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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

The high level trigger and express data production at STAR

To meet the demands of the Beam Energy Scan phase-II (BES-II) program, the STAR experiment at the Relativistic Heavy Ion Collider (RHIC) developed a dual real-time framework consisting of a High Level Trigger (HLT) and an Express Data Production system (xProduction). The HLT operates online within the Data Acquisition (DAQ) chain on a dedicated multi-core CPU cluster with the option to offload compute-intensive kernels to Xeon Phi coprocessors. It uses parallelized algorithms, such as the Cellular Automaton (CA) Track Finder, to perform rapid tracking, vertexing, and event filtering. This allows it to select events of interest in real time and provide immediate feedback on detector and beam conditions. In contrast, the xProduction workflow runs concurrently and independently of the DAQ loop. It applies near offline-quality calibration and reconstruction within hours of data collection. The xProduction input is the express data stream, whose content can be enriched by HLT trigger/priority selections under DAQ/HLT resource constraints, and it uses the STAR calibration/conditions framework, incorporating online calibration/QA information when available. This enables early preliminary physics analysis, including the reconstruction of rare signals, such as hyperons and hypernuclei. It also provides collaboration-wide access to analysis-ready datasets. Together, the HLT and xProduction systems form a complementary architecture: the HLT performs online event selection while the xProduction chain delivers high-quality results within a short amount of time. This integrated framework has enabled the prompt reconstruction of the $^5_Λ$ He hypernucleus with high statistical significance and the efficient processing of hundreds of millions of heavy-ion collision events. In conclusion, its demonstrated scalability and robustness establish a model for future high-luminosity experiments requiring both online event filtering and rapid access to analysis-quality data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Quantification of electron correlation for approximate quantum calculations

State-of-the-art many-body wave function techniques rely on heuristics to achieve high accuracy at an attainable computational cost to solve the many-body Schrödinger equation. By far, the most common property used to assess accuracy has been the total energy; however, total energies do not give a complete picture of electron correlation. In this work, we assess the von Neumann entropy of the one-particle reduced density matrix (1-RDM) to compare selected configuration interaction (CI), coupled cluster, variational Monte Carlo, and fixed-node diffusion Monte Carlo for benchmark hydrogen chains. A new algorithm, the circle reject method, is presented, which improves the efficiency of evaluating the von Neumann entropy using quantum Monte Carlo by several orders of magnitude. The von Neumann entropy of the 1-RDM and the eigenvalues of the 1-RDM are shown to distinguish between the dynamic correlation introduced by the Jastrow and the static correlation introduced by determinants with large weights, confirming some of the lore in the field concerning the difference between the selected CI and Slater–Jastrow wave functions.

Chemistry↗
DOE OSTI2024

Smart pixel sensors: towards on-sensor filtering of pixel clusters with deep learning

Highly granular pixel detectors allow for increasingly precise measurements of charged particle tracks. Next-generation detectors require that pixel sizes will be further reduced, leading to unprecedented data rates exceeding those foreseen at the High- Luminosity Large Hadron Collider. Signal processing that handles data incoming at a rate of $\mathcal{O}$(40 MHz) and intelligently reduces the data within the pixelated region of the detector at rate will enhance physics performance at high luminosity and enable physics analyses that are not currently possible. Using the shape of charge clusters deposited in an array of small pixels, the physical properties of the traversing particle can be extracted with locally customized neural networks. In this first demonstration, we present a neural network that can be embedded into the on-sensor readout and filter out hits from low momentum tracks, reducing the detector's data volume by 57.1%–75.7%. The network is designed and simulated as a custom readout integrated circuit with 28 nm CMOS technology and is expected to operate at less than 300 μW with an area of less than 0.2 mm 2 . The temporal development of charge clusters is investigated to demonstrate possible future performance gains, and there is also a discussion of future algorithmic and technological improvements that could enhance efficiency, data reduction, and power per area.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Clustering at Massive Scale

ClaMS provides hierarchical clustering technology for use on massive, high-dimensional datasets that require distributed memory for processing. The algorithm employed is inspired by the popular HDBSCAN algorithm but makes use of computational kernels better suited for distributed computing. ClaMS is built on scalable nearest neighbor graph construction, metric forest completion, and approximate minimum spanning tree techniques.

Stanley, ThomasA [Lawrence Livermore National Labo↗
NASA NTRS2024

Smallsat 2024 - Starling Cubesat Swarm Technology Demonstration Flight Results

The Starling swarm of four 6U CubeSats launched in July 2023 to test four key technologies to enable future swarm missions: 1) Mobile Ad-Hoc Networking (MANET) over a crosslink radio network 2) Autonomous onboard decision-making for operations 3) Optical-based absolute and relative navigation 4) Autonomous maneuver planning and execution The Starling team implemented the Better Approach to Mobile Ad-hoc Networking (B.A.T.M.A.N.) protocol to automatically manage the crosslink network of four satellites. The B.A.T.M.A.N. protocol uses a decentralized approach to managing a multi-hop mesh network of devices, in this case, a satellite swarm. The four satellites were able to successfully establish a network at multiple data rates and demonstrate file transfer and command issuance between spacecraft over the network. Starling incorporated Distributed Spacecraft Autonomy's (DSA) software to demonstrate onboard decision-making. The DSA software takes L1/L2 band GPS measurements and uses them to estimate the relative Total Electron Count (TEC) in the ionosphere. The onboard software then determines if there are any features of interest and provides that information to the other satellites over the crosslink network. The swarm of satellites then reaches a consensus on the optimal TEC observation strategy and adjusts its measurement collection tactics autonomously. The Starling Formation-Flying Optical Experiment (StarFOX), produced by Stanford's Space Rendezvous Laboratory, uses the onboard star trackers to collect images of the other swarm spacecraft and produce angles-only navigation estimates. This system is envisioned to be valuable in applications in which Global Navigation Satellite Systems (GNSS) are not available, such as in cis-lunar or deep space. StarFOX successfully applied its algorithms to multiple simultaneous spacecraft targets using the star tracker imagery. Finally, Starling used Emergent Space's Cluster Flight Application (CFA) software suite for the Reconfiguration and Orbit Maintenance Experiments Onboard (ROMEO) demonstration of autonomously planning and executing propulsive maneuvers. Large swarms will need to be able to maintain formation requirements with minimal operator involvement, especially as the size of the swarm scales up. Results from the ROMEO experiment are presented. Starling is funded by the Small Spacecraft Technology (SST) program out of NASA's Space Technology Mission Directorate (STMD).

distributed systems↗
DOE OSTI2021

Neutrino event selection in the MicroBooNE liquid argon time projection chamber using Wire-Cell 3D imaging, clustering, and charge-light matching

An accurate and efficient event reconstruction is required to realize the full scientific capability of liquid argon time projection chambers (LArTPCs). The current and future neutrino experiments that rely on massive LArTPCs create a need for new ideas and reconstruction approaches. Wire-Cell, proposed in recent years, is a novel tomographic event reconstruction method for LArTPCs. The Wire-Cell 3D imaging approach capitalizes on charge, sparsity, time, and geometry information to reconstruct a topology-agnostic 3D image of the ionization electrons prior to pattern recognition. A second novel method, the many-to-many charge-light matching, then pairs the TPC charge activity to the detected scintillation light signal, thus enabling a powerful rejection of cosmic-ray muons in the MicroBooNE detector. A robust processing of the scintillation light signal and an appropriate clustering of the reconstructed 3D image are fundamental to this technique. In this paper, we describe the principles and algorithms of these techniques and their successful application in the MicroBooNE experiment. A quantitative evaluation of the performance of these techniques is presented. Using these techniques, a 95% efficient pre-selection of neutrino charged-current events is achieved with a 30-fold reduction of non-beam-coincident cosmic-ray muons, and about 80% of the selected neutrino charged-current events are reconstructed with at least 70% completeness and 80% purity.

3D imaging↗
NASA NTRS1995

Stereo-Based Region-Growing using String Matching

We present a novel stereo algorithm based on a coarse texture segmentation preprocessing phase. Matching is performed using a string comparison. Matching sub-strings correspond to matching sequences of textures. Inter-scanline clustering of matching sub-strings yields regions of matching texture. The shape of these regions yield information concerning object's height, width and azimuthal position relative to the camera pair. Hence, rather than the standard dense depth map, the output of this algorithm is a segmentation of objects in the scene. Such a format is useful for the integration of stereo with other sensor modalities on a mobile robotic platform. It is also useful for localization; the height and width of a detected object may be used for landmark recognition, while depth and relative azimuthal location determine pose. The algorithm does not rely on the monotonicity of order of image primitives. Occlusions, exposures, and foreshortening effects are not problematic. The algorithm can deal with certain types of transparencies. It is computationally efficient, and very amenable to parallel implementation. Further, the epipolar constraints may be relaxed to some small but significant degree. A version of the algorithm has been implemented and tested on various types of images. It performs best on random dot stereograms, on images with easily filtered backgrounds (as in synthetic images), and on real scenes with uncontrived backgrounds.

Mandelbaum, Robert↗
NASA NTRS1990

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

Dongarra, Jack↗
DOE OSTI2024

Forming a database to study reversed magnetic shear from the National Spherical Torus eXperiment using machine learning

Achieving a long-lived reversed magnetic shear (RMS) target plasma in the National Spherical Torus eXperiment Upgrade will require developing various sustainment scenarios. To help with the ongoing plasma control efforts, the development of a new analysis for the motional Stark effect (MSE) diagnostic using a machine learning algorithm, namely, MSE-ML, is described. MSE-ML will be used to identify patterns during RMS discharges, some of which suffer magnetohydrodynamic (MHD) events resulting in current redistribution and monotonic q-profiles. A database consisting of q and magnetic shear profiles is being constructed primarily based on the existing National Spherical Torus eXperiment data with equilibrium reconstructions constrained by the magnetic field pitch angle profile measured using the multi-channel MSE diagnostic. An unsupervised k-means clustering of the data is developed to study the RMS formation as a function of time. The initial clustering from the q-profiles shows significant differences in both amplitude and the duration of the RMS period. As a goal, the clustering results that detect and distinguish shots with substantial and sustained RMS are to be used as a preprocessing step in a supervised algorithm to identify the underlying conditions that lead to long-lasting improved confinement with RMS. Another aim of the MSE-ML study is to identify precursors of RMS-destroying MHD events in either derived data such as the q-profile or directly measured data such as the magnetic field pitch angle profile.

Uzun-Kaymak, I. U. (ORCID:0000000276251493)↗
DOE OSTI2022

Toward Accurate Modeling of Galaxy Clustering on Small Scales: Constraining the Galaxy-halo Connection with Optimal Statistics

Applying halo models to analyze the small-scale clustering of galaxies is a proven method for characterizing the connection between galaxies and their host halos. Such works are often plagued by systematic errors or limited to clustering statistics that can be predicted analytically. In this work, we employ a numerical mock-based modeling procedure to examine the clustering of Sloan Digital Sky Survey DR7 galaxies. We apply a standard halo occupation distribution (HOD) model to dark matter only simulations with a ΛCDM cosmology. To constrain the theoreStical models, we utilize a combination of galaxy number density and selected scales of the projected correlation function, redshift-space correlation function, group multiplicity function, average group velocity dispersion, mark correlation function, and counts-in-cells statistics. We design an algorithm to choose an optimal combination of measurements that yields tight and accurate constraints on our model parameters. Compared to previous work using fewer clustering statistics, we find a significant improvement in the constraints on all parameters of our halo model for two different luminosity-threshold galaxy samples. Most interestingly, we obtain unprecedented high-precision constraints on the scatter in the relationship between galaxy luminosity and halo mass. However, our best-fit model results in significant tension (>4σ) for both samples, indicating the need to add second-order features to the standard HOD model. To guarantee the robustness of these results, we perform an extensive analysis of the systematic and statistical errors in our modeling procedure, including a first of its kind study of the sensitivity of our constraints to changes in the halo mass function due to baryonic physics.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2003

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗
DOE OSTI2021

Multi-channel Imager Algorithm (MIA): A novel cloud-top phase classification algorithm

The current Geostationary Operational Environmental Satellites (GOES-16 and 17) cloud-top phase classification algorithm is based primarily on empirical thresholds at multiple wavelengths that have varying absorption capabilities for water and ice. The performance of current GOES-16 cloud-top phase product largely depends on the accuracy of the selection of reflectance ratios. Here this study aims at presenting a novel cloud-top phase classification algorithm (the Multi-channel Imager Algorithm, MIA) that provides a more judicious selection of relationships between channels using a supervised K-mean clustering method on multi-channel Red-Green-Blue images. The K-mean clustering method works analogously to how human eyes separate different colors in a microphysical color rendering set of satellite images, which differentiates water, ice and unclassified thin clouds. For water phase, cloud-top temperature information is used to further distinguish supercooled water. To evaluate the performance of the MIA, an extensive comparison with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), Moderate Resolution Imaging Spectroradiometer, and current GOES-16 cloud-top phase products is conducted, using CALIOP as the benchmark. Compared to the current GOES-16 cloud-top phase product, MIA demonstrates a substantial improvement in phase classification, where hit rate increases from 69% to 76% over the Continental United States and 58% to 66% over the full disk domain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes

Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus’ genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Community detection in hypergraphs via mutual information maximization

Abstract The hypergraph community detection problem seeks to identify groups of related vertices in hypergraph data. We propose an information-theoretic hypergraph community detection algorithm which compresses the observed data in terms of community labels and community-edge intersections. This algorithm can also be viewed as maximum-likelihood inference in a degree-corrected microcanonical stochastic blockmodel. We perform the compression/inference step via simulated annealing. Unlike several recent algorithms based on canonical models, our microcanonical algorithm does not require inference of statistical parameters such as vertex degrees or pairwise group connection rates. Through synthetic experiments, we find that our algorithm succeeds down to recently-conjectured thresholds for sparse random hypergraphs. We also find competitive performance in cluster recovery tasks on several hypergraph data sets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

GPU-based Image Compression for Efficient Compositing in Distributed Rendering Applications

Visualizations of large-scale data sets are often created on graphics clusters that distribute the rendering task amongst many processes. When using real-time GPU-based graphics algorithms, the most time-consuming aspect of distributed rendering is typically the com-positing phase - combining all partial images from each rendering process into the final visualization. Compo siting requires image data to be copied off the GPU and sent over a network to other processes. While compression has been utilized in existing distributed rendering compositors to reduce the data being sent over the network, this compression tends to occur after the raw images are transferred from the GPU to main memory. In this paper, we present work that leverages OpenGL / CUDA interoperability to compress raw images on the GPU prior to transferring the data to main memory. This approach can significantly reduce the device-to-host data transfer time, thus enabling more efficient compositing of images generated by distributed rendering applications.

Lipinksi, Riley↗
DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Summer Proceedings 2019

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers and heterogeneous computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program includes the organization of a weekly seminar series and the publication of this summer proceedings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

CSRI Summer Proceedings 2020

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program is organized by CSRI and typically includes the organization of a weekly seminar series and the publication of a summer proceedings. In 2020, the CSRI summer program was executed completely virtually; all student interns worked from home, due to the COVID-19 pandemic.

97 MATHEMATICS AND COMPUTING↗