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At least 1,117 records · Page 62

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗

Uncertainty guided online ensemble for non-stationary data streams in fusion science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior with distribution drifts, resulted by both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with such non-stationary data streams. Online learning techniques have been leveraged in other domains, however it has been largely unexplored for fusion applications. In this paper, we investigate online learning for continuous adaptation to drifting data streams in the prediction of Toroidal Field (TF) coils deflection at the DIII-D fusion facility. We further address the short-term performance degradation inherent to standard online learning, which arises because ground truth is unavailable at prediction time. To mitigate this issue, we propose an uncertainty-guided online ensemble framework. The method leverages the Deep Gaussian Process Approximation (DGPA) for calibrated uncertainty estimation and uses these uncertainty measures to guide a meta-algorithm that aggregates predictions from learners trained over different historical horizons. Our results show that online learning reduces prediction error by 80% compared to a static model. The online ensemble and the proposed uncertainty-guided ensemble further reduce error by approximately 6%, and 10% respectively, relative to standard single-model online learning, while also providing calibrated uncertainty estimates to support operational decision-making.

AI↗

Radioisotope Identification with List-Mode Gamma-Ray Data

This work explores the potential of utilizing temporal data from gamma-ray detectors, known as list-mode data, to enhance radioisotope identification. Traditional identification methods, which rely on full gamma-ray spectrum analysis, often require long dwell times and struggle with spectra containing similarly spaced spectral peaks. We hypothesize that by leveraging the probabilistic nature of nuclear decay and the time-encoded information from decay sequences and interactions with surrounding materials, we can improve classification accuracy over static spectral analysis. This research examines the temporal content of list-mode data through exploratory data analysis via correlation discovery and qualitative distribution analysis. Additionally, we propose a probabilistic classification model that can utilize spectral data, temporal data, or both to determine if the incorporation of temporal information improves radioisotope identification. Our findings suggest that the temporal information present in list-mode gamma-ray data has merit and should be further investigated to develop more robust and optimal methods for utilizing this temporal information in applications requiring radioisotope identification.

List-mode data↗

Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems

Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.

59 BASIC BIOLOGICAL SCIENCES↗

Situational awareness-enhancing community-level load mapping with opportunistic machine learning

Motivated by present and forthcoming challenges in the adoption and integration of distributed renewable energy, we develop a machine learning (ML) approach that builds short-fuse mappings connecting the occasionally-unobservable true load in one target community with information-rich signals collected from relatively more instrumented reference communities. Our setting is inspired by and tailored to target communities with significant unobservable behind-the-meter solar generation, where true load (a relatively well-behaved quantity of interest to grid operators) is hard to discern during daytime due to insufficient instrumentation and/or privacy reasons, but that can be related to reference communities with low unobservable distributed variable generation or with sufficient instrumentation. The developed mapping, herein realized with Support Vector Machine regression, is built using nighttime data from all communities, when their distributed generation is low or zero. Our ML algorithm opportunistically learns to correlate signals of interest and then is operationally used the next day to shed light into target community load evolution. The mapping is subsequently rebuilt, rolling its short-fuse scope perpetually forward in time. Here, we demonstrate the efficacy of our approach on nine synthetically generated topologies and associated timeseries stemming from real-world data, on which we observe cumulative error performance that yields lower than 10% and 15% daily-averaged mean absolute percentage errors in target community load estimation on more than about 75% and 90% of days, respectively, in multiple yearly evaluations that shed light on long-term performance also under seasonal and one-off effects. The proposed ML-powered methodology can offer grid operators much-improved visibility into a previously obscure space and can also serve as an additional source of information in broader, multi-modal solar disaggregation solutions.

14 SOLAR ENERGY↗

GridDS: Data Science Toolkit for Energy Grid Data

According to the U.S. Energy Information Administration (EIA), the demand for energy is expected to increase 50% by the year 20501. While energy standards, such as the Institute of Electrical and Electronics Engineers (IEEE) Standard 1547, (Basso 2015) and monitoring with wide area management systems (WAMS) (Liu 2017, Zhou 2016) have enabled large scale data collection and storage, the application of this data in mitigating costs associated with increased consumer demand is an ongoing focus for energy research. This ubiquitous data collection presents a promising opportunity for machine learning and data science to improve efficiency of distributed energy resources (DERs). The GridDS software toolkit is designed to leverage advanced metering infrastructure (AMI), outage management systems data (OMS), Supervisory control Data Acquisition (SCADA), and geographic information systems (GIS) to forecast future energy demands and detect incipient grid failures. GridDS is a python software library designed to be modular and generalizable to data recorded by DERs. In adapting to disparate datasets recorded by various WAMS, GridDS provides a range of unique functionality not presently implemented in current WAMS which have highly specific software infrastructure by design. GridDS functionality ranges from data specification and preparation, to training and validation for state of the art machine learning, to interactive data visualization. For data intake, GridDS combines: Pandera: a library for creating data specifications. TimeScaleDB: a postgresSQL database infrastructure for efficient storage of timeseries data. Dataset class: A custom dataset class / interface that ensures modularity between a range of synthetic and live recorded datasets. Is

Ladd, Alexander↗

Cloud-based Testbed for Adaptive Under-Frequency Load Shedding with High DER Penetration

Increasing penetration of distributed energy resources and behind-the-meter renewables may soon disrupt the efficacy of critical protection schemes, such as under-frequency load shedding (UFLS). Improved data exchange and coordination across the transmission-distribution boundary will be required to maintain reliability of bulk electric system. Standards-based data integration platforms using agreed-upon semantic vocabularies, such as the Common Information Model, will be key to enabling adaptive protection schemes requiring synthesized data from both the bulk power system and behind-the-meter resources. This paper introduces a cloud-based open-source data integration environment and UFLS clustering algorithm being developed to enable adaptive relay coordination between transmission and distribution utilities in the state of Vermont.

Anderson, Alexander A.↗

PhytoOracle: Scalable, modular phenomics data processing pipelines

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

59 BASIC BIOLOGICAL SCIENCES↗

A robust synthetic data generation framework for machine learning in high-resolution transmission electron microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapid generation of complex nanoscale atomic structures which enables fast, systematic sampling of realistic nanomaterial structures and can be used as a random structure generator for large, diverse synthetic datasets. Using Construction Zone, we develop an end-to-end machine learning workflow for training neural network models to analyze experimental atomic resolution HRTEM images on the task of nanoparticle image segmentation purely with simulated databases. Further, we study the data curation process to understand how various aspects of the curated simulated data—including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions—affect model performance across three benchmark experimental HRTEM image datasets. Using our workflow, we are able to achieve state-of-the-art segmentation performance on these experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data. Construction Zone and its documentation are available at https://github.com/lerandc/construction_zone.

36 MATERIALS SCIENCE↗

Impact of jet-production data on the next-to-next-to-leading-order determination of HERAPDF2.0 parton distributions

The HERAPDF2.0 ensemble of parton distribution functions (PDFs) was introduced in 2015. The final stage is presented, a next-to-next-to-leading-order (NNLO) analysis of the HERA data on inclusive deep inelastic ep scattering together with jet data as published by the H1 and ZEUS collaborations. A perturbative QCD fit, simultaneously of $\alpha _s(M_Z^2)$ and the PDFs, was performed with the result $\alpha _s(M_Z^2)= 0.1156 \pm 0.0011~\mathrm{(exp)}~ ^{+0.0001}_{-0.0002}~ \mathrm{(model}$ $\mathrm{+ parameterisation)}~ \pm 0.0029~\mathrm{(scale)}$. The PDF sets of HERAPDF2.0Jets NNLO were determined with separate fits using two fixed values of $\alpha _s(M_Z^2)$, $\alpha _s(M_Z^2)$ = 0.1155 and 0.118, since the latter value was already chosen for the published HERAPDF2.0 NNLO analysis based on HERA inclusive DIS data only. The different sets of PDFs are presented, evaluated and compared. The consistency of the PDFs determined with and without the jet data demonstrates the consistency of HERA inclusive and jet-production cross-section data. The inclusion of the jet data reduced the uncertainty on the gluon PDF. Predictions based on the PDFs of HERAPDF2.0Jets NNLO give an excellent description of the jet-production data used as input.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

FTS3: Data Movement Service in containers deployed in OKD [Slides]

The File Transfer Service (FTS3) is a data movement service developed at CERN which is used to distribute the majority of the Large Hadron Collider's data across the Worldwide LHC Computing Grid (WLCG) infrastructure. At Fermilab, we have deployed FTS3 instances for Intensity Frontier experiments (e.g. DUNE) to transfer data in America and Europe, using a container-based strategy. In this article we summarize our experience building docker images based on work from the SLATE project (slateci.io) and deployed in OKD, the community distribution of Red Hat OpenShift. Additionally, we discuss our method of certificate management and maintenance utilizing Kubernetes CronJobs. Finally, we also report on the two different configurations currently running at Fermilab, comparing and contrasting a Docker-based OKD deployment against a traditional RPM-based deployment.

97 MATHEMATICS AND COMPUTING↗

FTS3: Data Movement Service in containers deployed in OKD

The File Transfer Service (FTS3) is a data movement service developed at CERN which is used to distribute the majority of the Large Hadron Collider's data across the Worldwide LHC Computing Grid (WLCG) infrastructure. At Fermilab, we have deployed FTS3 instances for Intensity Frontier experiments (e.g. DUNE) to transfer data in America and Europe, using a container-based strategy. In this article we summarize our experience building docker images based on work from the SLATE project (slateci.io) and deployed in OKD, the community distribution of Red Hat OpenShift. Additionally, we discuss our method of certificate management and maintenance utilizing Kubernetes CronJobs. Finally, we also report on the two different configurations currently running at Fermilab, comparing and contrasting a Docker-based OKD deployment against a traditional RPM-based deployment.

Lobato Pardavila, Lorena↗

SuperLab 2.0 Showcase: Connecting Five Labs to Tackle Grid Complexity and Unlock Unique Grid Asset Potential

SuperLab 2.0 (5-Lab Demo) is a collaborative, national-scale experiment showcasing the coordination of geographically distributed energy assets in real time. The demonstration integrates 25 physical and digital assets, spanning wind, PV, batteries, electrolyzers, DC fast chargers, microgrid controllers, building automation systems, small modular reactor (SMR), control centers, and gas turbines, across five DOE national laboratories-NLR, INL, NETL, LBNL, and SNL. These assets are unified using Energy Sciences Network (ESnet), a low-latency, high-performance U.S. Department of Energy's (DOE) network, and controlled via a centralized energy controller hosted at NLR's ARIES facility. The demonstration validates the ability to stress-test hybrid energy systems under dynamic scenarios to de-risk advanced control strategies for greater resilience and flexibility. SuperLab 2.0 (5-Lab Demo) showcased a major advancement in federated national laboratory collaboration, enabling real-time, cross-laboratory experimentation to coordinate geographically dispersed distributed energy resources (DERs) using various communication protocols and networks. SuperLab 2.0 (5-Lab Demo) built on previous demonstrations conducted between NLR-PNNL and NLR-INL connecting diverse assets including distant protection devices, a SMR simulator, and a high temperature electrolyzer (HTE). Previous demos were based on a single connection between two labs with minimal coordination challenges. The 5-Lab demo with a centralized controller, distributed testbeds across different geographical locations, and use of protocols-based communication represents a scenario closer to real-world grid operations that coordinate resources across a region to meet system needs. This experiment studied how local DER controllers interact with a centralized energy controller during normal and abnormal events to maintain reliability. The SuperLab team across the five labs implemented a notional power system model equivalent of transmission and distribution lines, represented by the data networks interconnecting the labs. Each lab continuously exchanged local parameters (such as P and Q) from its Hardware-In-Loop (CHIL) and Power Hardware-In-Loop (PHIL) assets through centralized energy controller at NLR, enabling real-time interaction and coordination across sites. By leveraging ESnet as the communication backbone, the team successfully operated the distributed assets as a unified power system, with each bus represented by a different laboratory. This setup mirrors how assets interact in real-world power systems across dispersed locations with various protocols and latencies. At each lab site, assets were operated using their own local controllers which were coordinated through an overarching operation and control layer of centralized energy controller, equivalent to how an energy management system (EMS) orchestrates assets across a regional or national grid. SuperLab's federated connectivity utilized a Digital Real-Time Simulators (DRTS)-type gateway to connect Controller Hardware-In-Loop (CHIL) and PHIL assets between labs. To enable this federated connection through ESnet, a deterministic network was established where latency variations were consistent. This consistency allowed the development of digital filters for the power system assets across CHIL and PHIL interfaces to avoid unstable and unreliable grid conditions. This report provides an overview of the cross-laboratory configuration and offers insights into interconnecting geographically distributed research assets to test them as if they were co-located. This experiment represents a step toward linking nine DOE national laboratories, enabling nation-wide simulations that can address utility-driven challenges with grid resilience, flexibility, and modernization.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Learning-Accelerated ADMM for Distributed DC Optimal Power Flow

We suggest a novel data-driven method to accelerate the convergence of Alternating Direction Method of Multipliers (ADMM) for solving distributed DC optimal power flow (DC-OPF) where lines are shared between independent network partitions. Using previous observations of ADMM trajectories for a given system under varying load, the method trains a recurrent neural network (RNN) to predict the converged values of dual and consensus variables. Given a new realization of system load, a small number of initial ADMM iterations is taken as input to infer the converged values and directly inject them into the iteration. We empirically demonstrate that the online injection of these values into the ADMM iteration accelerates convergence by a significant factor for partitioned 14-, 118-and 2848-bus test systems under differing load scenarios. The proposed method has several advantages: it maintains the security of private decision variables inherent in consensus ADMM; inference is fast and so may be used in online settings; RNN-generated predictions can dramatically improve time to convergence but, by construction, can never result in infeasible ADMM subproblems; it can be easily integrated into existing software implementations. While we focus on the ADMM formulation of distributed DC-OPF in this paper, the ideas presented are naturally extended to other distributed optimization problems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra: Supporting Data

High-resolution classification maps derived from occupied aerial systems (UASs). The UAS data were collected in August 2021 using a Skydio 2+ drone equipped with a 4K resolution red-green-blue (RGB) camera (2024 Skydio Inc) and a 3DR SOLO Quadcopter carried a Parrot Sequoia+ Multispectral Sensor (2023 Parrot Drone SAS). This package includes vegetation classification maps at four locations around Next Generation Ecosystem Experiment Arctic (NGEE Arctic) Council watershed study site on the Seward Peninsula, Alaska. The classification maps were generated using a combination of RGB and canopy height information. The map data and metadata are provided as ENVI image (.dat) and text (.txt, *hdr) formats. Additional map quicklooks are provided as GIS *.kml files. These datasets are provided in support of Yang et al., (In review), “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Data Services for Visualization and Analysis - ASC Level II Milestone (7186)

A new in transit Data Service is presented and compared to the traditional file-based workflow and the newly refactored in situ Catalyst workflow. Each workflow is enabled by the IOSS mesh interface equipped with data management layers for Exodus and CGNS (file-based), Catalyst (in situ), and FAODEL (in transit). FAODEL is a distributed object store that can transmit data across MPI allocations. Catalyst is a Para View-based visualization capability developed as part of the CSSE Data Services effort. The workflows considered here take SPARC data into Catalyst for visualization post-processing. Although still in unoptimized form, we show that the in transit approach is a viable alternative to file-based and in situ workflows and offers several advantages to both simulation and post-processing developers. Since IOSS is a mature interface with wide adoption across Sandia and externally, each workflow can be reconfigured to use different simulations that generate mesh data and post-processing tools that consume it.

97 MATHEMATICS AND COMPUTING↗

Impact of heavy quark and quarkonium data on nuclear gluon PDFs

A clear understanding of nuclear parton distribution functions (nPDFs) plays a crucial role in the interpretation of collider data taken at the Relativistic Heavy Ion Collider, the Large Hadron Collider (LHC), and in the near future at the Electron-Ion Collider. Even with the recent inclusions of vector boson and light meson production data, the uncertainty of the gluon PDF remains substantial and limits the interpretation of heavy ion collision data. To obtain new constraints on the nuclear gluon PDF, we extend our recent nCTEQ15WZ+SIH analysis to inclusive quarkonium and open heavy-flavor meson production data from the LHC. This vast new data set covers a wide kinematic range and puts strong constraints on the nuclear gluon PDF down to x ≲ 10 -5 . The theoretical predictions for these data sets are obtained from a data-driven approach, where proton-proton data are used to determine effective scattering matrix elements. This approach is validated with detailed comparisons to existing next-to-leading order calculations in nonrelativistic QCD for quarkonia and in the general-mass variable-flavor-number scheme for the open heavy-flavored mesons. In addition, the uncertainties from the data-driven approach are determined using the Hessian method and accounted for in the PDF fits. This extension of our previous analyses represents an important step toward the next generation of PDFs not only by including new data sets, but also by exploring new methods for future analyses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗