tristructural isotropic (TRISO) fuels, two developmental activities were conducted. The first activity was to determine how best to analyze uranium nitride TRISO fuel kernels using electron probe microanalysis, while the second activity focused on developing a method to deconsolidate TRISO fuel particles that have been encased in a silicon carbide matrix. Because these two activities were unrelated, they have been presented separately in this report. Initial EPMA analyses showed nitrogen contents that far exceeded the concentration expected for UN--a line compound. Further examination showed that current literature values for the mass absorption coefficient (MAC) for the N ka X-ray absorbed by U ranged from approximately 1600 to 9500, with most values tending toward 9500. Measuring UN with five different progressively increasing accelerating voltages followed by using the modeling program xMAC suggests the actual MAC is approximately 2115. Additional MAC modifications were required to produce reasonable analytical results. Because of the inaccuracies of necessary MAC coefficients, UN analysis via scanning electron microscopy (SEM) is likely to produce inaccurate results. This is because SEM software does not typically allow the user to alter MACs. Tests have been performed to examine the feasibility of an electrochemical technique to liberate irradiated TRISO fuel from a SiC matrix without damaging the outer pyrolytic carbon layer of the fuel particle. The method is performed by electrochemically exposing the SiC to magnesium metal forming Mg2Si and C. Following exposure, the small SiC samples showed slight mass increases with no evidence of conversion to Mg2Si and C nor obvious degradation of the SiC samples.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

How does C-VIEW image quality compare with conventional 2D FFDM?

Purpose: The FDA approved the use of digital breast tomosynthesis (DBT) in 2011 as an adjunct to 2D full field digital mammography (FFDM) with the constraint that all DBT acquisitions must be paired with a 2D image to assure adequate interpretative information is provided. Recently manufacturers have developed methods to provide a synthesized 2D image generated from the DBT data with the hope of sparing patients the radiation exposure from the FFDM acquisition. While this much needed alternative effectively reduces the total radiation burden, differences in image quality must also be considered. The goal of this study was to compare the intrinsic image quality of synthesized 2D C-VIEW and 2D FFDM images in terms of resolution, contrast, and noise. Methods: Two phantoms were utilized in this study: the American College of Radiology mammography accreditation phantom (ACR phantom) and a novel 3D printed anthropomorphic breast phantom. Both phantoms were imaged using a Hologic Selenia Dimensions 3D system. Analysis of the ACR phantom includes both visual inspection and objective automated analysis using in-house software. Analysis of the 3D anthropomorphic phantom includes visual assessment of resolution and Fourier analysis of the noise. Results: Using ACR-defined scoring criteria for the ACR phantom, the FFDM images scored statistically higher than C-VIEW according to both the average observer and automated scores. In addition, between 50% and 70% of C-VIEW images failed to meet the nominal minimum ACR accreditation requirements—primarily due to fiber breaks. Software analysis demonstrated that C-VIEW provided enhanced visualization of medium and large microcalcification objects; however, the benefits diminished for smaller high contrast objects and all low contrast objects. Visual analysis of the anthropomorphic phantom showed a measureable loss of resolution in the C-VIEW image (11 lp/mm FFDM, 5 lp/mm C-VIEW) and loss in detection of small microcalcification objects. Spectral analysis of the anthropomorphic phantom showed higher total noise magnitude in the FFDM image compared with C-VIEW. Whereas the FFDM image contained approximately white noise texture, the C-VIEW image exhibited marked noise reduction at midfrequency and high frequency with far less noise suppression at low frequencies resulting in a mottled noise appearance. Conclusions: Their analysis demonstrates many instances where the C-VIEW image quality differs from FFDM. Compared to FFDM, C-VIEW offers a better depiction of objects of certain size and contrast, but provides poorer overall resolution and noise properties. Based on these findings, the utilization of C-VIEW images in the clinical setting requires careful consideration, especially if considering the discontinuation of FFDM imaging. Not explicitly explored in this study is how the combination of DBT + C-VIEW performs relative to DBT + FFDM or FFDM alone.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Quantitative Imaging with a Mobile Phone Microscope

Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone–based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Flash-X: A multiphysics simulation software instrument

Flash-X is a highly composable multiphysics software system that can be used to simulate physical phenomena in several scientific domains. It derives some of its solvers from FLASH, which was first released in 2000. Flash-X has a new framework that relies on abstractions and asynchronous communications for performance portability across a range of increasingly heterogeneous hardware platforms. Flash-X is meant primarily for solving Eulerian formulations of applications with compressible and/or incompressible reactive flows. It also has a built-in, versatile Lagrangian framework that can be used in many different ways, including implementing tracers, particle-in-cell simulations, and immersed boundary methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Enabling kilometer-scale E3SM land model simulation over North America: A new integrated framework solution

This study introduces a novel framework designed to enhance the performance, scalability, and portability of the kilometer-scale E3SM Land Model (km-ELM) within the E3SM modeling infrastructure. By seamlessly integrating cutting-edge data tools, we address existing challenges such as slow performance, limited scalability, and difficulties in software integration in current data-driven ELM simulation over large geographic areas. Our innovative approach leverages the KiloCraft data toolkit to generate unified inputs for simulations ranging from a single-cite case, to a 72,083-cell regional case to a continental configuration encompassing 21.6 million land grid cells at a 1 km × 1 km resolution. We conduct extensive strong- and weak-scaling experiments on three state-of-the-art supercomputers, utilizing up to 100,800 CPU cores across 2400 compute nodes to evaluate end-to-end metrics including wall-clock time, simulation-years-per-day (SYPD), initialization costs, and I/O throughput. Our results reveal the land (LND) component’s efficient scaling, demonstrating near-ideal weak scaling and strong-scaling parallel efficiencies reaching up to 87% at 50,400 cores. We confirm portability and reproducibility through bitwise-equivalent outputs across different machines using identical inputs over supported machines. Notably, at extreme scales, we identify I/O as a critical bottleneck and that leads to effective solution with the SCORPIO/ADIOS stack. Collectively, these findings validate the deployment of km-ELM at a continental scale with high parallel efficiency and provide essential guidance on configuration, decomposition, and I/O settings for optimized kilometer-scale land simulations in E3SM. This work emphasizes the innovative design and practical solutions that enhance the operational capabilities of km-ELM, focusing on software performance and scalability while leaving detailed scientific evaluations of simulated land processes for future investigations.

E3SM land model (ELM), km-ELM, scalability, perfor↗

DOE OSTI2017

Informed-Proteomics: open-source software package for top-down proteomics

Top-down proteomics involves the analysis of intact proteins. This approach is very attractive as it allows for analyzing proteins in their endogenous form without proteolysis, preserving valuable information about post-translation modifications, isoforms, proteolytic processing or their combinations collectively called proteoforms. Moreover, the quality of the top-down LC-MS/MS datasets is rapidly increasing due to advances in the liquid chromatography and mass spectrometry instrumentation and sample processing protocols. However, the top-down mass spectra are substantially more complex compare to the more conventional bottom-up data. To take full advantage of the increasing quality of the top-down LC-MS/MS datasets there is an urgent need to develop algorithms and software tools for confident proteoform identification and quantification. In this study we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer. The presented tool along with several other popular tools were evaluated using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2024

Guest Editorial

The design of X-ray optical systems is very different from that of conventional optical systems, whether it be for the peculiarities of synchrotron radiation or the grazing incidence operation of most X-ray optical components. Further, specific simulation tools are thus required to ensure that designs work as expected, and there is now a vibrant landscape of open-source, freely available software that can be used to that end, and explore new design concepts.

47 OTHER INSTRUMENTATION↗

DOE OSTI2017

Big Data in HEP: A comprehensive use case study

Experimental Particle Physics has been at the forefront of analyzing the worlds largest datasets for decades. The HEP community was the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems collectively called Big Data technologies have emerged to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and promise a fresh look at analysis of very large datasets and could potentially reduce the time-to-physics with increased interactivity. In this talk, we present an active LHC Run 2 analysis, searching for dark matter with the CMS detector, as a testbed for Big Data technologies. We directly compare the traditional NTuple-based analysis with an equivalent analysis using Apache Spark on the Hadoop ecosystem and beyond. In both cases, we start the analysis with the official experiment data formats and produce publication physics plots. Lastly, we will discuss advantages and disadvantages of each approach and give an outlook on further studies needed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

SU-E-T-418: Explore the Sensitive of the Planar Quality Assurance to the MLC Error with Different Beam Complexity in Intensity-Modulate Radiation Therapy

Purpose: The purpose of this study is to investigate the sensitivity of the planar quality assurance to MLC errors with different beam complexities in intensity-modulate radiation therapy. Methods: sixteen patients’ planar quality assurance (QA) plans in our institution were enrolled in this study, including 10 dynamic MLC (DMLC) IMRT plans measured by Portal Dosimetry and 6 static MLC (SMLC) IMRT plans measured by Mapcheck. The gamma pass rate was calculated using vender’s software. The field numbers were 74 and 40 for DMLC and SMLC, respectively. A random error was generated and introduced to these fields. The modified gamma pass rate was calculated by comparing the original measured fluence and modified fields’ fluence. A decreasing gamma pass rate was acquired using the original gamma pass rate minus the modified gamma pass rate. Eight complexity scores were calculated in MATLAB based on the fluence and MLC sequence of these fields. The complexity scores include fractal dimension, monitor unit of field, modulation index, fluence map complexity, weighted average of field area, weighted average of field perimeter, and small aperture ratio ( <5cm{sup 2} and <50cm{sup 2}). The Spearman’s rank correlation coefficient was implemented to analyze the correlation between these scores and decreasing gamma rate. Results: The relation between the decreasing gamma pass rate and field complexity was insignificant for most complexity scores. The most significant complexity score was fluence map complexity for SMLC, which have ρ =0.4274 (p-value=0.0063). For DMLC, the most significant complex score was fractal dimension, which have ρ=−0.3068 (p-value=0.0081). Conclusions: According to the primarily Result of this study, the sensitivity gamma pass rate was not strongly relate to the field complexity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Two-Photon Absorption of Nonchain HF Laser Radiation in Germanium Single Crystals

Some results of experimental and numerical studies on the transmission of a nonchain high-frequency (HF) laser beam through germanium (Ge) single crystals of differing thickness and specific resistance are presented. Based on the experimental data for the HF(DF) lasing spectrum, the coefficient of two-photon absorption in germanium has been estimated as K{sub 2} = 55 ± 10 cm/GW at λ = 2.8 μm. The results are in good agreement with theory. The developed experimental data-processing software has enabled the numerical study of the transmission of a high-power beam with λ = 2.6–3 μm through Ge at any laser-pulse-impact moment. It has been shown that thin germanium coatings can efficiently smoothen the distribution of energy over the beam aperture for high-power laser radiation with λ = 2.6–4 μm.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Design, Integration and Synthesis Platform to Advance Tightly Coupled Hybrid Energy Systems (DISPATCHES) v0.1.0

The DISPATCHES software will enable the design and optimization of Integrated Energy Systems (IES). The platform will support hybridizing existing generation facilities (such as nuclear and coal plants) as well as greenfield hybrid designs that incorporate advanced technologies (such as Advanced Modular Reactors and Coal FIRST), and it will enable the consideration of multiple technology options with different time constants. The design of the IES will be optimized for operation within the bulk power system via energy market signals (day ahead, real-time, and ancillary services) obtained from a production cost model. The goal of DISPATCHES is to identify flexible, dynamic designs that are responsive to grid market signals resulting in highly efficient, cost effective tightly coupled hybrid energy systems that can act as a "black box" to the grid to provide increased flexibility and resiliency.

Gunter, Daniel↗

DOE OSTI2023

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Imaging effectiveness calculator for non-design microscope samples

When attempting to integrate single-molecule fluorescence microscopy with microfabricated devices such as microfluidic channels, fabrication constraints may prevent using traditional coverslips. Instead, the fabricated devices may require imaging through material with a different thickness or index of refraction. Altering either can easily reduce the quality of the image formation (measured by the Strehl ratio) by a factor of 2 or more, reducing the signal-to-noise ratio accordingly. In such cases, successful detection of single-molecule fluorescence may prove difficult or impossible. Furthermore, we provide software to calculate the effect of non-design materials upon the Strehl ratio or ensquared energy and explore the impact of common materials used in microfabrication.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

AmeriFlux FLUXNET-1F US-VT1 Vermillion Tributary Paired Cropland – Site 1 (Corn/Soy; No Cover Crops)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-VT1 Vermillion Tributary Paired Cropland – Site 1 (Corn/Soy; No Cover Crops). This is the FLUXNET version of the carbon flux data for the site US-VT1 Vermillion Tributary Paired Cropland – Site 1 (Corn/Soy; No Cover Crops) produced by applying the standard ONEFlux (1F) software. Site Description - US-VT1 is located on flat, actively managed farmland operated by working farmers, following a conventional no-till corn–soybean rotation in the U.S. Midwest. US-VT1 is one of two paired working farm sites on the same property; both are managed using similar conventional practices, with the key difference being that the paired site (US-VT2) incorporates cover crops into its rotation. This paired design enables direct site-to-site comparisons to assess the impacts of cover cropping on carbon, water, and energy fluxes.

Key, Kesondra [Indiana University - Bloomington]↗

DOE OSTI2017

Operation of the NSLS-II Injector with a Lower Booster Injection Energy

The NSLS-II injector consists of a 200 MeV linac and a 3 GeV full-energy booster synchrotron. The linac contains five traveling-wave S-band accelerating structures driven by two high-power klystrons. Optimization of the NSLS-II injector has continued since user operation started in October 2014. Beam losses have been minimized by the injector tuning and stabilization, and high level software has been developed to characterize the booster and injection parameters. However, due to the recently increased frequency of klystrons arcing which shortens the lifetime of the klystron, operation of the linac with lowered klystron output power would allow injection to be maintained with fewer trips and extended lifetime of klystrons. Apart from the energy difference, the low energy klystron operation is quite similar to the nominal 200 MeV operation. Injection trials were carried out with scaled magnet settings of the linac, linac-to- booster (LtB) transport line, and the booster. The beam was successfully injected into the booster on May 31, 2017 at the low energy mode of the 170 MeV LtB injection. Overall transfer efficiency from the linac to the storage ring is identical to the standard 200 MeV operation. The 170 MeV injection mode has been adopted in NSLS-II user operation ever since the beam study. In the most recent injector studies on June 28 and July 3, 2017, the booster injection energy was further decremented to the final target value of 100 MeV via applying the same method established in the 170 MeV operation. The ultimate value of 100 MeV is determined by the special requirement of operating the injector at single klystron while repairing the other klystron or with two klystrons with significantly reduced outputs for the purpose of maximizing klystron lifetimes.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Rapid Gamma Simulations of TRISO Fuel Elements

As energy demand rises, nuclear energy, particularly from reactors that use tristructural isotropic (TRISO) fuels, has gained attention due to the fuel’s enhanced resistance to radiation damage and high temperatures. This report investigates the modeling capabilities of the Gamma Detector Response and Analysis Software (GADRAS) for TRISO fuels, focusing on the gamma signatures of TRISO particles, which have not been extensively explored. Using the Monte Carlo N-Particle (MCNP) code as a benchmark, we developed both homogeneous and heterogeneous models of TRISO pebbles to analyze gamma spectra. Our findings reveal that the homogeneous and heterogeneous models produced different gamma signatures. Additionally, the GADRAS heterogeneous model significantly reduces computation times compared to MCNP, enabling effective modeling of gamma signatures for safeguards applications. This advancement is essential for the International Atomic Energy Agency (IAEA) in detecting anomalies and potential smuggling attempts in TRISO reactor fuel elements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

The Analysis Description Language Ecosystem: Latest developments and physics applications

We present latest developments in Analysis Description Language (ADL), a declarative domain-specific language describing the physics algorithm of a HEP data analysis decoupled from software frameworks. Analyses written in ADL can be integrated into any framework for various tasks. ADL is a multipurpose construct with uses ranging from analysis design to preservation, reinterpretation, queries, visualisation, combination, etc. The most advanced infrastructure to execute ADL on events is the CutLang runtime interpreter. Recent technical developments include an automated interface with different data types, generation of the abstract syntax tree, a visualization tool that that auto-converts analysis flows to graphs, incorporation of trained machine learning models and a Jupyter-based plotting tool. We also report physics implications including a large scale LHC analysis implementation and validation effort for beyond the standard model reinterpretation purposes and studies with ATLAS and CMS open data.

Sekmen, Sezen [Kyungpook National Univ., Daegu (Ko↗